from the XML. * \return ctkCmdLineModuleReference the reference corresponding to the fullName, or an invalid reference if non found. */ ctkCmdLineModuleReference GetReferenceByFullName(QString fullName); /** * \brief Raises a message box asking the user to select a module first. */ void AskUserToSelectAModule() const; /** * \brief Enables or Disables the Run Button. */ void UpdateRunButtonEnabledStatus(); /** * \brief The GUI controls contain a reset and run button, and a QWidget container, and the GUI component * for each command line module is added to the QWidget dynamically at run time. */ CommandLineModulesViewControls *m_Controls; /** * \brief We store the parent, passed in via CommandLineModulesView::CreateQtPartControl, * as this class itself is not a QWidget. */ QWidget *m_Parent; /** * \brief We keep a local layout, and arrange a display of QmitkCmdLineModuleProgressWidget, * where each QmitkCmdLineModuleProgressWidget represents a single running job. */ QVBoxLayout *m_Layout; /** * \brief The manager is responsible for loading and instantiating command line modules. */ ctkCmdLineModuleManager *m_ModuleManager; /** * \brief We are using a back-end that runs locally installed command line programs. */ ctkCmdLineModuleBackendLocalProcess *m_ModuleBackend; /** * \brief The ctkCmdLineModuleDirectoryWatcher maintains the list of directories * we are using to load modules, to provide automatic updates. */ ctkCmdLineModuleDirectoryWatcher *m_DirectoryWatcher; /** * \brief We store a temporary folder name, accessible via user preferences. */ QString m_TemporaryDirectoryName; /** * \brief We store an output folder name, accessible via user preferences for when * the file specified in a default output path is not within a writable directory. */ QString m_OutputDirectoryName; /** * \brief Cache the list of directory paths locally to avoid repeatedly trying to update Directory Watcher. */ QStringList m_DirectoryPaths; /** * \brief Cache the list of module/executable paths locally to avoid repeatedly trying to update Directory Watcher. */ QStringList m_ModulePaths; /** - * \brief We store the validation mode, accessisble via user preferences. + * \brief We store the validation mode, accessible via user preferences. */ ctkCmdLineModuleManager::ValidationMode m_ValidationMode; /** * \brief We store the maximum number of concurrent processes, and disable the run button accordingly. */ int m_MaximumConcurrentProcesses; /** * \brief Counts the number of currently running processes. */ int m_CurrentlyRunningProcesses; /** * \brief Member variable, taken from preference page. */ bool m_DebugOutput; /** * \brief Member variable, taken from preferences page. */ int m_XmlTimeoutSeconds; /** * \brief We keep a list of front ends to match the m_TabWidget. */ QList<ctkCmdLineModuleFrontend*> m_ListOfModules; }; #endif // CommandLineModulesView_h diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleRunner.h b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleRunner.h index 8a43d18fca..e750b9a539 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleRunner.h +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleRunner.h @@ -1,232 +1,232 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkCmdLineModuleRunner_h #define QmitkCmdLineModuleRunner_h #include <QWidget> #include <QTimer> #include <QList> #include <ctkCmdLineModuleParameter.h> #include <mitkDataNode.h> class QVBoxLayout; class QTemporaryFile; class QmitkCmdLineModuleGui; class ctkCmdLineModuleManager; class ctkCmdLineModuleFutureWatcher; namespace Ui { class QmitkCmdLineModuleProgressWidget; } namespace mitk { class DataStorage; } /** * \class QmitkCmdLineModuleRunner * \brief Based on ctkCmdLineModuleExplorerProgressWidget, implements a progress widget * with console output, and space for storing the GUI widgets. * \author Matt Clarkson (m.clarkson@ucl.ac.uk) * \ingroup org_mitk_gui_qt_cmdlinemodules_internal * \sa ctkCmdLineModuleExplorerProgressWidget */ class QmitkCmdLineModuleRunner : public QWidget { Q_OBJECT public: QmitkCmdLineModuleRunner(QWidget *parent = nullptr); ~QmitkCmdLineModuleRunner() override; /** * \brief Sets the manager on this object, and must be called immediately * after construction, before using the widget. */ void SetManager(ctkCmdLineModuleManager* manager); /** * \brief Sets the DataStorage on this object, and must be called immediately * after construction, before using the widget. */ void SetDataStorage(mitk::DataStorage* dataStorage); /** * \brief Sets the Output Directory on this widget, and must be called * immediately after construction, before using the widget. */ void SetOutputDirectory(const QString& directoryName); /** * \brief Tells this widget, which module frontend it is running * \param frontEnd our QmitkCmdLineModuleGui class derived from ctkCmdLineModuleFrontend */ void SetFrontend(QmitkCmdLineModuleGui* frontEnd); /** * \brief Runs the module that this widget is currently referring to. */ void Run(); Q_SIGNALS: // These signals so that container classes such as CommandLineModuleView // can keep track of how many modules are running simultaneously. - void started(); // emmitted when the module is started. - void finished(); // emmitted when the module is completely finished. + void started(); // emitted when the module is started. + void finished(); // emitted when the module is completely finished. private Q_SLOTS: void OnCheckModulePaused(); void OnPauseButtonToggled(bool toggled); void OnRemoveButtonClicked(); void OnModuleStarted(); void OnModuleCanceled(); void OnModuleFinished(); void OnModuleResumed(); void OnModuleProgressRangeChanged(int progressMin, int progressMax); void OnModuleProgressTextChanged(const QString& progressText); void OnModuleProgressValueChanged(int progressValue); void OnOutputDataReady(); void OnErrorDataReady(); private: /** * \brief Simply returns true if this widget is considered as having been started. */ bool IsStarted() const; /** * \brief Used to write output to the console widget, and also to qDebug(). */ void PublishMessage(const QString& message); /** * \brief Used to write output to the console widget, and also to qDebug(). */ void PublishByteArray(const QByteArray& array); /** * \brief Destroys any images listed in m_TemporaryFileNames. */ void ClearUpTemporaryFiles(); /** * \brief Loads any data listed in m_OutputDataToLoad into the m_DataStorage. */ void LoadOutputData(); /** * \brief Saves temporary image to file. * \param[in] node non-nullptr pointer to node containing a non-nullptr mitk::Image. * \param[out] errorMessage which if not empty means an error occurred. * \return QTemporaryFile temporary file that the caller is responsible for deleting. * * If the returned QTemporaryFile is nullptr, check errorMessage. * If the returned QTemporaryFile is not-nullptr, there could still be data in the errorMessage. * It could be that this method tried n file extensions, before finding a successful one. * In this case, the returned QTemporaryFile is the successful one, and the errorMessage contains error messages of all the failed attempts. */ QTemporaryFile* SaveTemporaryImage(const ctkCmdLineModuleParameter& parameter, mitk::DataNode::ConstPointer node, QString& errorMessage) const; /** * \brief Utility method to look up the title from the description. */ QString GetTitle(); /** * \brief Returns <category>.<title>, derived from the ctkCmdLineModuleReference and * hence from the ctkCmdLineModuleDescription. */ QString GetFullName() const; /** * \brief Takes nodeName, and makes sure that it only contains A-Z, a-z, 0-9, hyphen and underscore, * and does not use hyphen as the first character. * * Inspired by <a href="https://www.boost.org/doc/libs/1_43_0/libs/filesystem/doc/portability_guide.htm">boost recommendations</a>. */ QString GetValidNodeName(const QString& nodeName) const; /** * \brief This must be injected before the Widget is used. */ ctkCmdLineModuleManager *m_ModuleManager; /** * \brief This must be injected before the Widget is used. */ mitk::DataStorage *m_DataStorage; /** * \brief This must be injected before the Widget is used. */ QString m_OutputDirectoryName; /** * \brief We instantiate the main widgets from this .ui file. */ Ui::QmitkCmdLineModuleProgressWidget *m_UI; /** * \brief The m_ParametersGroupBox needs a layout. */ QVBoxLayout *m_Layout; /** * \brief The QmitkCmdLineModuleGui is created by the QmitkCmdLineModuleFactoryGui outside * of this class and injected into this class before being run. */ QmitkCmdLineModuleGui *m_ModuleFrontEnd; /** * \brief Main object to keep track of a running command line module. */ ctkCmdLineModuleFutureWatcher *m_FutureWatcher; /** * \brief Due to Qt bug 12152, we use a timer to correctly check for a paused module. */ QTimer m_PollPauseTimer; /** * \brief We store a list of temporary file names that are saved to disk before * launching a command line app, and then must be cleared up when the command line * app successfully finishes. */ QList<QTemporaryFile*> m_TemporaryFiles; /** * \brief We store a list of output images, so that on successful completion of * the command line module, we automatically load the output data into the mitk::DataStorage. */ QStringList m_OutputDataToLoad; /** * \brief We track how many times the OnOutputDataReady is called. */ int m_OutputCount; /** * \brief We track how many times the OnErrorDataReady is called. */ int m_ErrorCount; }; #endif diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.h b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.h index a714712aa0..3e280b20e0 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.h +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.h @@ -1,56 +1,56 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUiLoader_h #define QmitkUiLoader_h #include <ctkCmdLineModuleQtUiLoader.h> #include <QStringList> #include "mitkDataStorage.h" /** * \class QmitkUiLoader * \brief Derived from ctkCmdLineModuleQtGuiLoader to enable us to instantiate widgets from Qmitk at runtime, - * and currently we instatiate QmitkDataStorageComboBoxWithSelectNone, used for image input widgets. + * and currently we instantiate QmitkDataStorageComboBoxWithSelectNone, used for image input widgets. * \author Matt Clarkson (m.clarkson@ucl.ac.uk) * \ingroup org_mitk_gui_qt_cmdlinemodules_internal * \sa ctkCmdLineModuleQtUiLoader */ class QmitkUiLoader : public ctkCmdLineModuleQtUiLoader { Q_OBJECT public: QmitkUiLoader(const mitk::DataStorage* dataStorage, QObject *parent=nullptr); ~QmitkUiLoader() override; /** * \brief Returns the list of available widgets in ctkCmdLineModuleQtGuiLoader and also QmitkDataStorageComboBoxWithSelectNone. * \see ctkCmdLineModuleQtGuiLoader::availableWidgets() */ QStringList availableWidgets () const; /** * \brief If className is QmitkDataStorageComboBox, instantiates QmitkDataStorageComboBoxWithSelectNone and * otherwise delegates to base class. * \see ctkCmdLineModuleQtGuiLoader::createWidget() */ QWidget* createWidget(const QString & className, QWidget * parent = nullptr, const QString & name = QString() ) override; private: const mitk::DataStorage* m_DataStorage; }; // end class #endif diff --git a/Plugins/org.mitk.gui.qt.common/resources/icon-license.txt b/Plugins/org.mitk.gui.qt.common/resources/icon-license.txt new file mode 100644 index 0000000000..683e7f7561 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.common/resources/icon-license.txt @@ -0,0 +1,2 @@ +See [Font Awesome 4] in Licenses/ICONS.md for: +- times.svg \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractRenderEditor.h b/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractRenderEditor.h index d1eb9bf302..1860c2d453 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractRenderEditor.h +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractRenderEditor.h @@ -1,166 +1,166 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkAbstractRenderEditor_h #define QmitkAbstractRenderEditor_h #include <berryQtEditorPart.h> #include "mitkIRenderWindowPart.h" #include <mitkIDataStorageReference.h> #include <mitkDataStorage.h> #include <org_mitk_gui_qt_common_Export.h> class QmitkAbstractRenderEditorPrivate; namespace mitk { class IPreferences; } /** * \ingroup org_mitk_gui_qt_common * * \brief A convenient base class for MITK render window BlueBerry Editors. * * QmitkAbstractRenderEditor provides several convenience methods that ease the introduction of * a new editor for rendering a MITK DataStorage: * * <ol> * <li> Access to the DataStorage (~ the shared data repository) * <li> Access to and update notification for the editor's preferences * <li> Default implementation of some mitk::IRenderWindowPart methods * </ol> * * When inheriting from QmitkAbstractRenderEditor, you must implement the following methods: * <ul> * <li>void CreateQtPartControl(QWidget* parent) * <li>void SetFocus() * </ul> * * You may reimplement the following private virtual methods to be notified about certain changes: * <ul> * <li>void OnPreferencesChanged(const mitk::IPreferences*) * </ul> * * \see IRenderWindowPart * \see ILinkedRenderWindowPart */ class MITK_QT_COMMON QmitkAbstractRenderEditor : public berry::QtEditorPart, public virtual mitk::IRenderWindowPart { Q_OBJECT Q_INTERFACES(mitk::IRenderWindowPart) public: berryObjectMacro(QmitkAbstractRenderEditor, QtEditorPart, mitk::IRenderWindowPart); /** * \see mitk::IRenderWindowPart::GetSelectedTimePoint() This default implementation assumes that all renderer use the same TimeNavigationControl provided by this class (GetTimeNavigationControl()). */ mitk::TimePointType GetSelectedTimePoint(const QString& id = QString()) const override; QmitkAbstractRenderEditor(); ~QmitkAbstractRenderEditor() override; protected: /** * Initializes this editor by checking for a valid mitk::DataStorageEditorInput as <code>input</code>. * * \see berry::IEditorPart::Init */ void Init(berry::IEditorSite::Pointer site, berry::IEditorInput::Pointer input) override; /** * Get a reference to the DataStorage set by the editor input. */ virtual mitk::IDataStorageReference::Pointer GetDataStorageReference() const; /** * Get the DataStorage set by the editor input. */ virtual mitk::DataStorage::Pointer GetDataStorage() const; /** * Get the preferences for this editor. */ virtual mitk::IPreferences* GetPreferences() const; /** * Get the RenderingManager used by this editor. This default implementation uses the * global MITK RenderingManager provided by mitk::RenderingManager::GetInstance(). * * \see mitk::IRenderWindowPart::GetRenderingManager */ mitk::IRenderingManager* GetRenderingManager() const override; /** * Request an update of this editor's render windows. * This implementation calls mitk::IRenderingManager::RequestUpdate on the rendering * manager interface returned by GetRenderingManager(); * * \param requestType The type of render windows for which an update is requested. * * \see mitk::IRenderWindowPart::RequestUpdate */ void RequestUpdate(mitk::RenderingManager::RequestType requestType = mitk::RenderingManager::REQUEST_UPDATE_ALL) override; /** * Force an immediate update of this editor's render windows. * This implementation calls mitk::IRenderingManager::ForceImmediateUpdate() on the rendering * manager interface returned by GetRenderingManager(); * - * \param requestType The type of render windows for which an immedate update is forced. + * \param requestType The type of render windows for which an immediate update is forced. * * \see mitk::IRenderWindowPart::ForceImmediateUpdate */ void ForceImmediateUpdate(mitk::RenderingManager::RequestType requestType = mitk::RenderingManager::REQUEST_UPDATE_ALL) override; /** * Get the time navigation controller for this editor. * This implementation returns the TimeNavigationController returned by the mitk::IRenderingManager::GetTimeNavigationController() * method of the interface implementation returned by GetRenderingManager(). * * \see mitk::IRenderingManager::GetTimeNavigationController */ mitk::TimeNavigationController* GetTimeNavigationController() const override; /** \see berry::IEditorPart::DoSave */ void DoSave() override; /** \see berry::IEditorPart::DoSaveAs */ void DoSaveAs() override; /** \see berry::IEditorPart::IsDirty */ bool IsDirty() const override; /** \see berry::IEditorPart::IsSaveAsAllowed */ bool IsSaveAsAllowed() const override; private: virtual void OnPreferencesChanged(const mitk::IPreferences*); private: QScopedPointer<QmitkAbstractRenderEditorPrivate> d; }; #endif diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.h b/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.h index b98a39219a..afe6788eb5 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.h +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.h @@ -1,356 +1,356 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkAbstractView_h #define QmitkAbstractView_h //# blueberry stuff #include <berryQtViewPart.h> #include <berryISelectionListener.h> //# mitk stuff #include <org_mitk_gui_qt_common_Export.h> #include "mitkDataNodeSelection.h" #include "mitkIRenderWindowPart.h" #include <mitkWorkbenchUtil.h> #include <mitkDataStorage.h> #include <mitkRenderingManager.h> #include <mitkIDataStorageReference.h> #include <QItemSelectionModel> namespace mitk { class DataNode; class IPreferences; } class QmitkAbstractViewPrivate; class QmitkAbstractViewSelectionProvider; /** * \ingroup org_mitk_gui_qt_common * * \brief A convenient base class for MITK related BlueBerry Views. * * QmitkAbstractView provides several convenience methods that ease the introduction of a new view: * * <ol> * <li> Access to the DataStorage (~ the shared data repository) * <li> Access to the active IRenderWindowPart * <li> Access to and update notification for the view's preferences * <li> Access to and update notification for the current DataNode selection / to DataNode selection events send through the SelectionService * <li> Access to and update notification for DataNode events (added/removed/modified) * <li> Methods to send DataNode selections through the SelectionService * <li> Some minor important convenience methods (like changing the mouse cursor/exception handling) * </ol> * * Usually all MITK Views inherit from QmitkAbstractView to achieve a consistent Workbench behavior. * * When inheriting from QmitkAbstractView, you must implement the following methods: * <ul> * <li>void CreateQtPartControl(QWidget* parent) * <li>void SetFocus() * </ul> * * You may reimplement the following private virtual methods to customize your View's behavior: * <ul> * <li>void SetSelectionProvider() * <li>QItemSelectionModel* GetDataNodeSelectionModel() const * </ul> * * You may reimplement the following private virtual methods to be notified about certain changes: * <ul> * <li>void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer> &nodes) * <li>void OnNullSelection(berry::IWorkbenchPart::Pointer part) * <li>void OnPreferencesChanged(const mitk::IPreferences*) * <li>void NodeAdded(const mitk::DataNode* node) * <li>void NodeChanged(const mitk::DataNode* node) * <li>void NodeRemoved(const mitk::DataNode* node) * <li>void DataStorageModified() * <li>void DataStorageChanged(mitk::IDataStorageReference::Pointer dsRef) * </ul> * * \see mitk::ILifecycleAwarePart * \see mitk::IZombieViewPart * \see mitk::IRenderWindowPartListener */ class MITK_QT_COMMON QmitkAbstractView : public berry::QtViewPart { public: /** * Creates smartpointer typedefs */ berryObjectMacro(QmitkAbstractView); /** - * Nothing to do in the standard ctor. Initiliaze your GUI in CreateQtPartControl(QWidget*) + * Nothing to do in the standard ctor. Initialize your GUI in CreateQtPartControl(QWidget*) * \see berry::QtViewPart::CreateQtPartControl(QWidget*) */ QmitkAbstractView(); /** * Disconnects all standard event listeners */ ~QmitkAbstractView() override; protected: /** * Informs other parts of the workbench that node is selected via the blueberry selection service. * * \note This method should not be used if you have set your own selection provider via * SetSelectionProvider() or your own QItemSelectionModel via GetDataNodeSelectionModel(). */ void FireNodeSelected(mitk::DataNode::Pointer node); /** * Informs other parts of the workbench that the nodes are selected via the blueberry selection service. * * \note This method should not be used if you have set your own selection provider via * SetSelectionProvider() or your own QItemSelectionModel via GetDataNodeSelectionModel(). */ virtual void FireNodesSelected(const QList<mitk::DataNode::Pointer>& nodes); /** * \return The selection of the currently active part of the workbench or an empty list * if there is no selection or if it is empty. * * \see IsCurrentSelectionValid */ QList<mitk::DataNode::Pointer> GetCurrentSelection() const; /** * Queries the state of the current selection. * * \return If the current selection is <code>nullptr</code>, this method returns * <code>false</code> and <code>true</code> otherwise. */ bool IsCurrentSelectionValid() const; /** * Returns the current selection made in the datamanager bundle or an empty list * if there is no selection or if it is empty. * * \see IsDataManagerSelectionValid */ QList<mitk::DataNode::Pointer> GetDataManagerSelection() const; /** * Queries the state of the current selection of the data manager view. * * \return If the current data manager selection is <code>nullptr</code>, this method returns * <code>false</code> and <code>true</code> otherwise. */ bool IsDataManagerSelectionValid() const; /** * Sets the selection of the data manager view if available. * * \param selection The new selection for the data manager. * \param flags The Qt selection flags for controlling the way how the selection is updated. */ void SetDataManagerSelection(const berry::ISelection::ConstPointer& selection, QItemSelectionModel::SelectionFlags flags = QItemSelectionModel::ClearAndSelect) const; /** * Takes the current selection and sets it on the data manager. Only matching nodes in the * data manager view will be selected. */ void SynchronizeDataManagerSelection() const; /** * Returns the Preferences object for this View. - * Important: When refering to this preferences, e.g. in a PreferencePage: The ID + * Important: When referring to this preferences, e.g. in a PreferencePage: The ID * for this preferences object is "/<VIEW-ID>", e.g. "/org.mitk.views.datamanager" */ mitk::IPreferences* GetPreferences() const; /** * Returns a reference to the currently active DataStorage. */ mitk::IDataStorageReference::Pointer GetDataStorageReference() const; /** * Returns the currently active DataStorage. */ mitk::DataStorage::Pointer GetDataStorage() const; /** * Returns the currently active mitk::IRenderWindowPart. * * \param strategies Strategies for returning a mitk::IRenderWindowPart instance if there * is currently no active one. * \return The active mitk::IRenderWindowPart. */ mitk::IRenderWindowPart* GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategies strategies = mitk::WorkbenchUtil::NONE) const; /** * Request an update of all render windows of the currently active IRenderWindowPart. * * \param requestType Specifies the type of render windows for which an update will be requested. */ void RequestRenderWindowUpdate(mitk::RenderingManager::RequestType requestType = mitk::RenderingManager::REQUEST_UPDATE_ALL); /** * Outputs an error message to the console and displays a message box containing * the exception description. * \param e the exception which should be handled * \param parent * \param showDialog controls, whether additionally a message box should be * displayed to inform the user that something went wrong */ void HandleException( std::exception& e, QWidget* parent = nullptr, bool showDialog = true ) const; /** * Calls HandleException ( std::exception&, QWidget*, bool ) internally * \see HandleException ( std::exception&, QWidget*, bool ) */ void HandleException( const char* str, QWidget* parent = nullptr, bool showDialog = true ) const; /** * Convenient method to set and reset a wait cursor ("hourglass") */ void WaitCursorOn(); /** * Convenient method to restore the standard cursor */ void WaitCursorOff(); /** * Convenient method to set and reset a busy cursor */ void BusyCursorOn(); /** * Convenient method to restore the standard cursor */ void BusyCursorOff(); /** * Convenient method to restore the standard cursor */ void RestoreOverrideCursor(); private: /** * Reimplement this method to set a custom selection provider. This method is * called once after CreateQtPartControl(). * * The default implementation registers a QmitkDataNodeSelectionProvider with * a QItemSelectionModel returned by GetDataNodeSelectionModel(). */ virtual void SetSelectionProvider(); /** * Reimplement this method to supply a custom Qt selection model. The custom * model will be used with the default selection provider QmitkDataNodeSelectionProvider * to inform the MITK Workbench about selection changes. * * If you reimplement this method, the methods FireNodeSelected() and FireNodesSelected() * will have no effect. Use your custom selection model to notify the MITK Workbench * about selection changes. * * The Qt item model used with the custom selection model must return mitk::DataNode::Pointer * objects for model indexes when the role is QmitkDataNodeRole. */ virtual QItemSelectionModel* GetDataNodeSelectionModel() const; /** * Called when the selection in the workbench changed. * May be reimplemented by deriving classes. * * \param part The source part responsible for the selection change. * \param nodes A list of selected nodes. * * \see OnNullSelection */ virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer> &nodes); /** * Called when a <code>nullptr</code> selection occurs. * * \param part The source part responsible for the selection change. */ virtual void OnNullSelection(berry::IWorkbenchPart::Pointer part); /** * Called when the preferences object of this view changed. * May be reimplemented by deriving classes. * * \see GetPreferences() */ virtual void OnPreferencesChanged(const mitk::IPreferences*); /** * Called when a DataStorage Add event was thrown. May be reimplemented * by deriving classes. */ virtual void NodeAdded(const mitk::DataNode* node); /** * Called when a DataStorage Changed event was thrown. May be reimplemented * by deriving classes. */ virtual void NodeChanged(const mitk::DataNode* node); /** * Called when a DataStorage Remove event was thrown. May be reimplemented * by deriving classes. */ virtual void NodeRemoved(const mitk::DataNode* node); /** * Called when a DataStorage add *or* remove *or* change event from the currently active * data storage is thrown. * * May be reimplemented by deriving classes. */ virtual void DataStorageModified(); /** * Called when the currently active DataStorage changed. * May be reimplemented by deriving classes. * * \param dsRef A reference to the new active DataStorage. */ virtual void DataStorageChanged(mitk::IDataStorageReference::Pointer dsRef); /** * Creates a scroll area for this view and calls CreateQtPartControl then */ void CreatePartControl(QWidget* parent) override; /** * Called immediately after CreateQtPartControl(). * Here standard event listeners for a QmitkAbstractView are registered */ void AfterCreateQtPartControl(); private: friend class QmitkAbstractViewPrivate; friend class QmitkViewCoordinator; Q_DISABLE_COPY(QmitkAbstractView) const QScopedPointer<QmitkAbstractViewPrivate> d; }; #endif diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h b/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h index d075f60572..8329792ce1 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h @@ -1,137 +1,137 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSliceNavigationListener_h #define QmitkSliceNavigationListener_h #include <mitkTimeGeometry.h> #include <mitkPoint.h> #include <itkEventObject.h> #include <QObject> #include <org_mitk_gui_qt_common_Export.h> namespace itk { class Object; } namespace mitk { class SliceNavigationController; struct IRenderWindowPart; } /** @brief Helper class to allow QmitkAbstractView and derived classes to react on changes of the slice/time navigation. - Purpose of the class to be used in view and to give the respective view class (by composition) the posibility to react + Purpose of the class to be used in view and to give the respective view class (by composition) the possibility to react on changes of the currently selected timepoint or position in the world geometry.\n - It also offers convinient signals that are only triggered when the selected timepoint or the selected possition of the - active render window have realy changed.\n + It also offers convenient signals that are only triggered when the selected timepoint or the selected position of the + active render window have really changed.\n In order to setup this class properly the following things must be regarded: - View class must also derive public from mitk::IRenderWindowPartListener - View class must implement void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) and pass the renderWindowPart to the listener. void QmitkMyView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceNavigationListener.RenderWindowPartActivated(renderWindowPart); } - View class must implement void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) and pass the renderWindowPart to the listener. void QmitkMyView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceNavigationListener.RenderWindowPartDeactivated(renderWindowPart); } - View class must pass its on render window part in its CreateQtPartControl(QWidget* parent) this->m_SliceNavigationListener.RenderWindowPartActivated(this->GetRenderWindowPart()); - View class must connect the SliceChanged signal of the listener as see fit. */ class MITK_QT_COMMON QmitkSliceNavigationListener : public QObject { Q_OBJECT public: QmitkSliceNavigationListener(); ~QmitkSliceNavigationListener() override; mitk::TimePointType GetCurrentSelectedTimePoint() const; mitk::Point3D GetCurrentSelectedPosition() const; signals: /** Signal triggered as soon as there is any change. It may be a change in the position/slice or of the selected timepoint.*/ void SliceChanged(); - /** Convinience signal that can be used if you are only interested in changes of the current selected time point. + /** Convenience signal that can be used if you are only interested in changes of the current selected time point. Changes in spatial position will be ignored.*/ void SelectedTimePointChanged(const mitk::TimePointType& newTimePoint); - /** Convinience signal that can be used if you are only interested in changes of the current selected position. + /** Convenience signal that can be used if you are only interested in changes of the current selected position. Changes in time will be ignored.*/ void SelectedPositionChanged(const mitk::Point3D& newPoint); public slots: void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart); void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart); void RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderWindowPart); protected slots: /** Overwrite function to implement the behavior on slice/time changes. */ void OnSliceChangedDelayed(); protected: /** @brief Calls OnSliceChangedDelayed so the event isn't triggered multiple times. */ void OnSliceChangedInternal(const itk::EventObject& e); void OnTimeChangedInternal(itk::Object* sender, const itk::EventObject& e); void OnSliceNavigationControllerDeleted(const itk::Object* sender, const itk::EventObject& /*e*/); /** Initializes and sets the observers that are used to monitor changes in the selected position or time point in order to actualize the view.h*/ bool InitObservers(); void RemoveObservers(const mitk::SliceNavigationController* deletedSlicer); /** Removes all observers of the deletedPart. If null pointer is passed all observers will be removed.*/ void RemoveAllObservers(mitk::IRenderWindowPart* deletedPart = nullptr); bool ObserversInitialized(mitk::SliceNavigationController* controller); mitk::IRenderWindowPart* m_renderWindowPart; // Needed for observing the events for when a slice or time step is changed. bool m_PendingSliceChangedEvent; /**Helper structure to manage the registered observer events.*/ struct ObserverInfo { mitk::SliceNavigationController* controller; int observerTag; std::string renderWindowName; mitk::IRenderWindowPart* renderWindowPart; ObserverInfo(mitk::SliceNavigationController* controller, int observerTag, const std::string& renderWindowName, mitk::IRenderWindowPart* part); }; typedef std::multimap<const mitk::SliceNavigationController*, ObserverInfo> ObserverMapType; ObserverMapType m_ObserverMap; unsigned int m_ControllerToTimeObserverTag; mitk::Point3D m_CurrentSelectedPosition; mitk::TimePointType m_CurrentSelectedTimePoint; }; #endif diff --git a/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.ui b/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.ui index 1599ef75ad..039ae9cc68 100644 --- a/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.ui +++ b/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.ui @@ -1,165 +1,165 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkNodeSelectionPreferencePage</class> <widget class="QWidget" name="QmitkNodeSelectionPreferencePage"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>715</width> <height>713</height> </rect> </property> <property name="windowTitle"> <string>Form</string> </property> <layout class="QGridLayout" name="gridLayout"> <item row="4" column="0"> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QPushButton" name="btnUp"> <property name="text"> <string>Up</string> </property> </widget> </item> <item> <widget class="QPushButton" name="btnDown"> <property name="text"> <string>Down</string> </property> </widget> </item> </layout> </item> <item row="1" column="0"> <widget class="QComboBox" name="comboPreferred"> <property name="toolTip"> - <string><html><head/><body>The preferred inspector is always visible.Additionally the preferred inspector has always the focus when opening a node selection dialoge.</body></html></string> + <string><html><head/><body>The preferred inspector is always visible.Additionally the preferred inspector has always the focus when opening a node selection dialog.</body></html></string> </property> <item> <property name="text"> <string>Neues Element</string> </property> </item> <item> <property name="text"> <string>2</string> </property> </item> </widget> </item> <item row="7" column="0"> <widget class="QLabel" name="label_2"> <property name="text"> <string><html><head/><body>Instruction: Only checked inspectors will be shown in node selection dialogs. You may change the order in the inspector list, to change the order of the tabs in the node selection dialog.</body></html></string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item row="3" column="0"> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QLabel" name="label"> <property name="text"> <string>Inspector visiblitiy and order:</string> </property> </widget> </item> <item> <widget class="QListWidget" name="listInspectors"> <property name="maximumSize"> <size> <width>16777215</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string>List of all available inspectors. Checked inspectores will be display</string> </property> <item> <property name="text"> <string>TreeInspector</string> </property> <property name="toolTip"> <string>ffffff</string> </property> <property name="checkState"> <enum>Checked</enum> </property> </item> <item> <property name="text"> <string>List</string> </property> <property name="checkState"> <enum>Checked</enum> </property> </item> </widget> </item> </layout> </item> <item row="8" column="0"> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item row="0" column="0"> <widget class="QLabel" name="label_3"> <property name="text"> <string>Preferred inspector:</string> </property> </widget> </item> <item row="5" column="0"> <widget class="QCheckBox" name="checkShowFav"> <property name="text"> <string>Show favorites inspector</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="2" column="0"> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>20</height> </size> </property> </spacer> </item> <item row="6" column="0"> <widget class="QCheckBox" name="checkShowHistory"> <property name="text"> <string>Show history inspector</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </widget> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox index 7c7326558c..bcf86c0feb 100644 --- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox +++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox @@ -1,192 +1,192 @@ /** \page org_mitk_views_datamanager The Data Manager View \imageMacro{data-manager-dox.svg,"Icon of the Data Manager", 2.00} \tableofcontents \section DataManagerIntroduction Introduction The Datamanager is the central component to manage medical data like images, segmentation masks, registrations, surfaces, point sets, annotations, measurements, etc.. After loading data into the Datamanager the data is shown in the four-view window, the so-called Standard Display. The user can now start working on the data by interacting with the data inside the Standard Display, by using the MITK-plugins such as Segmentation or Basic Image Processing or by using the context menu inside the data manager. \section DataManagerLoadingData Loading Data There are several ways of loading data into the Datamanager as so-called data nodes: <ul> <li> drag and drop data (e.g. from a file explorer or desktop) into the Datamanager <li> drag and drop data (e.g. from a file explorer or desktop) into one of the four windows of the Standard Display <li> use the keyboard shortcut Ctrl + o <li> use the Open File Button in the left upper corner and use the Open Dialog <li> use File -> Open File... from the top menu </ul> A lot of file-formats can be loaded into MITK, for example: <ul> <li> 2D-images / 3D-volumes with or without several time steps (*.dcm, *.ima, *.nrrd, ...) <li> Surfaces (*.stl, *.vtk, ...) <li> Point sets (*.mps) <li> and many more </ul> The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume. To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key. Note: What really happens is that the data nodes are stored inside a "Data storage" and the Datamanager is just a visual representation of the data inside the "Data storage". That's why the documentation sometimes uses the term "Data storage" instead of "Datamanager". \section DataManagerSavingData Saving Data There are several ways of saving data from the Datamanager: <ul> <li> use the keyboard shortcut Ctrl + s on a single data node <li> use the keyboard shortcut Ctrl + s on multiple data nodes <li> use the context menu right-click -> Save on a single data node <li> use the context menu right-click -> Save on multiple data nodes <li> use File -> Save... from the top menu on a single data node <li> use File -> Save... from the top menu on multiple data nodes </ul> \section DataManagerWorking Working with the Datamanager After loading data into the Datamanager the data appears as data nodes in a sorted list inside the Datamanager. The user can change the order of the data nodes manually by dragging one or multiple data nodes and dropping them at any position inside the Datamanager. Data nodes can also be sorted hierarchically as a parent-child-relation. For example after using the Segmentation-Plugin to create a segmentation on DataNode, the result is created as ChildNode, which is a child of DataNode (see \ref ParentChild "Parent-Child-Relation" screenshot). A parent-child-relation can be changed by dragging a child of a data node and dropping it onto another data node. For this the Property Allow changing of parent nodes needs to be enabled (see \ref DataManagerPreferences "Preferences"). \anchor ParentChild \imageMacro{QmitkDatamanager_ParentChild.png, "Parent-Child-Relation", 16.00} \subsection DataManagerNodeVisibility Visibility of data nodes By default all loaded data nodes are visible in the Standard Display. The visibility is indicated by the checkbox in front of the data node name in the Datamanager. If a data node is visible, the checkbox is filled - an empty checkbox indicates a hidden data node (see \ref ParentChild "Parent-Child-Relation" screenshot). Hint: The data nodes are rendered on top of each other, such that the topmost visible data node is always displayed on top of other data nodes. By hiding the topmost visible data node the next data node becomes the topmost visible data node and the hidden data node is not rendered anymore. Note: "Visible" does not mean that the node is correctly displayed inside the render windows. The user might have to re-initialize a data node to have it correctly displayed. \subsection DataManagerNodeSelection Selection of data nodes Some MITK-plugins contain widgets to control the data nodes that are used for plugin-specific data processing. These widgets can be configured such that they listen to the current selection of the Datamanager. Having such a plugin active each selection change of data nodes inside the data manager will change the respective selection of the plugin. The data node selection widgets can have specific node predicates, which means that only specific data nodes can be controlled by the widgets. It might happen that a selected data node will not be represented in such a selection widget or that the selection widget will be emptied. \subsection DataManagerNodeRenaming Renaming data nodes There are two ways of changing the name of a data node inside the Datamanager: <ul> <li> use the F2 key on a single data node <li> double-click on a single data node </ul> In both cases the new name can be accepted by hitting Enter or by clicking somewhere else. \section DataManagerContextMenu Context Menu The Datamanager provides a context menu for each data node that can be opened by right-clicking on a data node. An example of the context-menu can be seen in the \ref ContextMenu "Context menu" screenshot. The context menu allows to quickly perform common actions on data nodes. These actions differ according to the data type. Some of these actions are described here. For more actions see the respective modules and plugins (e.g. <tt>QmitkCreatePolygonModelAction</tt> inside the <tt>org_mitk_gui_qt_segmentation</tt>-plugin. <ul> <li> Global Reinit: Re-initializes the render windows to the common bounding box of all data nodes of the data storage that <ul> <li> have not set <tt>"includeInBoundingBox"</tt> to false <li> are <tt>"visible"</tt>. </ul> In this case it does not matter on which node this action is performed. <li> Reinit: Re-initializes the render windows to the common bounding box of all selected data nodes of the data storage that <ul> <li> have not set <tt>"includeInBoundingBox"</tt> to false <li> are <tt>"visible"</tt>. </ul> <li> Save: see \ref DataManagerSavingData "Saving Data" section <li> Remove: Removes all selected data nodes from the data storage. <li> Show only selected nodes: Enables the visibility of all selected data nodes and hides all other data nodes. <li> Toggle visibility: Shows / hides each selected data node according to each node's current visibility state. <li> Show details: Opens a pop-up window with detailed information about each node, like data type, geometry, DICOM information, file path etc. <li> Opacity: Sets the opacity via a slider for the rendering of the selected data node. <li> Color: Opens a pop-up window that allows to pick an arbitrary color for the rendering of all selected data nodes. <li> Colormap: Opens another submenu with a list of different colormaps that can be chosen for the rendering of all selected data nodes. <li> Component: Sets the currently visible data component for the rendering of this particular component of the selected data node. <li> Texture Interpolation: Smooths the data visualization for rendering of a selected data node. <li> Surface Representation: Opens another submenu with the following entries: <ul> <li> Points: Visually represents a surface (a data type) as a set of points. <li> Wireframe: Visually represents a surface (a data type) as a wireframe model. <li> Surface: Visually represents a surface (a data type) as a solid surface. </ul> </ul> As the description of the actions showed, it is possible to open / use the context menu with a single data node or with a set of selected data nodes. If the data types of multiple selected data nodes differ, the actions might not appear / work as expected. Also some actions are not available for a set of selected data nodes. \anchor ContextMenu \imageMacro{QmitkDatamanager_ContextMenu.png, "Context menu", 16.00} \section DataManagerPreferences Preferences The MITK Workbench provides a preference page for specific plugins. The preference page provided for the Datamanager can be seen in the \ref PreferencePage "Preference page" screenshot. The user can open the preference page by <ul> <li> using the keyboard shortcut Ctrl + p <li> using Window -> Preferences... from the top menu. </ul> It allows to set the following preferences for the Datamanager, which define the behavior of the Datamanager: <ul> <li> Place new nodes on top: If enabled, newly added data nodes will be inserted at the top of the list of data nodes inside the Datamanager. If disabled, newly added nodes will be inserted at the bottom of the list. <li> Show helper objects: If enabled, data nodes that have set <tt>"helper object"</tt> to true will be displayed in the Datamanager. If disabled, data nodes that have set <tt>"helper object"</tt> to true will not be visible in the Datamanager. <li> Show nodes containing no data: If enabled, data nodes that have no underlying base data defined will be displayed in the Datamanager. If disabled, data nodes that have no underlying base data defined will not be visible in the Datamanager. If disabled, the surface will have its original number of triangles in the triangle mesh. <li> Allow changing of parent node: If enabled, the user can change the hierarchy of the data nodes manually by dragging one or multiple data nodes and dropping them at any position inside the Datamanager (see \ref DataManagerWorking "Working with the Datamanager") for changing the order of the data nodes manually). </ul> \anchor PreferencePage \imageMacro{QmitkDatamanager_PreferencePage.png, "Preference page", 16.00} \section DataManagerHotkeys Hotkeys The MITK Workbench provides hotkeys for specific plugins. The hotkeys provided for the Datamanager can be seen in the \ref Hotkeys "Hotkeys" screenshot. They allow to expedite common operations in relation to data nodes or the Datamanager. The user can customize the hotkeys by accessing the preference page: <ul> <li> using the keyboard shortcut Ctrl + p - <li> useing Window -> Preferences... from the top menu + <li> using Window -> Preferences... from the top menu </ul> <ul> <li> Delete selected nodes Removes all selected data nodes from the data storage. <li> Global reinit Re-initializes the render windows to the common bounding box of all data nodes of the data storage that <ul> <li> have not set <tt>"includeInBoundingBox"</tt> to false <li> are <tt>"visible"</tt> </ul> In this case it does not matter on which node this action is performed. <li> Make all nodes invisible Hides all data nodes of the data storage. <li> Reinit selected nodes Re-initializes the render windows to the common bounding box of all selected data nodes of the data storage that <ul> <li> have not set <tt>"includeInBoundingBox"</tt> to false <li> are <tt>"visible"</tt> </ul> <li> Show node information Opens a pop-up window with detailed information about each node, like data type, geometry, DICOM information, file path etc. <li> Toggle visibility of selected nodes: Shows / hides each selected data node according to each node's current visibility state. </ul> \anchor Hotkeys \imageMacro{QmitkDatamanager_Hotkeys.png, "Hotkeys", 16.00} */ diff --git a/Plugins/org.mitk.gui.qt.datastorageviewertest/src/internal/QmitkDataStorageViewerTestControls.ui b/Plugins/org.mitk.gui.qt.datastorageviewertest/src/internal/QmitkDataStorageViewerTestControls.ui index 52a3edab6c..6d496bcf2e 100644 --- a/Plugins/org.mitk.gui.qt.datastorageviewertest/src/internal/QmitkDataStorageViewerTestControls.ui +++ b/Plugins/org.mitk.gui.qt.datastorageviewertest/src/internal/QmitkDataStorageViewerTestControls.ui @@ -1,210 +1,210 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkDataStorageViewerTestControls</class> <widget class="QWidget" name="QmitkDataStorageViewerTestControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>945</width> <height>456</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>Data storage viewer test</string> </property> <layout class="QGridLayout" name="gridLayout"> <item row="0" column="0"> <widget class="QmitkDataStorageListInspector" name="listInspector"/> </item> <item row="0" column="1"> <widget class="QmitkDataStorageTreeInspector" name="treeInspector"/> </item> <item row="1" column="0"> <widget class="QCheckBox" name="selectionProviderCheckBox1"> <property name="text"> <string>Set as selection provider</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QCheckBox" name="selectionProviderCheckBox2"> <property name="text"> <string>Set as selection provider</string> </property> </widget> </item> <item row="2" column="0"> <widget class="QCheckBox" name="selectionListenerCheckBox1"> <property name="text"> <string>Set as selection listener</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QCheckBox" name="selectionListenerCheckBox2"> <property name="text"> <string>Set as selection listener</string> </property> </widget> </item> <item row="3" column="0"> <widget class="QmitkSingleNodeSelectionWidget" name="singleSlot" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="3" column="1"> <widget class="QmitkMultiNodeSelectionWidget" name="multiSlot" native="true"/> </item> <item row="4" column="0"> <widget class="QCheckBox" name="selectionProviderCheckBox3"> <property name="text"> <string>Set as selection provider</string> </property> </widget> </item> <item row="4" column="1"> <widget class="QCheckBox" name="selectionProviderCheckBox4"> <property name="text"> <string>Set as selection provider</string> </property> </widget> </item> <item row="5" column="0"> <widget class="QCheckBox" name="selectionListenerCheckBox3"> <property name="text"> - <string>Set as selection listner</string> + <string>Set as selection listener</string> </property> </widget> </item> <item row="5" column="1"> <widget class="QCheckBox" name="selectionListenerCheckBox4"> <property name="text"> - <string>Set as selection listner</string> + <string>Set as selection listener</string> </property> </widget> </item> <item row="6" column="0"> <widget class="QCheckBox" name="checkOnlyVisible1"> <property name="text"> <string>Only valid nodes</string> </property> </widget> </item> <item row="6" column="1"> <widget class="QCheckBox" name="checkOnlyVisible2"> <property name="text"> <string>Only valid nodes</string> </property> </widget> </item> <item row="7" column="0"> <widget class="QCheckBox" name="checkOnlyImages1"> <property name="text"> <string>Allow only images </string> </property> </widget> </item> <item row="7" column="1"> <widget class="QCheckBox" name="checkOnlyImages2"> <property name="text"> <string>Allow only images (using NodePredicate feature and general invalid message)</string> </property> </widget> </item> <item row="8" column="1"> <widget class="QCheckBox" name="checkOnlyUneven"> <property name="text"> <string>Allow only uneven selection count (using check funcktion feature)</string> </property> </widget> </item> <item row="9" column="0"> <widget class="QCheckBox" name="checkOptional1"> <property name="text"> <string>Is Optional</string> </property> </widget> </item> <item row="9" column="1"> <widget class="QCheckBox" name="checkOptional2"> <property name="text"> <string>Is Optional</string> </property> </widget> </item> <item row="10" column="0"> <widget class="QCheckBox" name="checkEnabled1"> <property name="text"> <string>Is Enabled</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="10" column="1"> <widget class="QCheckBox" name="checkEnabled2"> <property name="text"> <string>Is Enabled</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="11" column="0"> <widget class="QCheckBox" name="checkAuto"> <property name="text"> <string>Auto select node</string> </property> </widget> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkDataStorageListInspector</class> <extends>QWidget</extends> <header location="global">QmitkDataStorageListInspector.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkDataStorageTreeInspector</class> <extends>QWidget</extends> <header location="global">QmitkDataStorageTreeInspector.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkMultiNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkMultiNodeSelectionWidget.h</header> <container>1</container> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox index feb3c7e1f5..e4eb5ea593 100644 --- a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox +++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox @@ -1,73 +1,73 @@ /** \page org_mitk_views_deformableclippingplane The Clipping Plane View \imageMacro{QmitkClippingPlane_Icon.png,"Icon of the Clipping Plane Plugin",5.00} \imageMacro{QmitkClippingPlane_Overview2.png,"Clipping Plane view",16.00} \tableofcontents \section org_mitk_views_clippingPlaneManualOverview Overview -The Clipping Plane view allows you to create clipping planes and calculate the volumina of the devided parts. +The Clipping Plane view allows you to create clipping planes and calculate the volumina of the divided parts. \section org_mitk_views_clippingPlaneTechnicalIssue Technical Issue To use the Update Volumina function your image should be binary. \section org_mitk_views_clippingPlaneManualImageSelection Image Selection The Clipping Plane view makes use of the Data Manager view to give you an overview of all images, segmentations and clipping planes. \imageMacro{QmitkClippingPlane_DataManager.png,"Data Manager is used for selecting the current clipping plane. The reference plane is selected in the drop down box of the control area.",8.00} To select the reference plane use the drop down box in the control area of the Clipping Plane view or the Data Manager. The clipping plane selected in the Data Manager is displayed below the drop down box. If no clipping plane exists or none is selected create a new clipping plane by using the "Create new clipping plane" button. Some items of the graphical user interface might be disabled when no plane is selected. In any case, the application will give you hints if a selection is needed. \section org_mitk_views_clippingPlaneCreating Creating New Clipping Plane If you want to create a new clipping plane select an image from the Data Manager and press the button "Create new clipping plane". Optionally you can enable the "...with surface model" option. \section org_mitk_views_clippingPlaneInteraction Interaction with the planes \imageMacro{QmitkClippingPlane_Interaction.png,"The interaction buttons",5.00} You have different options to interact with the clipping planes: \subsection org_mitk_views_clippingPlaneTranslation Translation In Translation mode you can change the position of the clipping plane. - Click the Translation Button - Move mouse over the selected clipping plane (the plane changes its color from blue to green) - Hold mouse-left button and move the mouse orthogonally to the plane \subsection org_mitk_views_clippingPlaneRotation Rotation In Rotation mode you can change the angle of the clipping plane. - Click the Rotation Button - Move mouse over the selected clipping plane (the plane changes its color from blue to green) - Hold mouse-left button and move the mouse in the direction it should be rotated \subsection org_mitk_views_clippingPlaneDeformation Deformation In Deformation mode you can change the surface of the clipping plane. - Click the Deformation Button - Move mouse over the selected clipping plane (the plane changes its color from blue to green). The deformation area is highlighted in red and yellow. - On mouse-scrolling you can change the size of the deformation area (Scroll-Down = smaller / Scroll-Up = bigger). - Hold mouse-left button and move the mouse orthogonally to the plane to deformate the plane \section org_mitk_views_clippingPlaneUpdateVolumina Update Volumina \imageMacro{QmitkClippingPlane_UpdateVolumina.png,"The 'Update Volumina' button",5.00} -Calculating the volumina of the segmentation parts, which are devided by the clipping plane(s). +Calculating the volumina of the segmentation parts, which are divided by the clipping plane(s). - Create a segmentation (see Segmentation-Manual) - Create one or more clipping plane(s) - Use the interaction buttons (Translation, Rotation, Deformation) to adjust the clipping plane for intersecting the segmentation - - (You can decide which planes shouldnt be included for the calculation by changing their visibility to invisible) + - (You can decide which planes shouldn't be included for the calculation by changing their visibility to invisible) - Click button "Update Volumina" button - The intersected parts are displayed in different colors and their volumina are shown beneath the "Update Volumina" button **/ diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp index 095153cb34..2d2ffa0a09 100644 --- a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp +++ b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp @@ -1,584 +1,584 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkDeformableClippingPlaneView.h" #include <usModuleRegistry.h> // mitk core #include <mitkImageToSurfaceFilter.h> #include <mitkInteractionConst.h> #include <mitkLevelWindowProperty.h> #include <mitkLookupTableProperty.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateNot.h> #include <mitkRenderingModeProperty.h> #include <mitkRotationOperation.h> #include <mitkSurfaceVtkMapper3D.h> #include <mitkVtkRepresentationProperty.h> #include <mitkVtkResliceInterpolationProperty.h> #include <mitkHeightFieldSurfaceClipImageFilter.h> #include <mitkClippingPlaneInteractor3D.h> #include <mitkLabeledImageLookupTable.h> #include <mitkLabeledImageVolumeCalculator.h> #include <mitkSurfaceDeformationDataInteractor3D.h> #include <vtkFloatArray.h> #include <vtkPointData.h> #include <vtkPlaneSource.h> #include <vtkProperty.h> #include <mitkILinkedRenderWindowPart.h> #include <array> const std::string QmitkDeformableClippingPlaneView::VIEW_ID = "org.mitk.views.deformableclippingplane"; QmitkDeformableClippingPlaneView::QmitkDeformableClippingPlaneView() : QmitkAbstractView() , m_Controls(new Ui::QmitkDeformableClippingPlaneViewControls) , m_WorkingNode(nullptr) { auto isImage = mitk::TNodePredicateDataType<mitk::Image>::New(); auto isNotHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); m_IsImagePredicate = mitk::NodePredicateAnd::New(isImage, isNotHelperObject); m_IsClippingPlanePredicate = mitk::NodePredicateProperty::New("clippingPlane", mitk::BoolProperty::New(true)); } QmitkDeformableClippingPlaneView::~QmitkDeformableClippingPlaneView() { if (m_WorkingNode.IsNotNull()) m_WorkingNode->SetDataInteractor(nullptr); } void QmitkDeformableClippingPlaneView::SetFocus() { m_Controls->createNewPlanePushButton->setFocus(); } void QmitkDeformableClippingPlaneView::CreateQtPartControl(QWidget *parent) { m_Controls->setupUi(parent); m_Controls->imageSelectionWidget->SetDataStorage(GetDataStorage()); m_Controls->imageSelectionWidget->SetNodePredicate(m_IsImagePredicate); m_Controls->imageSelectionWidget->SetSelectionIsOptional(false); m_Controls->imageSelectionWidget->SetInvalidInfo("Select an image or segmentation."); m_Controls->imageSelectionWidget->SetPopUpTitel("Select an image or segmentation."); m_Controls->clippingPlaneSelector->SetDataStorage(this->GetDataStorage()); m_Controls->clippingPlaneSelector->SetPredicate(m_IsClippingPlanePredicate); m_Controls->volumeGroupBox->setEnabled(false); m_Controls->interactionSelectionBox->setEnabled(false); m_Controls->planesWarningLabel->hide(); this->CreateConnections(); m_Controls->imageSelectionWidget->SetAutoSelectNewNodes(true); } void QmitkDeformableClippingPlaneView::OnCurrentSelectionChanged(const QList<mitk::DataNode::Pointer>& /*nodes*/) { this->UpdateView(); } void QmitkDeformableClippingPlaneView::OnComboBoxSelectionChanged(const mitk::DataNode* node) { this->DeactivateInteractionButtons(); auto selectedNode = const_cast<mitk::DataNode*>(node); if(nullptr != selectedNode) { if(m_WorkingNode.IsNotNull()) selectedNode->SetDataInteractor(m_WorkingNode->GetDataInteractor()); m_WorkingNode = selectedNode; } this->UpdateView(); } void QmitkDeformableClippingPlaneView::OnCreateNewClippingPlane() { this->DeactivateInteractionButtons(); auto plane = mitk::Surface::New(); auto planeSource = vtkSmartPointer<vtkPlaneSource>::New(); planeSource->SetOrigin(-32.0, -32.0, 0.0); planeSource->SetPoint1(32.0, -32.0, 0.0); planeSource->SetPoint2(-32.0, 32.0, 0.0); planeSource->SetResolution(128, 128); planeSource->Update(); plane->SetVtkPolyData(planeSource->GetOutput()); mitk::ScalarType imageDiagonal = 200.0; auto selectedNode = m_Controls->imageSelectionWidget->GetSelectedNode(); if (selectedNode.IsNotNull()) { auto selectedImage = dynamic_cast<mitk::Image*>(selectedNode->GetData()); if (nullptr != selectedImage) { // check if user wants a surface model if (m_Controls->surfaceModelCheckBox->isChecked()) { //Check if there is a surface node from the image. If not, create one bool createSurfaceFromImage = true; auto isSurface = mitk::NodePredicateDataType::New("Surface"); auto childNodes = GetDataStorage()->GetDerivations(selectedNode, isSurface, true); for (mitk::DataStorage::SetOfObjects::ConstIterator it = childNodes->Begin(); it != childNodes->End(); it++) { if (it.Value().IsNotNull() && it->Value()->GetName() == selectedNode->GetName()) { createSurfaceFromImage = false; it.Value()->SetVisibility(true); } } if (createSurfaceFromImage) { //Lsg 2: Surface for the 3D-perspective auto surfaceFilter = mitk::ImageToSurfaceFilter::New(); surfaceFilter->SetInput(selectedImage); surfaceFilter->SetThreshold(1); surfaceFilter->SetSmooth(true); //Downsampling surfaceFilter->SetDecimate(mitk::ImageToSurfaceFilter::DecimatePro); auto surfaceNode = mitk::DataNode::New(); surfaceNode->SetData(surfaceFilter->GetOutput()); surfaceNode->SetProperty("color", selectedNode->GetProperty("color")); surfaceNode->SetOpacity(0.5); surfaceNode->SetName(selectedNode->GetName()); this->GetDataStorage()->Add(surfaceNode, selectedNode); } } //If an image is selected trim the plane to this. imageDiagonal = selectedImage->GetGeometry()->GetDiagonalLength(); plane->SetOrigin(selectedImage->GetGeometry()->GetCenter()); // Rotate plane mitk::Vector3D rotationAxis; mitk::FillVector3D(rotationAxis, 0.0, 1.0, 0.0); mitk::RotationOperation op(mitk::OpROTATE, selectedImage->GetGeometry()->GetCenter(), rotationAxis, 90.0); plane->GetGeometry()->ExecuteOperation(&op); } } // equivalent to the extent and resolution function of the clipping plane const auto x = imageDiagonal * 0.9; planeSource->SetOrigin(-x / 2.0, -x / 2.0, 0.0); planeSource->SetPoint1(x / 2.0, -x / 2.0, 0.0); planeSource->SetPoint2(-x / 2.0, x / 2.0, 0.0); planeSource->SetResolution(64, 64); planeSource->Update(); plane->SetVtkPolyData(planeSource->GetOutput()); // Set scalars (for colorization of plane) vtkFloatArray *scalars = vtkFloatArray::New(); scalars->SetName("Distance"); scalars->SetNumberOfComponents(1); const auto numerOfPoints = plane->GetVtkPolyData(0)->GetNumberOfPoints(); for (std::remove_const_t<decltype(numerOfPoints)> i = 0; i < plane->GetVtkPolyData(0)->GetNumberOfPoints(); ++i) { scalars->InsertNextValue(-1.0); } plane->GetVtkPolyData(0)->GetPointData()->SetScalars(scalars); plane->GetVtkPolyData(0)->GetPointData()->Update(); auto planeNode = mitk::DataNode::New(); planeNode->SetData(plane); std::stringstream planeName; planeName << "ClippingPlane "; planeName << this->GetAllClippingPlanes()->Size() + 1; planeNode->SetName(planeName.str()); planeNode->AddProperty("clippingPlane", mitk::BoolProperty::New(true)); // Make plane pickable planeNode->SetBoolProperty("pickable", true); mitk::SurfaceVtkMapper3D::SetDefaultProperties(planeNode); // Don't include plane in bounding box! planeNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); // Set lookup table for plane surface visualization auto lookupTablevtk = vtkSmartPointer<vtkLookupTable>::New(); lookupTablevtk->SetHueRange(0.6, 0.0); lookupTablevtk->SetSaturationRange(1.0, 1.0); lookupTablevtk->SetValueRange(1.0, 1.0); lookupTablevtk->SetTableRange(-1.0, 1.0); lookupTablevtk->Build(); auto lookupTable = mitk::LookupTable::New(); lookupTable->SetVtkLookupTable(lookupTablevtk); auto prop = mitk::LookupTableProperty::New(lookupTable); planeNode->SetProperty("LookupTable", prop); planeNode->SetBoolProperty("scalar visibility", true); planeNode->SetBoolProperty("color mode", true); planeNode->SetFloatProperty("ScalarsRangeMinimum", -1.0); planeNode->SetFloatProperty("ScalarsRangeMaximum", 1.0); // Configure material so that only scalar colors are shown planeNode->SetColor(0.0f, 0.0f, 0.0f); planeNode->SetOpacity(1.0f); planeNode->SetFloatProperty("material.wireframeLineWidth", 2.0f); //Set view of plane to wireframe planeNode->SetProperty("material.representation", mitk::VtkRepresentationProperty::New(VTK_WIREFRAME)); //Add the plane to data storage this->GetDataStorage()->Add(planeNode); //Change the index of the selector to the new generated node m_Controls->clippingPlaneSelector->setCurrentIndex(m_Controls->clippingPlaneSelector->Find(planeNode)); m_Controls->interactionSelectionBox->setEnabled(true); if (auto renderWindowPart = dynamic_cast<mitk::ILinkedRenderWindowPart*>(this->GetRenderWindowPart())) { renderWindowPart->EnableSlicingPlanes(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkDeformableClippingPlaneView::OnCalculateClippingVolume() { auto selectedNode = m_Controls->imageSelectionWidget->GetSelectedNode(); if (selectedNode.IsNull()) { MITK_ERROR << "No segmentation selected! Can't calculate volume"; return; } bool isSegmentation = false; selectedNode->GetBoolProperty("binary", isSegmentation); if (!isSegmentation) { MITK_ERROR << "No segmentation selected! Can't calculate volume"; return; } std::vector<mitk::Surface*> clippingPlanes; mitk::DataStorage::SetOfObjects::ConstPointer allClippingPlanes = this->GetAllClippingPlanes(); for (mitk::DataStorage::SetOfObjects::ConstIterator itPlanes = allClippingPlanes->Begin(); itPlanes != allClippingPlanes->End(); itPlanes++) { bool isVisible = false; itPlanes.Value()->GetBoolProperty("visible", isVisible); auto plane = dynamic_cast<mitk::Surface*>(itPlanes.Value()->GetData()); if (isVisible && nullptr != plane) clippingPlanes.push_back(plane); } if (clippingPlanes.empty()) { MITK_ERROR << "No clipping plane selected! Can't calculate volume"; return; } // deactivate Tools this->DeactivateInteractionButtons(); //Clear the list of volumes, before calculating the new values m_Controls->volumeList->clear(); selectedNode->SetBoolProperty("visible", false); - //set some properties for clipping the image-->Output: labled Image + //set some properties for clipping the image-->Output: labeled Image mitk::HeightFieldSurfaceClipImageFilter::Pointer surfaceClipFilter = mitk::HeightFieldSurfaceClipImageFilter::New(); surfaceClipFilter->SetInput(dynamic_cast<mitk::Image*>(selectedNode->GetData())); surfaceClipFilter->SetClippingModeToMultiPlaneValue(); surfaceClipFilter->SetClippingSurfaces(clippingPlanes); surfaceClipFilter->Update(); //delete the old clipped image node mitk::DataStorage::SetOfObjects::ConstPointer oldClippedNode = this->GetDataStorage()->GetSubset(mitk::NodePredicateProperty::New("name", mitk::StringProperty::New("Clipped Image"))); if (oldClippedNode.IsNotNull()) this->GetDataStorage()->Remove(oldClippedNode); //add the new clipped image node auto clippedNode = mitk::DataNode::New(); mitk::Image::Pointer clippedImage = surfaceClipFilter->GetOutput(); clippedImage->DisconnectPipeline(); clippedNode->SetData(clippedImage); clippedNode->SetName("Clipped Image"); clippedNode->SetColor(1.0, 1.0, 1.0); // color property will not be used, labeled image lookuptable will be used instead clippedNode->SetProperty("use color", mitk::BoolProperty::New(false)); clippedNode->SetProperty("reslice interpolation", mitk::VtkResliceInterpolationProperty::New(VTK_RESLICE_NEAREST)); clippedNode->SetOpacity(0.4); this->GetDataStorage()->Add(clippedNode); auto volumeCalculator = mitk::LabeledImageVolumeCalculator::New(); volumeCalculator->SetImage(clippedImage); volumeCalculator->Calculate(); auto volumes = volumeCalculator->GetVolumes(); auto lookupTable = mitk::LabeledImageLookupTable::New(); int lablesWithVolume = 0; const auto numberOfVolumes = volumes.size(); for (std::remove_const_t<decltype(numberOfVolumes)> i = 1; i < numberOfVolumes; ++i) { if (0 != volumes[0]) { lablesWithVolume++; mitk::Color color(GetLabelColor(lablesWithVolume)); lookupTable->SetColorForLabel(i, color.GetRed(), color.GetGreen(), color.GetBlue(), 1.0); QColor qcolor; qcolor.setRgbF(color.GetRed(), color.GetGreen(), color.GetBlue(), 0.7); //output volume as string "x.xx ml" std::stringstream stream; stream << std::fixed << std::setprecision(2) << 0.001 * volumes[i] << " ml"; stream << " ml"; auto item = new QListWidgetItem(); item->setText(QString::fromStdString(stream.str())); item->setBackgroundColor(qcolor); m_Controls->volumeList->addItem(item); } } //set the rendering mode to use the lookup table and level window clippedNode->SetProperty("Image Rendering.Mode", mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR)); mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New(lookupTable.GetPointer()); clippedNode->SetProperty("LookupTable", lutProp); // it is absolutely important, to use the LevelWindow settings provided by // the LUT generator, otherwise, it is not guaranteed, that colors show // up correctly. clippedNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(lookupTable->GetLevelWindow())); } void QmitkDeformableClippingPlaneView::OnTranslationMode(bool check) { if (check) { //uncheck all other buttons m_Controls->rotationPushButton->setChecked(false); m_Controls->deformationPushButton->setChecked(false); mitk::ClippingPlaneInteractor3D::Pointer affineDataInteractor = mitk::ClippingPlaneInteractor3D::New(); affineDataInteractor->LoadStateMachine("ClippingPlaneInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetEventConfig("ClippingPlaneTranslationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetDataNode(m_WorkingNode); } else m_WorkingNode->SetDataInteractor(nullptr); } void QmitkDeformableClippingPlaneView::OnRotationMode(bool check) { if (check) { //uncheck all other buttons m_Controls->translationPushButton->setChecked(false); m_Controls->deformationPushButton->setChecked(false); mitk::ClippingPlaneInteractor3D::Pointer affineDataInteractor = mitk::ClippingPlaneInteractor3D::New(); affineDataInteractor->LoadStateMachine("ClippingPlaneInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetEventConfig("ClippingPlaneRotationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); affineDataInteractor->SetDataNode(m_WorkingNode); } else m_WorkingNode->SetDataInteractor(nullptr); } void QmitkDeformableClippingPlaneView::OnDeformationMode(bool check) { if (check) { //uncheck all other buttons m_Controls->translationPushButton->setChecked(false); m_Controls->rotationPushButton->setChecked(false); mitk::SurfaceDeformationDataInteractor3D::Pointer surfaceDataInteractor = mitk::SurfaceDeformationDataInteractor3D::New(); surfaceDataInteractor->LoadStateMachine("ClippingPlaneInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); surfaceDataInteractor->SetEventConfig("ClippingPlaneDeformationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt")); surfaceDataInteractor->SetDataNode(m_WorkingNode); } else m_WorkingNode->SetDataInteractor(nullptr); } void QmitkDeformableClippingPlaneView::CreateConnections() { connect(m_Controls->imageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkDeformableClippingPlaneView::OnCurrentSelectionChanged); connect(m_Controls->translationPushButton, &QPushButton::toggled, this, &QmitkDeformableClippingPlaneView::OnTranslationMode); connect(m_Controls->rotationPushButton, &QPushButton::toggled, this, &QmitkDeformableClippingPlaneView::OnRotationMode); connect(m_Controls->deformationPushButton, &QPushButton::toggled, this, &QmitkDeformableClippingPlaneView::OnDeformationMode); connect(m_Controls->createNewPlanePushButton, &QPushButton::clicked, this, &QmitkDeformableClippingPlaneView::OnCreateNewClippingPlane); connect(m_Controls->updateVolumePushButton, &QPushButton::clicked, this, &QmitkDeformableClippingPlaneView::OnCalculateClippingVolume); connect(m_Controls->clippingPlaneSelector, &QmitkDataStorageComboBox::OnSelectionChanged, this, &QmitkDeformableClippingPlaneView::OnComboBoxSelectionChanged); } void QmitkDeformableClippingPlaneView::NodeRemoved(const mitk::DataNode* node) { if (m_IsClippingPlanePredicate->CheckNode(node)) { if (this->GetAllClippingPlanes()->Size() <= 1) { m_WorkingNode = nullptr; this->UpdateView(); } } } void::QmitkDeformableClippingPlaneView::NodeChanged(const mitk::DataNode*) { this->UpdateView(); } void QmitkDeformableClippingPlaneView::UpdateView() { auto selectedNode = m_Controls->imageSelectionWidget->GetSelectedNode(); if (selectedNode.IsNotNull()) { m_Controls->selectedReferenceImageLabel->setText(QString::fromUtf8(selectedNode->GetName().c_str())); if (m_WorkingNode.IsNotNull()) { bool isSegmentation = false; selectedNode->GetBoolProperty("binary", isSegmentation); m_Controls->interactionSelectionBox->setEnabled(true); m_Controls->volumeGroupBox->setEnabled(isSegmentation); //clear list --> than search for all shown clipping plans (max 7 planes) m_Controls->selectedClippingPlanesLabel->setText(""); m_Controls->planesWarningLabel->hide(); int volumePlanes = 0; auto allClippingPlanes = this->GetAllClippingPlanes(); for (mitk::DataStorage::SetOfObjects::ConstIterator itPlanes = allClippingPlanes->Begin(); itPlanes != allClippingPlanes->End(); itPlanes++) { bool isVisible = false; itPlanes.Value()->GetBoolProperty("visible", isVisible); if (isVisible) { if (volumePlanes < 7) { ++volumePlanes; m_Controls->selectedClippingPlanesLabel->setText(m_Controls->selectedClippingPlanesLabel->text().append(QString::fromStdString(itPlanes.Value()->GetName()+"\n"))); } else { m_Controls->planesWarningLabel->show(); return; } } } } else { m_Controls->volumeGroupBox->setEnabled(false); m_Controls->interactionSelectionBox->setEnabled(false); m_Controls->selectedClippingPlanesLabel->setText(""); m_Controls->volumeList->clear(); } } else { m_Controls->volumeGroupBox->setEnabled(false); m_Controls->selectedReferenceImageLabel->setText(""); m_Controls->selectedClippingPlanesLabel->setText(""); m_Controls->planesWarningLabel->hide(); m_Controls->interactionSelectionBox->setEnabled(m_WorkingNode.IsNotNull()); } } mitk::DataStorage::SetOfObjects::ConstPointer QmitkDeformableClippingPlaneView::GetAllClippingPlanes() { auto allPlanes = GetDataStorage()->GetSubset(m_IsClippingPlanePredicate); return allPlanes; } mitk::Color QmitkDeformableClippingPlaneView::GetLabelColor(int label) { std::array<float, 3> color = { 0.0f, 0.0f, 0.0f }; switch (label % 6) { case 0: // red color[0] = 1.0f; break; case 1: // green color[1] = 1.0f; break; case 2: // blue color[2] = 1.0f; break; case 3: // yellow color[0] = 1.0f; color[1] = 1.0f; break; case 4: // magenta color[0] = 1.0f; color[2] = 1.0f; break; case 5: // cyan color[1] = 1.0f; color[2] = 1.0f; default: // black break; } int outerCycleNr = label / 6; int cycleSize = std::min(1, static_cast<int>(std::pow(2.0, std::log(outerCycleNr) / std::log(2.0)))); int insideCycleCounter = outerCycleNr % cycleSize; float factor; if (0 == outerCycleNr) { factor = 255.0f; } else { factor = 256.0f / (2.0f * cycleSize) + insideCycleCounter * (256.0f / cycleSize); } color = { std::min(1.0f, color[0] / 256.0f * factor), std::min(1.0f, color[1] / 256.0f * factor), std::min(1.0f, color[2] / 256.0f * factor) }; return mitk::Color(color.data()); } void QmitkDeformableClippingPlaneView::DeactivateInteractionButtons() { m_Controls->translationPushButton->setChecked(false); m_Controls->rotationPushButton->setChecked(false); m_Controls->deformationPushButton->setChecked(false); } diff --git a/Plugins/org.mitk.gui.qt.dicombrowser/CMakeLists.txt b/Plugins/org.mitk.gui.qt.dicombrowser/CMakeLists.txt index f8c21fc0fe..9be5362901 100644 --- a/Plugins/org.mitk.gui.qt.dicombrowser/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.dicombrowser/CMakeLists.txt @@ -1,29 +1,29 @@ project(org_mitk_gui_qt_dicombrowser) # Note: # If we use an installed version of DCMTK then DCMTK_DIR points to the subdirectory # of the installation directory (share/dcmtk) that contains DCMTKConfig.cmake. # Therefore we look for the the storescp command in the '../../bin' directory, too. find_program(DCMTK_STORESCP NAMES storescp storescp${DCMTK_CMAKE_DEBUG_POSTFIX} storescp${CMAKE_DEBUG_POSTFIX} PATHS "${MITK_EXTERNAL_PROJECT_PREFIX}/bin" PATH_SUFFIXES Release Debug - DOC "Dcmtk storage provider which is used to store dicom files which are transfered over network." + DOC "Dcmtk storage provider which is used to store dicom files which are transferred over network." NO_DEFAULT_PATH ) mark_as_advanced(DCMTK_STORESCP) if(NOT EXISTS ${DCMTK_STORESCP}) message(WARNING "Couldn't find program storescp: Query/retrieve of the DICOM plugin won't work!") else() configure_file( org_mitk_gui_qt_dicombrowser_config.h.in org_mitk_gui_qt_dicombrowser_config.h @ONLY) MITK_INSTALL_HELPER_APP(EXECUTABLES ${DCMTK_STORESCP}) mitk_create_plugin( EXPORT_DIRECTIVE DICOM_EXPORT EXPORTED_INCLUDE_SUFFIXES src MODULE_DEPENDS MitkContourModel MitkQtWidgetsExt MitkDICOMUI MitkRT MitkRTUI MitkDICOM PACKAGE_DEPENDS CTK|CTKDICOMWidgets ) endif() diff --git a/Plugins/org.mitk.gui.qt.dicombrowser/documentation/UserManual/QmitkDicom.dox b/Plugins/org.mitk.gui.qt.dicombrowser/documentation/UserManual/QmitkDicom.dox index d69c4c5e55..913fea2601 100644 --- a/Plugins/org.mitk.gui.qt.dicombrowser/documentation/UserManual/QmitkDicom.dox +++ b/Plugins/org.mitk.gui.qt.dicombrowser/documentation/UserManual/QmitkDicom.dox @@ -1,118 +1,118 @@ /** \page org_mitk_editors_dicombrowser The Dicom Browser Plugin \imageMacro{dicombrowser-dox.svg,"Icon of the DICOM Plugin",2.00} \note This article requires a basic knowledge of the DICOM Standard. \tableofcontents \section org_mitk_gui_qt_dicomOverview Overview The DICOM editor is an experimental editor which allows for loading of DICOM images as well as server communication. It features a highly experimental query/retrieve (you need to configure your PACS correspondingly) as well as a DICOM browser. The DICOM browser allows you to navigate the DICOM folder/cd depending on its metadata (patient/study/series) and import selected series for viewing in your MITK based application. It also allows you to store your dicom data in an internal database so you can easily access often used dicom images. It is based on the <a href="https://commontk.org/index.php/Documentation/DICOM_Overview">commonTK (CTK) DICOM funcionality</a>. \section org_mitk_gui_qt_dicomDataHandling Data handling \imageMacro{QmitkDicom_PluginControls.png,"The dicom Plugin controls",7.37} In the image above you see the start page of the dicom plugin. On top of the start page you see four buttons. The Local Storage, the Import CD, the Import Folder and the Query Retrieve button. If you press one of these buttons, the dicom plugin will switch to your local dicom image storage or will start importing dicom images from CD or a folder on your hard drive or it will open the query retrieve screen. <ul> <li> Click the 'Local Storage' button to open the local storage screen. <li> Click the 'Import CD' button to import DICOM data from a CD. <li> Click the 'Import Folder' button to import DICOM date from a directory. <li> Click the 'Query Retrieve' button to open the query retrieve screen. </ul> \subsection org_mitk_gui_qt_dicomStorage Data storage \imageMacro{QmitkDicom_PluginExtended.png,"The DICOM data storage",16.00} If you open the dicom plugin the dicom data storage will be displayed. You are able to see all your stored dicom image data. You can browse your data by clicking on the left arrow beside the name of your data. There are three levels available. The first level is the patient level where you can see the patient data. On the second level you can see the dicom studies for the patient. -on the third level you can see all available series refering to it's study. +on the third level you can see all available series referring to its study. You can delete the data by selecting it and pressing the delete button. -Be careful if you have selected a patient or a study all refering data be deleted. -So if you delete a patient the patient and all studies and series refered to the patient will be deleted. +Be careful if you have selected a patient or a study all referring data be deleted. +So if you delete a patient the patient and all studies and series referred to the patient will be deleted. If you delete a study all series of the study will be deleted. If you want to view the dicom data you have to select a series and click on the View button. -The data will appear in the DataManager and will be dispayed. +The data will appear in the DataManager and will be displayed. \imageMacro{QmitkDicom_DisplayDataManager.png,"Viewed image",16.00} <ul> <li> Click on the arrow on the left of your data to expand or hide dicom data levels. <li> Click the 'Delete' button to delete selected DICOM data. <li> Click the 'View' button to view DICOM data. </ul> \subsection org_mitk_gui_qt_dicomImport Data import \imageMacro{QmitkDicom_ImportDialog.png,"The import dialog checked",9.53} -There are two diffrent ways to import DICOM data. -The First one is to directly imort it into your DICOM data storage. To achieve this you should toggle the checkbox 'Copy on import'. +There are two different ways to import DICOM data. +The First one is to directly import it into your DICOM data storage. To achieve this you should toggle the checkbox 'Copy on import'. The second approach is, to have a look at the data first before importing it. To do that you simply don't check 'Copy on import'. -This will leed you to the leed you to the 'External Dicom Data' screen which provides you a preview of the data containing in youre choosen folder. +This will leed you to the leed you to the 'External Dicom Data' screen which provides you a preview of the data containing in you're chosen folder. You can import the data here by selecting it and pressing the 'Download' button. It is also possible to view DICOM series directly in Mitk by selecting it here and pressing the 'View' button. <ul> <li> Click 'Import Folder' or 'Import CD' button to open the import dialog.</li> <ul> <li> Enable the 'Copy on import' checkbox and choose a folder to import into data storage directly.</li> <li> Disable the 'Copy on import' checkbox to get to the 'External Dicom Data' screen.</li> <ul> <li> Click on the arrow on the left of your data to expand or hide dicom data levels. <li> Click the 'Download' button to download selected DICOM data to your DICOM data storage. <li> Click the 'View' button to view DICOM data. </ul> </ul> </ul> \section org_mitk_gui_qt_dicomQueryRetrieve Query/Retrieve \warning This plugin is experimental and not all of the described features behave as expected. \note The query retrieve plugin only works if the PACS you are calling knows your machine settings. There are also issues when you are running a firewall. The query retrieve workflow allows you to get DICOM data from a server. \imageMacro{QmitkDicom_QueryRetrieve.png,"The query retrieve screen",16.00} \subsection org_mitk_gui_qt_dicomQuery Query \imageMacro{QmitkDicom_Nodes.png,"The DICOM network configuration",11.26} By performing a DICOM query you will ask a server for it's DICOM data. This requires to setup the DICOM network configuration of your system and the server. By clicking on 'Add Server' a new plain server field will appear. Now you can give it a name of your choice. -Fill the servers "DICOM name" the AETitle. Type in it's url, it's port and the specific DICOM protocoll you want to use for image transfer. -\note I recommend not to use CGET because most of the PACS systems (Image Servers) don't support that protocoll. +Fill the servers "DICOM name" the AETitle. Type in it's url, it's port and the specific DICOM protocol you want to use for image transfer. +\note I recommend not to use CGET because most of the PACS systems (Image Servers) don't support that protocol. You can configure the DICOM network configuration of your machine by editing the 'Calling AETiltle', the 'Storage AETitle' and The 'Storage Port' text fields. -But normaly you don't have to change your configuration. +But normally you don't have to change your configuration. \imageMacro{QmitkDicom_FilterWidget.png,"The DICOM search options",3.66} After you have finished your network configuration and before you start the query you should use the 'Search Options' to specify your query. Otherwise all data on the server will be queried and you will have to wait for a long time. You can specify your query by searching for a specific patient name or a study or a serie or a specific DICOM object by it's id. -You are allowed to include or exclude DICOM modalities from your query and you can specify a specific time in which the DICOM images you are searching fo might been captured. +You are allowed to include or exclude DICOM modalities from your query and you can specify a specific time in which the DICOM images you are searching for might been captured. When you finished that you can click the query button and the queried DICOM data will appear. <ul> <li> Click on the 'Add Server' button. <ul> <li> Edit 'Name' field. <li> Edit 'AETitle' field. - <li> Edit 'Adress' field. + <li> Edit 'Address' field. <li> Edit 'Port' field. </ul> <li> Set search options. <li> Click on 'Query' button. </ul> \subsection org_mitk_gui_qt_dicomRetrieve Retrieve \imageMacro{QmitkDicom_Retrieve.png,"The queried DICOM data.",15.22} After the query you are able to select the queried data and click the 'Retrieve' button. This will store the queried DICOM data into your DICOM storage. Click on the 'Local Storage' button and work with your new data. <ul> <li> Click on the 'Retrieve' button to retrieve the data to your DICOM storage. <li> Click on the 'Local Storage' button. </ul> */ diff --git a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomBrowser.h b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomBrowser.h index a30841bbba..40cf1e6355 100644 --- a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomBrowser.h +++ b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomBrowser.h @@ -1,149 +1,149 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkDicomBrowser_h #define QmitkDicomBrowser_h // Blueberry #include <berryIPartListener.h> #include <berryISelectionListener.h> #include <berryQtEditorPart.h> // MITK #include "DicomEventHandler.h" #include "QmitkDicomDataEventPublisher.h" #include "QmitkDicomDirectoryListener.h" #include "QmitkStoreSCPLauncher.h" #include "QmitkStoreSCPLauncherBuilder.h" #include "ui_QmitkDicomBrowserControls.h" #include <org_mitk_gui_qt_dicombrowser_Export.h> // Qt #include <QObject> #include <QString> #include <QStringList> #include <QThread> #include <QVariant> namespace mitk { class IPreferences; } /** * \brief QmitkDicomBrowser is an editor providing functionality for dicom storage and import and query retrieve functionality. * * \sa berry::IPartListener * \ingroup ${plugin_target}_internal */ class DICOM_EXPORT QmitkDicomBrowser : public berry::QtEditorPart, virtual public berry::IPartListener { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: berryObjectMacro(QmitkDicomBrowser); static const std::string EDITOR_ID; static const QString TEMP_DICOM_FOLDER_SUFFIX; /** * \brief QmitkDicomBrowser constructor. */ QmitkDicomBrowser(); /** * \brief QmitkDicomBrowser destructor. */ ~QmitkDicomBrowser() override; /** * \brief Init initialize the editor. */ void Init(berry::IEditorSite::Pointer site, berry::IEditorInput::Pointer input) override; void SetFocus() override; void DoSave() override {} void DoSaveAs() override {} bool IsDirty() const override { return false; } bool IsSaveAsAllowed() const override { return false; } virtual void OnPreferencesChanged(const mitk::IPreferences* prefs); signals: /** * \brief SignalStartDicomImport is enitted when dicom directory for import was selected. */ void SignalStartDicomImport(const QString&); protected slots: /// \brief Called when import is finished. void OnDicomImportFinished(); /// \brief Called when Query Retrieve or Import Folder was clicked. void OnTabChanged(int); /// \brief Called when view button is clicked. Sends out an event for adding the current selected file to the mitkDataStorage. void OnViewButtonAddToDataManager(QHash<QString, QVariant> eventProperties); /// \brief Called when status of dicom storage provider changes. void OnStoreSCPStatusChanged(const QString& status); /// \brief Called when dicom storage provider emits a network error. void OnDicomNetworkError(const QString& status); protected: /// \brief StartStoreSCP starts dicom storage provider. void StartStoreSCP(); /// \brief StopStoreSCP stops dicom storage provider. void StopStoreSCP(); /// \brief TestHandler initializes event handler. void TestHandler(); - /// \brief CreateTemporaryDirectory creates temporary directory in which temorary dicom objects are stored. + /// \brief CreateTemporaryDirectory creates temporary directory in which temporary dicom objects are stored. void CreateTemporaryDirectory(); /// \brief StartDicomDirectoryListener starts dicom directory listener. void StartDicomDirectoryListener(); /** * \brief CreateQtPartControl(QWidget *parent) sets the view objects from ui_QmitkDicomBrowserControls.h. * * \param parent is a pointer to the parent widget */ void CreateQtPartControl(QWidget *parent) override; /// \brief SetPluginDirectory Sets plugin directory. void SetPluginDirectory(); Events::Types GetPartEventTypes() const override; ctkFileDialog* m_ImportDialog; Ui::QmitkDicomBrowserControls m_Controls; QmitkDicomDirectoryListener* m_DicomDirectoryListener; QmitkStoreSCPLauncherBuilder m_Builder; QmitkStoreSCPLauncher* m_StoreSCPLauncher; DicomEventHandler* m_Handler; QmitkDicomDataEventPublisher* m_Publisher; QString m_PluginDirectory; QString m_TempDirectory; QString m_DatabaseDirectory; }; #endif diff --git a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomDirectoryListener.h b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomDirectoryListener.h index c65217c047..aeff79f078 100644 --- a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomDirectoryListener.h +++ b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkDicomDirectoryListener.h @@ -1,120 +1,120 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkDicomDirectoryListener_h #define QmitkDicomDirectoryListener_h #include<QObject> #include<QString> #include<QHash> #include <QStringList> #include <QFileSystemWatcher> #include <QDir> #include<QTimer> /** * \brief QmitkDicomDirectoryListener class listens on a given directory for incomng files. */ class QmitkDicomDirectoryListener : public QObject { Q_OBJECT public: /** * \brief QmitkDicomDirectoryListener default constructor. */ QmitkDicomDirectoryListener(); /** * \brief QmitkDicomDirectoryListener default destructor. */ ~QmitkDicomDirectoryListener() override; /** * \brief sets listened directory. * \note that only one directory can be set. */ void SetDicomListenerDirectory(const QString&); /** * \brief get filepath to the listened directory. */ QString GetDicomListenerDirectory(); /** * \brief get the status whether the directorey listener is listening or not. */ bool IsListening(); /** * \brief set the directory listener listening. Id listening is set false the listener won't listen anymore. */ void SetListening(bool listening); /** * \brief set m_DicomFolderSuffix. */ void SetDicomFolderSuffix(QString suffix); signals: /** * \brief signal starts the dicom import with given file list. */ void SignalStartDicomImport(const QStringList&); public slots: /** * \brief called when listener directory changes */ void OnDirectoryChanged(const QString&); /** - * \brief called when error occours during dicom store request + * \brief called when error occurs during dicom store request */ void OnDicomNetworkError(const QString&); protected: /** * \brief creates directory if it's not already existing. */ void CreateListenerDirectory(const QDir& directory); /** * \brief Composes the filename and initializes m_LastRetrievedFile with it. */ void SetFilesToImport(); /** * \brief removes files from listener directory. */ void RemoveTemporaryFiles(); QString m_DicomFolderSuffix; QFileSystemWatcher* m_FileSystemWatcher; QStringList m_FilesToImport; QHash<QString,QString> m_AlreadyImportedFiles; QDir m_DicomListenerDirectory; bool m_IsListening; }; #endif diff --git a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.cpp b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.cpp index b9ee7254b4..1ef4353f0e 100644 --- a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.cpp +++ b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.cpp @@ -1,199 +1,199 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkStoreSCPLauncher.h" #include <QMessageBox> #include <QProcessEnvironment> #include <mitkLog.h> #include <fstream> #include <iostream> #include <QFile> #include <QTextStream> #include <QIODevice> #include <QDir> #include <QDirIterator> #include <QCoreApplication> #include "org_mitk_gui_qt_dicombrowser_config.h" QmitkStoreSCPLauncher::QmitkStoreSCPLauncher(QmitkStoreSCPLauncherBuilder* builder) : m_StoreSCP(new QProcess()) { m_StoreSCP->setProcessChannelMode(QProcess::MergedChannels); connect( m_StoreSCP, SIGNAL(error(QProcess::ProcessError)),this, SLOT(OnProcessError(QProcess::ProcessError))); connect( m_StoreSCP, SIGNAL(stateChanged(QProcess::ProcessState)),this, SLOT(OnStateChanged(QProcess::ProcessState))); connect( m_StoreSCP, SIGNAL(readyReadStandardOutput()),this, SLOT(OnReadyProcessOutput())); SetArgumentList(builder); } QmitkStoreSCPLauncher::~QmitkStoreSCPLauncher() { disconnect( m_StoreSCP, SIGNAL(error(QProcess::ProcessError)),this, SLOT(OnProcessError(QProcess::ProcessError))); disconnect( m_StoreSCP, SIGNAL(stateChanged(QProcess::ProcessState)),this, SLOT(OnStateChanged(QProcess::ProcessState))); disconnect( m_StoreSCP, SIGNAL(readyReadStandardOutput()),this, SLOT(OnReadyProcessOutput())); m_StoreSCP->close(); m_StoreSCP->waitForFinished(1000); delete m_StoreSCP; } void QmitkStoreSCPLauncher::StartStoreSCP() { FindPathToStoreSCP(); m_StoreSCP->start(m_PathToStoreSCP,m_ArgumentList); } void QmitkStoreSCPLauncher::FindPathToStoreSCP() { QString appPath= QCoreApplication::applicationDirPath(); if(m_PathToStoreSCP.isEmpty()) { QString fileName; #ifdef _WIN32 fileName = "/storescp.exe"; #else fileName = "/storescp"; #endif m_PathToStoreSCP = appPath + fileName; - //In developement the storescp isn't copied into bin directory + //In development the storescp isn't copied into bin directory if(!QFile::exists(m_PathToStoreSCP)) { m_PathToStoreSCP = static_cast<QString>(DCMTK_STORESCP); } } } void QmitkStoreSCPLauncher::OnReadyProcessOutput() { QString out(m_StoreSCP->readAllStandardOutput()); QStringList allDataList,importList; allDataList = out.split("\n",QString::SkipEmptyParts); QStringListIterator it(allDataList); while(it.hasNext()) { QString output = it.next(); if (output.contains("E: ")) { output.replace("E: ",""); m_ErrorText = output; OnProcessError(QProcess::UnknownError); return; } if(output.contains("I: storing DICOM file: ")) { output.replace("I: storing DICOM file: ",""); output.replace("\\", "/"); // cannot handle backslashes output.replace("\r", ""); // cannot handle carriage return importList += output; } } if(!importList.isEmpty()) { emit SignalStartImport(importList); } } void QmitkStoreSCPLauncher::OnProcessError(QProcess::ProcessError err) { switch(err) { case QProcess::FailedToStart: m_ErrorText.prepend("Failed to start storage provider: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; case QProcess::Crashed: m_ErrorText.prepend("Storage provider closed: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; case QProcess::Timedout: m_ErrorText.prepend("Storage provider timeout: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; case QProcess::WriteError: m_ErrorText.prepend("Storage provider write error: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; case QProcess::ReadError: m_ErrorText.prepend("Storage provider read error: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; case QProcess::UnknownError: m_ErrorText.prepend("Storage provider unknown error: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; default: m_ErrorText.prepend("Storage provider unknown error: "); m_ErrorText.append(m_StoreSCP->errorString()); emit SignalStoreSCPError(m_ErrorText); m_ErrorText.clear(); break; } } void QmitkStoreSCPLauncher::OnStateChanged(QProcess::ProcessState status) { switch(status) { case QProcess::NotRunning: m_StatusText.prepend("Storage provider not running!"); emit SignalStatusOfStoreSCP(m_StatusText); m_StatusText.clear(); break; case QProcess::Starting: m_StatusText.prepend("Starting storage provider!"); emit SignalStatusOfStoreSCP(m_StatusText); m_StatusText.clear(); break; case QProcess::Running: m_StatusText.prepend(m_ArgumentList[0]).prepend(" Port: ").prepend(m_ArgumentList[2]).prepend(" AET: ").prepend("Storage provider running! "); emit SignalStatusOfStoreSCP(m_StatusText); m_StatusText.clear(); break; default: m_StatusText.prepend("Storage provider unknown error!"); emit SignalStatusOfStoreSCP(m_StatusText); m_StatusText.clear(); break; } } void QmitkStoreSCPLauncher::SetArgumentList(QmitkStoreSCPLauncherBuilder* builder) { m_ArgumentList << *builder->GetPort() << QString("-aet") <<*builder->GetAETitle() << *builder->GetTransferSyntax() << *builder->GetOtherNetworkOptions() << *builder->GetMode() << QString("-od") << *builder->GetOutputDirectory(); } QString QmitkStoreSCPLauncher::ArgumentListToQString() { QString argumentString; QStringListIterator argumentIterator(m_ArgumentList); while(argumentIterator.hasNext()) { argumentString.append(" "); argumentString.append(argumentIterator.next()); } return argumentString; } diff --git a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.h b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.h index 685fb5d394..dd66d73a4a 100644 --- a/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.h +++ b/Plugins/org.mitk.gui.qt.dicombrowser/src/internal/QmitkStoreSCPLauncher.h @@ -1,113 +1,113 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkStoreSCPLauncher_h #define QmitkStoreSCPLauncher_h #include <QProcess> #include <QString> #include "QmitkStoreSCPLauncherBuilder.h" /** * \brief QmitkStoreSCPLauncher launches the dcmtk storage provider commandline tool in another process and provides basic interoperability with it. */ class QmitkStoreSCPLauncher : public QObject { Q_OBJECT public: /** * \brief QmitkStoreSCPLauncher constructor. */ QmitkStoreSCPLauncher(QmitkStoreSCPLauncherBuilder* builder); /** * \brief QmitkStoreSCPLauncher constructor. */ ~QmitkStoreSCPLauncher() override; public slots: /** * \brief Starts a storage provider in a new process. */ void StartStoreSCP(); /** * \brief Called when storage provider process emits error. */ void OnProcessError(QProcess::ProcessError error); /** * \brief Called when storage provider process changes its state. */ void OnStateChanged(QProcess::ProcessState status); /** * \brief Called when storage provider process provides new information on its standard output. */ void OnReadyProcessOutput(); signals: /** * \brief signal is emitted if status of storage provider process has changend. * \param QString containing m_StatusText. */ void SignalStatusOfStoreSCP(const QString&); /** - * \brief signal is emitted an error occours while storage provider process is running. + * \brief signal is emitted an error occurs while storage provider process is running. * \param QString containing m_ErrorText. */ void SignalStoreSCPError(const QString& errorText = ""); /** * \brief signal is emitted when storage provider process starts storing dicom files. * \param QStringList& of processed dicom files. */ void SignalStartImport(const QStringList&); /** * \brief signal is emitted if import of storage provider process has finished. * \note currently not used. */ void SignalFinishedImport(); private: /** * \brief DicomEventHandler constructor. */ void FindPathToStoreSCP(); /** * \brief DicomEventHandler constructor. * \param QmitkStoreSCPLauncherBuilder* to builder object. */ void SetArgumentList(QmitkStoreSCPLauncherBuilder* builder); /** * \brief Converts the m_ArgumentList into a QString containing all arguments from list. */ QString ArgumentListToQString(); QString m_PathToStoreSCP; QString m_ErrorText; QString m_StatusText; QProcess* m_StoreSCP; QStringList m_ArgumentList; QStringList m_ImportFilesList; }; #endif diff --git a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/DoseVisualizationPreferencePage.cpp b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/DoseVisualizationPreferencePage.cpp index 09d2646799..1c5fa5c573 100644 --- a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/DoseVisualizationPreferencePage.cpp +++ b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/DoseVisualizationPreferencePage.cpp @@ -1,397 +1,397 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "DoseVisualizationPreferencePage.h" #include "mitkRTUIConstants.h" #include <QWidget> #include <QMessageBox> #include <QInputDialog> #include <QMenu> #include <mitkCoreServices.h> #include <mitkIPreferencesService.h> #include <mitkIPreferences.h> #include <QmitkDoseColorDelegate.h> #include <QmitkDoseValueDelegate.h> #include <QmitkDoseVisualStyleDelegate.h> #include <QmitkIsoDoseLevelSetModel.h> #include "mitkIsoLevelsGenerator.h" #include "org_mitk_gui_qt_dosevisualization_Activator.h" namespace { mitk::IPreferences* GetPreferences() { auto* preferencesService = mitk::CoreServices::GetPreferencesService(); return preferencesService->GetSystemPreferences()->Node(mitk::RTUIConstants::ROOT_DOSE_VIS_PREFERENCE_NODE_ID); } } DoseVisualizationPreferencePage::DoseVisualizationPreferencePage() : m_MainControl(nullptr), m_Controls(nullptr), m_referenceDoseChanged(false), m_presetMapChanged(false), m_globalVisChanged(false) { } DoseVisualizationPreferencePage::~DoseVisualizationPreferencePage() { delete m_LevelSetModel; delete m_DoseColorDelegate; delete m_DoseValueDelegate; delete m_DoseVisualDelegate; delete m_Controls; } void DoseVisualizationPreferencePage::Init(berry::IWorkbench::Pointer ) { } void DoseVisualizationPreferencePage::CreateQtControl(QWidget* parent) { m_LevelSetModel = new QmitkIsoDoseLevelSetModel(this); m_DoseColorDelegate = new QmitkDoseColorDelegate(this); m_DoseValueDelegate = new QmitkDoseValueDelegate(this); m_DoseVisualDelegate = new QmitkDoseVisualStyleDelegate(this); m_MainControl = new QWidget(parent); m_Controls = new Ui::DoseVisualizationPreferencePageControls; m_Controls->setupUi( m_MainControl ); this->m_Controls->isoLevelSetView->setModel(m_LevelSetModel); this->m_Controls->isoLevelSetView->setItemDelegateForColumn(0,m_DoseColorDelegate); this->m_Controls->isoLevelSetView->setItemDelegateForColumn(1,m_DoseValueDelegate); this->m_Controls->isoLevelSetView->setItemDelegateForColumn(2,m_DoseVisualDelegate); this->m_Controls->isoLevelSetView->setItemDelegateForColumn(3,m_DoseVisualDelegate); this->m_Controls->isoLevelSetView->setContextMenuPolicy(Qt::CustomContextMenu); connect(m_Controls->spinReferenceDose, SIGNAL(valueChanged(double)), m_LevelSetModel, SLOT(setReferenceDose(double))); connect(m_Controls->spinReferenceDose, SIGNAL(valueChanged(double)), this, SLOT(OnReferenceDoseChanged(double))); connect(m_Controls->checkGlobalSync, SIGNAL(toggled(bool)), m_Controls->spinReferenceDose, SLOT(setEnabled(bool))); connect(m_Controls->radioAbsDose, SIGNAL(toggled(bool)), m_LevelSetModel, SLOT(setShowAbsoluteDose(bool))); connect(m_Controls->isoLevelSetView, SIGNAL(customContextMenuRequested(const QPoint&)), this, SLOT(OnShowContextMenuIsoSet(const QPoint&))); connect(m_Controls->listPresets, SIGNAL(currentItemChanged ( QListWidgetItem *, QListWidgetItem *)), this, SLOT(OnCurrentItemChanged ( QListWidgetItem *, QListWidgetItem *))); connect(m_Controls->btnAddPreset, SIGNAL(clicked(bool)), this, SLOT(OnAddPresetClicked(bool))); connect(m_Controls->btnDelPreset, SIGNAL(clicked(bool)), this, SLOT(OnDelPresetClicked(bool))); connect(m_Controls->btnResetPreset, SIGNAL(clicked(bool)), this, SLOT(OnResetPresetClicked(bool))); connect(m_Controls->btnDelLevel, SIGNAL(clicked(bool)), this, SLOT(OnDelLevelClicked(bool))); connect(m_Controls->btnAddLevel, SIGNAL(clicked(bool)), this, SLOT(OnAddLevelClicked(bool))); connect(m_Controls->checkGlobalVisColorWash, SIGNAL(toggled(bool)), this, SLOT(OnGlobalVisChanged(bool))); connect(m_Controls->checkGlobalVisIsoLine, SIGNAL(toggled(bool)), this, SLOT(OnGlobalVisChanged(bool))); this->Update(); } QWidget* DoseVisualizationPreferencePage::GetQtControl() const { return m_MainControl; } bool DoseVisualizationPreferencePage::PerformOk() { auto* prefs = GetPreferences(); prefs->PutBool(mitk::RTUIConstants::DOSE_DISPLAY_ABSOLUTE_ID,m_Controls->radioAbsDose->isChecked()); prefs->PutBool(mitk::RTUIConstants::GLOBAL_VISIBILITY_COLORWASH_ID,m_Controls->checkGlobalVisColorWash->isChecked()); prefs->PutBool(mitk::RTUIConstants::GLOBAL_VISIBILITY_ISOLINES_ID,m_Controls->checkGlobalVisIsoLine->isChecked()); prefs->PutDouble(mitk::RTUIConstants::REFERENCE_DOSE_ID,m_Controls->spinReferenceDose->value()); prefs->PutBool(mitk::RTUIConstants::GLOBAL_REFERENCE_DOSE_SYNC_ID, m_Controls->checkGlobalSync->isChecked()); mitk::StorePresetsMap(this->m_Presets); if (this->m_Presets.find(this->m_selectedPresetName)==this->m_Presets.end()) { //the preset currently selected in the application is not available any more. Change it to a valid one. mitk::SetSelectedPresetName(this->m_Presets.begin()->first); } if (this->m_LevelSetModel->isModified()) { this->m_presetMapChanged = true; } if (m_referenceDoseChanged) { mitk::SignalReferenceDoseChange(m_Controls->checkGlobalSync->isChecked(), m_Controls->spinReferenceDose->value(), mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()); } if (m_presetMapChanged) { mitk::SignalPresetMapChange(mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()); } if(m_globalVisChanged) { mitk::SignalGlobalVisChange(m_Controls->checkGlobalSync->isChecked(), m_Controls->checkGlobalVisIsoLine->isChecked(), m_Controls->checkGlobalVisColorWash->isChecked(), mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()); } return true; } void DoseVisualizationPreferencePage::PerformCancel() { } void DoseVisualizationPreferencePage::Update() { auto* prefs = GetPreferences(); m_Controls->checkGlobalVisColorWash->setChecked(prefs->GetBool(mitk::RTUIConstants::GLOBAL_VISIBILITY_COLORWASH_ID, true)); m_Controls->checkGlobalVisIsoLine->setChecked(prefs->GetBool(mitk::RTUIConstants::GLOBAL_VISIBILITY_ISOLINES_ID, true)); m_Controls->radioAbsDose->setChecked(prefs->GetBool(mitk::RTUIConstants::DOSE_DISPLAY_ABSOLUTE_ID, true)); m_Controls->radioRelDose->setChecked(!(prefs->GetBool(mitk::RTUIConstants::DOSE_DISPLAY_ABSOLUTE_ID, false))); m_Controls->spinReferenceDose->setValue(prefs->GetDouble(mitk::RTUIConstants::REFERENCE_DOSE_ID, mitk::RTUIConstants::DEFAULT_REFERENCE_DOSE_VALUE)); m_Controls->checkGlobalSync->setChecked(prefs->GetBool(mitk::RTUIConstants::GLOBAL_REFERENCE_DOSE_SYNC_ID, true)); m_referenceDoseChanged = false; m_presetMapChanged = false; m_globalVisChanged = false; this->m_Presets = mitk::LoadPresetsMap(); if(m_Presets.empty()) return; this->m_selectedPresetName = mitk::GetSelectedPresetName(); UpdatePresetsWidgets(); } mitk::IsoDoseLevelSet* DoseVisualizationPreferencePage::GetSelectedIsoLevelSet() { QListWidgetItem* selectedItem = m_Controls->listPresets->currentItem(); mitk::IsoDoseLevelSet::Pointer result; if (selectedItem) { result = m_Presets[selectedItem->text().toStdString()]; } return result; } void DoseVisualizationPreferencePage::UpdateLevelSetWidgets() { this->m_Controls->btnAddLevel->setEnabled(this->GetSelectedIsoLevelSet()!=nullptr); QModelIndex selectedIndex = m_Controls->isoLevelSetView->currentIndex(); this->m_Controls->btnDelLevel->setEnabled(this->GetSelectedIsoLevelSet()!=nullptr && selectedIndex.isValid()); } void DoseVisualizationPreferencePage::UpdatePresetsWidgets() { m_Controls->listPresets->clear(); QListWidgetItem* selectedItem = nullptr; for (PresetMapType::iterator pos = m_Presets.begin(); pos != m_Presets.end(); ++pos) { QListWidgetItem* item = new QListWidgetItem(QString::fromStdString(pos->first)); if (!selectedItem) { selectedItem = item; } m_Controls->listPresets->addItem(item); } if (selectedItem) { m_Controls->listPresets->setCurrentItem(selectedItem); } if (this->m_LevelSetModel->isModified()) { this->m_presetMapChanged = true; } this->m_LevelSetModel->setIsoDoseLevelSet(this->GetSelectedIsoLevelSet()); m_Controls->btnDelPreset->setEnabled((m_Controls->listPresets->currentItem() != nullptr) && (m_Controls->listPresets->count()>1)); } void DoseVisualizationPreferencePage::OnCurrentItemChanged (QListWidgetItem*, QListWidgetItem*) { this->m_LevelSetModel->setIsoDoseLevelSet(this->GetSelectedIsoLevelSet()); } void DoseVisualizationPreferencePage::OnShowContextMenuIsoSet(const QPoint& pos) { QPoint globalPos = m_Controls->isoLevelSetView->viewport()->mapToGlobal(pos); QModelIndex selectedIndex = m_Controls->isoLevelSetView->currentIndex(); QMenu viewMenu; QAction* addLevelAct = viewMenu.addAction("Add new level"); QAction* delLevelAct = viewMenu.addAction("Delete selected level"); delLevelAct->setEnabled(selectedIndex.isValid()); viewMenu.addSeparator(); QAction* invertIsoLineAct = viewMenu.addAction("Invert iso line visibility"); QAction* activateIsoLineAct = viewMenu.addAction("Activate all iso lines"); QAction* deactivateIsoLineAct = viewMenu.addAction("Deactivate all iso lines"); viewMenu.addSeparator(); QAction* invertColorWashAct = viewMenu.addAction("Invert color wash visibility"); QAction* activateColorWashAct = viewMenu.addAction("Activate all color wash levels"); QAction* deactivateColorWashAct = viewMenu.addAction("Deactivate all color wash levels"); viewMenu.addSeparator(); QAction* swapAct = viewMenu.addAction("Swap iso line/color wash visibility"); QAction* selectedItem = viewMenu.exec(globalPos); if (selectedItem == invertIsoLineAct) { this->m_LevelSetModel->invertVisibilityIsoLines(); } else if (selectedItem == activateIsoLineAct) { this->m_LevelSetModel->switchVisibilityIsoLines(true); } else if (selectedItem == deactivateIsoLineAct) { this->m_LevelSetModel->switchVisibilityIsoLines(false); } else if (selectedItem == invertColorWashAct) { this->m_LevelSetModel->invertVisibilityColorWash(); } else if (selectedItem == activateColorWashAct) { this->m_LevelSetModel->switchVisibilityColorWash(true); } else if (selectedItem == deactivateColorWashAct) { this->m_LevelSetModel->switchVisibilityColorWash(false); } else if (selectedItem == swapAct) { this->m_LevelSetModel->swapVisibility(); } else if (selectedItem == addLevelAct) { this->m_LevelSetModel->addLevel(); } else if (selectedItem == delLevelAct) { this->m_LevelSetModel->deleteLevel(selectedIndex); } } void DoseVisualizationPreferencePage::OnAddPresetClicked(bool) { bool done = false; QString name = tr("new_preset"); while (!done) { bool ok; name = QInputDialog::getText(m_MainControl, tr("Define name of new preset."), tr("Preset name:"), QLineEdit::Normal, name, &ok); if (!ok) { - return; //cancled by user; + return; //canceled by user; } bool uniqueName = m_Presets.find(name.toStdString()) == m_Presets.end(); if (!uniqueName) { QMessageBox box; box.setText(tr("New preset name is not unique. Please, choose another one.")); box.exec(); } bool validName = name.indexOf(tr("/")) ==-1; if (!validName) { QMessageBox box; box.setText(tr("New preset name is not valid. Please don't use \"/\".")); box.exec(); } done = uniqueName && validName; } mitk::IsoDoseLevelSet::Pointer newSet = mitk::GenerateIsoLevels_Virtuos(); m_Presets.insert(std::make_pair(name.toStdString(),newSet)); m_presetMapChanged = true; UpdatePresetsWidgets(); } void DoseVisualizationPreferencePage::OnDelPresetClicked(bool) { QListWidgetItem* selectedItem = m_Controls->listPresets->currentItem(); if (selectedItem) { if (m_Controls->listPresets->count() > 1) { m_Presets.erase(selectedItem->text().toStdString()); m_presetMapChanged = true; this->UpdatePresetsWidgets(); } } } void DoseVisualizationPreferencePage::OnResetPresetClicked(bool) { QMessageBox box; box.setText("Do you want to reset the presets?"); box.setInformativeText("If you reset the presets. All user defined presets will be removed and the default presets will be loaded."); box.setStandardButtons(QMessageBox::Yes | QMessageBox::No); box.setDefaultButton(QMessageBox::No); int ret = box.exec(); if (ret == QMessageBox::Yes) { mitk::IsoDoseLevelSet::Pointer newSet = mitk::GenerateIsoLevels_Virtuos(); m_Presets.clear(); m_Presets.insert(std::make_pair("Virtuos",newSet)); m_presetMapChanged = true; UpdatePresetsWidgets(); } } void DoseVisualizationPreferencePage::OnAddLevelClicked(bool) { this->m_LevelSetModel->addLevel(); } void DoseVisualizationPreferencePage::OnDelLevelClicked(bool) { QModelIndex selectedIndex = m_Controls->isoLevelSetView->currentIndex(); if (!selectedIndex.isValid()) { selectedIndex = m_Controls->isoLevelSetView->indexAt(QPoint(1,1)); } this->m_LevelSetModel->deleteLevel(selectedIndex); } void DoseVisualizationPreferencePage::OnReferenceDoseChanged(double) { this->m_referenceDoseChanged = true; } void DoseVisualizationPreferencePage::OnGlobalVisChanged(bool) { this->m_globalVisChanged = true; } diff --git a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp index 4b5b2ff5f4..abce4fae23 100644 --- a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp +++ b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp @@ -1,821 +1,821 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Qt #include <QMessageBox> #include <QMenu> // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // MITK #include <mitkNodePredicateDataProperty.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateNot.h> #include <mitkDoseNodeHelper.h> #include <mitkPropertyNameHelper.h> #include <mitkRTConstants.h> #include <mitkIsoDoseLevelSetProperty.h> #include <mitkIsoDoseLevelVectorProperty.h> #include <mitkIsoLevelsGenerator.h> #include <mitkRTUIConstants.h> #include <mitkTransferFunction.h> #include <mitkTransferFunctionProperty.h> #include <service/event/ctkEventAdmin.h> #include <service/event/ctkEventConstants.h> // Qmitk #include "RTDoseVisualizer.h" #include <QmitkDoseColorDelegate.h> #include <QmitkDoseValueDelegate.h> #include <QmitkDoseVisualStyleDelegate.h> #include <QmitkIsoDoseLevelSetModel.h> #include <QmitkFreeIsoDoseLevelWidget.h> #include "QmitkRenderWindow.h" #include "org_mitk_gui_qt_dosevisualization_Activator.h" #include <vtkMath.h> #include "vtkDecimatePro.h" const std::string RTDoseVisualizer::VIEW_ID = "org.mitk.views.rt.dosevisualization"; const std::string RTDoseVisualizer::ISO_LINE_NODE_NAME = "dose iso lines"; namespace mitk { /** @brief Predicate to identify dose nodes. Didn't use NodePredicateeDataProperty, because we want only depend on the property value ('RTDOSE') and not on the property type (e.g. StringProperty or mitkTemperoSpatialStringProperty).*/ class NodePredicateDose : public NodePredicateBase { public: mitkClassMacro(NodePredicateDose, NodePredicateBase); itkNewMacro(NodePredicateDose); ~NodePredicateDose() override {}; bool CheckNode(const mitk::DataNode *node) const override { if (!node) return false; auto data = node->GetData(); if (!data) { return false; } auto modalityProperty = data->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str()); if (modalityProperty.IsNull()) { return false; } std::string modality = modalityProperty->GetValueAsString(); return modality == "RTDOSE"; }; protected: NodePredicateDose() {}; }; } // namespace mitk RTDoseVisualizer::RTDoseVisualizer() { m_selectedNode = nullptr; m_selectedPresetName = ""; m_PrescribedDose_Data = 0.0; m_freeIsoValuesCount = 0; m_internalUpdate = false; m_isDoseOrIsoPredicate = mitk::NodePredicateDose::New(); m_isIsoPredicate = mitk::NodePredicateProperty::New("name", mitk::StringProperty::New(ISO_LINE_NODE_NAME)); m_isDosePredicate = mitk::NodePredicateAnd::New(m_isDoseOrIsoPredicate, mitk::NodePredicateNot::New(m_isIsoPredicate)); } RTDoseVisualizer::~RTDoseVisualizer() { mitk::DataStorage::SetOfObjects::ConstPointer isoNodes = this->GetDataStorage()->GetSubset(m_isIsoPredicate); this->GetDataStorage()->Remove(isoNodes); delete m_LevelSetModel; delete m_DoseColorDelegate; delete m_DoseValueDelegate; delete m_DoseVisualDelegate; } void RTDoseVisualizer::SetFocus(){} void RTDoseVisualizer::CreateQtPartControl( QWidget *parent ) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi( parent ); m_LevelSetModel = new QmitkIsoDoseLevelSetModel(this); m_LevelSetModel->setVisibilityEditOnly(true); m_DoseColorDelegate = new QmitkDoseColorDelegate(this); m_DoseValueDelegate = new QmitkDoseValueDelegate(this); m_DoseVisualDelegate = new QmitkDoseVisualStyleDelegate(this); this->UpdateByPreferences(); auto doseNodes = this->GetDataStorage()->GetSubset(this->m_isDosePredicate); auto doseNodeIter = doseNodes->begin(); while (doseNodeIter != doseNodes->end()) { PrepareDoseNode(*doseNodeIter); ++doseNodeIter; } this->ActualizeIsoLevelsForAllDoseDataNodes(); this->ActualizeReferenceDoseForAllDoseDataNodes(); this->ActualizeDisplayStyleForAllDoseDataNodes(); this->m_Controls.isoLevelSetView->setModel(m_LevelSetModel); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(0,m_DoseColorDelegate); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(1,m_DoseValueDelegate); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(2,m_DoseVisualDelegate); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(3,m_DoseVisualDelegate); this->m_Controls.isoLevelSetView->setContextMenuPolicy(Qt::CustomContextMenu); this->m_Controls.btnRemoveFreeValue->setDisabled(true); this->m_Controls.doseBtn->setVisible(false); connect(m_Controls.spinReferenceDose, SIGNAL(valueChanged(double)), this, SLOT(OnReferenceDoseChanged(double))); connect(m_Controls.spinReferenceDose, SIGNAL(valueChanged(double)), m_LevelSetModel, SLOT(setReferenceDose(double))); connect(m_Controls.radioAbsDose, SIGNAL(toggled(bool)), m_LevelSetModel, SLOT(setShowAbsoluteDose(bool))); connect(m_Controls.radioAbsDose, SIGNAL(toggled(bool)), this, SLOT(OnAbsDoseToggled(bool))); connect(m_Controls.btnAddFreeValue, SIGNAL(clicked()), this, SLOT(OnAddFreeValueClicked())); connect(m_Controls.btnRemoveFreeValue, SIGNAL(clicked()), this, SLOT(OnRemoveFreeValueClicked())); connect(m_Controls.checkGlobalVisColorWash, SIGNAL(toggled(bool)), this, SLOT(OnGlobalVisColorWashToggled(bool))); connect(m_Controls.checkGlobalVisIsoLine, SIGNAL(toggled(bool)), this, SLOT(OnGlobalVisIsoLineToggled(bool))); connect(m_Controls.isoLevelSetView, SIGNAL(customContextMenuRequested(const QPoint&)), this, SLOT(OnShowContextMenuIsoSet(const QPoint&))); connect(m_Controls.comboPresets, SIGNAL(currentIndexChanged ( const QString&)), this, SLOT(OnCurrentPresetChanged(const QString&))); connect(m_Controls.btnUsePrescribedDose, SIGNAL(clicked()), this, SLOT(OnUsePrescribedDoseClicked())); connect(m_Controls.isoLevelSetView->model(), SIGNAL( modelReset()), this, SLOT(OnDataChangedInIsoLevelSetView())); ctkServiceReference ref = mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()->getServiceReference<ctkEventAdmin>(); ctkDictionary propsForSlot; if (ref) { ctkEventAdmin* eventAdmin = mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()->getService<ctkEventAdmin>(ref); propsForSlot[ctkEventConstants::EVENT_TOPIC] = mitk::RTCTKEventConstants::TOPIC_ISO_DOSE_LEVEL_PRESETS_CHANGED.c_str(); eventAdmin->subscribeSlot(this, SLOT(OnHandleCTKEventPresetsChanged(ctkEvent)), propsForSlot); propsForSlot[ctkEventConstants::EVENT_TOPIC] = mitk::RTCTKEventConstants::TOPIC_REFERENCE_DOSE_CHANGED.c_str(); eventAdmin->subscribeSlot(this, SLOT(OnHandleCTKEventReferenceDoseChanged(ctkEvent)), propsForSlot); propsForSlot[ctkEventConstants::EVENT_TOPIC] = mitk::RTCTKEventConstants::TOPIC_GLOBAL_VISIBILITY_CHANGED.c_str(); eventAdmin->subscribeSlot(this, SLOT(OnHandleCTKEventGlobalVisChanged(ctkEvent)), propsForSlot); } this->UpdateBySelectedNode(); } void RTDoseVisualizer::OnReferenceDoseChanged(double value) { if (! m_internalUpdate) { mitk::DoseValueAbs referenceDose = 0.0; bool globalSync = mitk::GetReferenceDoseValue(referenceDose); if (globalSync) { mitk::SetReferenceDoseValue(globalSync, value); this->ActualizeReferenceDoseForAllDoseDataNodes(); } else { if (this->m_selectedNode.IsNotNull()) { this->m_selectedNode->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) isoDoseNode->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); } } if (this->m_selectedNode.IsNotNull()) { this->UpdateColorWashTransferFunction(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void RTDoseVisualizer::OnAddFreeValueClicked() { QColor newColor; //Use HSV schema of QColor to calculate a different color depending on the //number of already existing free iso lines. newColor.setHsv((m_freeIsoValuesCount*85)%360,255,255); mitk::IsoDoseLevel::ColorType mColor; mColor[0]=newColor.redF(); mColor[1]=newColor.greenF(); mColor[2]=newColor.blueF(); mitk::IsoDoseLevelVector::Pointer freeIsoDoseVector; mitk::IsoDoseLevelVectorProperty::Pointer propIsoVector; mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) { propIsoVector = dynamic_cast<mitk::IsoDoseLevelVectorProperty*>(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); freeIsoDoseVector = propIsoVector->GetValue(); if (freeIsoDoseVector.IsNull()) mitk::IsoDoseLevelVector::Pointer freeIsoDoseVector = mitk::IsoDoseLevelVector::New(); mitk::IsoDoseLevel::Pointer newLevel = mitk::IsoDoseLevel::New(0.5, mColor, true, false); freeIsoDoseVector->InsertElement(m_freeIsoValuesCount, newLevel); propIsoVector = mitk::IsoDoseLevelVectorProperty::New(freeIsoDoseVector); isoDoseNode->SetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str(), propIsoVector); m_freeIsoValuesCount++; this->m_Controls.btnRemoveFreeValue->setEnabled(true); //Update Widget this->UpdateFreeIsoValues(); //Update Rendering this->ActualizeFreeIsoLine(); } } void RTDoseVisualizer::OnRemoveFreeValueClicked() { int index = this->m_Controls.listFreeValues->currentRow(); if (index > static_cast<int>(m_freeIsoValuesCount) || index < 0) return; mitk::IsoDoseLevelVectorProperty::Pointer propfreeIsoVec; mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); propfreeIsoVec = dynamic_cast<mitk::IsoDoseLevelVectorProperty*>(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); mitk::IsoDoseLevelVector::Pointer freeIsoDoseLevelVec = propfreeIsoVec->GetValue(); if(freeIsoDoseLevelVec->IndexExists(index)) { //freeIsoDoseLevelVec->DeleteIndex(index); freeIsoDoseLevelVec->erase(freeIsoDoseLevelVec->begin()+index); --m_freeIsoValuesCount; if(m_freeIsoValuesCount == 0) this->m_Controls.btnRemoveFreeValue->setEnabled(true); this->UpdateFreeIsoValues(); this->ActualizeFreeIsoLine(); } } void RTDoseVisualizer::OnUsePrescribedDoseClicked() { m_Controls.spinReferenceDose->setValue(this->m_PrescribedDose_Data); } void RTDoseVisualizer::OnDataChangedInIsoLevelSetView() { //colorwash visibility changed, update the colorwash this->UpdateColorWashTransferFunction(); if(m_selectedNode.IsNotNull()) { //Hack: This is a dirty hack to reinit the isodose contour node. Only if the node (or property) has changed the rendering process register the RequestUpdateAll //Only way to render the isoline by changes without a global reinit mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) isoDoseNode->Modified(); // Reinit if visibility of colorwash or isodoselevel changed mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void RTDoseVisualizer::OnShowContextMenuIsoSet(const QPoint& pos) { QPoint globalPos = m_Controls.isoLevelSetView->viewport()->mapToGlobal(pos); QMenu viewMenu; QAction* invertIsoLineAct = viewMenu.addAction("Invert iso line visibility"); QAction* activateIsoLineAct = viewMenu.addAction("Activate all iso lines"); QAction* deactivateIsoLineAct = viewMenu.addAction("Deactivate all iso lines"); viewMenu.addSeparator(); QAction* invertColorWashAct = viewMenu.addAction("Invert color wash visibility"); QAction* activateColorWashAct = viewMenu.addAction("Activate all color wash levels"); QAction* deactivateColorWashAct = viewMenu.addAction("Deactivate all color wash levels"); viewMenu.addSeparator(); QAction* swapAct = viewMenu.addAction("Swap iso line/color wash visibility"); // ... QAction* selectedItem = viewMenu.exec(globalPos); if (selectedItem == invertIsoLineAct) { this->m_LevelSetModel->invertVisibilityIsoLines(); } else if (selectedItem == activateIsoLineAct) { this->m_LevelSetModel->switchVisibilityIsoLines(true); } else if (selectedItem == deactivateIsoLineAct) { this->m_LevelSetModel->switchVisibilityIsoLines(false); } else if (selectedItem == invertColorWashAct) { this->m_LevelSetModel->invertVisibilityColorWash(); } else if (selectedItem == activateColorWashAct) { this->m_LevelSetModel->switchVisibilityColorWash(true); } else if (selectedItem == deactivateColorWashAct) { this->m_LevelSetModel->switchVisibilityColorWash(false); } else if (selectedItem == swapAct) { this->m_LevelSetModel->swapVisibility(); } } void RTDoseVisualizer::UpdateFreeIsoValues() { this->m_Controls.listFreeValues->clear(); mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) { mitk::IsoDoseLevelVectorProperty::Pointer propfreeIsoVec; propfreeIsoVec = dynamic_cast<mitk::IsoDoseLevelVectorProperty*>(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); mitk::IsoDoseLevelVector::Pointer freeIsoDoseLevelVec = propfreeIsoVec->GetValue(); for (mitk::IsoDoseLevelVector::Iterator pos = freeIsoDoseLevelVec->Begin(); pos != freeIsoDoseLevelVec->End(); ++pos) { QListWidgetItem* item = new QListWidgetItem; item->setSizeHint(QSize(0, 25)); QmitkFreeIsoDoseLevelWidget* widget = new QmitkFreeIsoDoseLevelWidget; float pref; m_selectedNode->GetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), pref); widget->setIsoDoseLevel(pos.Value()); widget->setReferenceDose(pref); connect(m_Controls.spinReferenceDose, SIGNAL(valueChanged(double)), widget, SLOT(setReferenceDose(double))); connect(widget, SIGNAL(ColorChanged(mitk::IsoDoseLevel*)), this, SLOT(ActualizeFreeIsoLine())); connect(widget, SIGNAL(ValueChanged(mitk::IsoDoseLevel*, mitk::DoseValueRel)), this, SLOT(ActualizeFreeIsoLine())); connect(widget, SIGNAL(VisualizationStyleChanged(mitk::IsoDoseLevel*)), this, SLOT(ActualizeFreeIsoLine())); this->m_Controls.listFreeValues->addItem(item); this->m_Controls.listFreeValues->setItemWidget(item, widget); } } } void RTDoseVisualizer::ActualizeFreeIsoLine() { if(m_selectedNode.IsNotNull()) { //Hack: This is a dirty hack to reinit the isodose contour node. Only if the node (or property) has changed the rendering process register the RequestUpdateAll //Only way to render the isoline by changes without a global reinit mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) isoDoseNode->Modified(); // Reinit if visibility of colorwash or isodoselevel changed mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void RTDoseVisualizer::OnAbsDoseToggled(bool showAbs) { if (! m_internalUpdate) { mitk::SetDoseDisplayAbsolute(showAbs); this->ActualizeDisplayStyleForAllDoseDataNodes(); } } void RTDoseVisualizer::OnGlobalVisColorWashToggled(bool showColorWash) { if (m_selectedNode.IsNotNull()) { m_selectedNode->SetBoolProperty(mitk::RTConstants::DOSE_SHOW_COLORWASH_PROPERTY_NAME.c_str(), showColorWash); //The rendering mode could be set in the dose mapper: Refactoring! mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New(); if(showColorWash) renderingMode->SetValue(mitk::RenderingModeProperty::COLORTRANSFERFUNCTION_COLOR); else renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR); m_selectedNode->SetProperty("Image Rendering.Mode", renderingMode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void RTDoseVisualizer::OnGlobalVisIsoLineToggled(bool showIsoLines) { if (m_selectedNode.IsNotNull()) { mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) { isoDoseNode->SetBoolProperty(mitk::RTConstants::DOSE_SHOW_ISOLINES_PROPERTY_NAME.c_str(), showIsoLines); //toggle the visibility of the free isolevel sliders this->m_Controls.listFreeValues->setEnabled(showIsoLines); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void RTDoseVisualizer::UpdateColorWashTransferFunction() { //Generating the Colorwash vtkSmartPointer<vtkColorTransferFunction> transferFunction = vtkSmartPointer<vtkColorTransferFunction>::New(); if(m_selectedNode.IsNotNull()) { mitk::IsoDoseLevelSetProperty::Pointer propIsoSet = dynamic_cast<mitk::IsoDoseLevelSetProperty* >(m_selectedNode->GetProperty(mitk::RTConstants::DOSE_ISO_LEVELS_PROPERTY_NAME.c_str())); mitk::IsoDoseLevelSet::Pointer isoDoseLevelSet = propIsoSet->GetValue(); float referenceDose; m_selectedNode->GetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(),referenceDose); mitk::TransferFunction::ControlPoints scalarOpacityPoints; scalarOpacityPoints.push_back( std::make_pair(0, 1 ) ); - //Backgroud + //Background transferFunction->AddHSVPoint(((isoDoseLevelSet->Begin())->GetDoseValue()*referenceDose)-0.001,0,0,0,1.0,1.0); for(mitk::IsoDoseLevelSet::ConstIterator itIsoDoseLevel = isoDoseLevelSet->Begin(); itIsoDoseLevel != isoDoseLevelSet->End(); ++itIsoDoseLevel) { float *hsv = new float[3]; //used for transfer rgb to hsv vtkSmartPointer<vtkMath> cCalc = vtkSmartPointer<vtkMath>::New(); if(itIsoDoseLevel->GetVisibleColorWash()) { cCalc->RGBToHSV(itIsoDoseLevel->GetColor()[0],itIsoDoseLevel->GetColor()[1],itIsoDoseLevel->GetColor()[2],&hsv[0],&hsv[1],&hsv[2]); transferFunction->AddHSVPoint(itIsoDoseLevel->GetDoseValue()*referenceDose,hsv[0],hsv[1],hsv[2],1.0,1.0); } else { scalarOpacityPoints.push_back( std::make_pair(itIsoDoseLevel->GetDoseValue()*referenceDose, 1 ) ); } } mitk::TransferFunction::Pointer mitkTransFunc = mitk::TransferFunction::New(); mitk::TransferFunctionProperty::Pointer mitkTransFuncProp = mitk::TransferFunctionProperty::New(); mitkTransFunc->SetColorTransferFunction(transferFunction); mitkTransFunc->SetScalarOpacityPoints(scalarOpacityPoints); mitkTransFuncProp->SetValue(mitkTransFunc); m_selectedNode->SetProperty("Image Rendering.Transfer Function", mitkTransFuncProp); } } /**Simple check if the passed node has dose visualization properties set.*/ bool hasDoseVisProperties(mitk::DataNode::Pointer doseNode) { return doseNode->GetProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str()) != nullptr; } void RTDoseVisualizer::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>&) { QList<mitk::DataNode::Pointer> dataNodes = this->GetDataManagerSelection(); mitk::DataNode* selectedNode = nullptr; if (!dataNodes.empty()) { bool isDoseNode = m_isDosePredicate->CheckNode(dataNodes[0].GetPointer()); if (isDoseNode) { selectedNode = dataNodes[0]; } } if (selectedNode != m_selectedNode.GetPointer()) { m_selectedNode = selectedNode; if (selectedNode) { PrepareDoseNode(m_selectedNode); } } UpdateBySelectedNode(); } void RTDoseVisualizer::PrepareDoseNode( mitk::DataNode* doseNode ) const { mitk::DoseValueAbs dose; mitk::GetReferenceDoseValue(dose); auto presetMap = mitk::LoadPresetsMap(); auto colorPreset = mitk::GenerateIsoLevels_Virtuos(); auto finding = presetMap.find(mitk::GetSelectedPresetName()); if (finding != presetMap.end()) { colorPreset = finding->second; } if (!hasDoseVisProperties(doseNode)) { mitk::ConfigureNodeAsDoseNode(doseNode, colorPreset, dose, true); } mitk::DataNode::Pointer doseOutlineNode = this->GetIsoDoseNode(doseNode); if (doseOutlineNode.IsNull()) { doseOutlineNode = mitk::DataNode::New(); doseOutlineNode->SetData(doseNode->GetData()); doseOutlineNode->SetName(ISO_LINE_NODE_NAME); mitk::ConfigureNodeAsIsoLineNode(doseOutlineNode, colorPreset, dose, true); this->GetDataStorage()->Add(doseOutlineNode, doseNode); } } void RTDoseVisualizer::UpdateBySelectedNode() { m_Controls.groupNodeSpecific->setEnabled(m_selectedNode.IsNotNull()); m_Controls.groupFreeValues->setEnabled(m_selectedNode.IsNotNull()); m_Controls.checkGlobalVisColorWash->setEnabled(m_selectedNode.IsNotNull()); m_Controls.checkGlobalVisIsoLine->setEnabled(m_selectedNode.IsNotNull()); m_Controls.isoLevelSetView->setEnabled(m_selectedNode.IsNotNull()); if(m_selectedNode.IsNull()) { m_Controls.NrOfFractions->setText(QString("N/A. No dose selected")); m_Controls.prescribedDoseSpecific->setText(QString("N/A. No dose selected")); } else { //dose specific information int fracCount = 1; m_selectedNode->GetIntProperty(mitk::RTConstants::DOSE_FRACTION_COUNT_PROPERTY_NAME.c_str(), fracCount); m_Controls.NrOfFractions->setText(QString::number(fracCount)); m_PrescribedDose_Data = 0.0; auto prescibedDoseProperty = m_selectedNode->GetData()->GetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str()); auto prescribedDoseGenericProperty = dynamic_cast<mitk::DoubleProperty*>(prescibedDoseProperty.GetPointer()); m_PrescribedDose_Data = prescribedDoseGenericProperty->GetValue(); m_Controls.prescribedDoseSpecific->setText(QString::number(m_PrescribedDose_Data)); //free iso lines mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode) { mitk::IsoDoseLevelVectorProperty::Pointer propIsoVector; propIsoVector = dynamic_cast<mitk::IsoDoseLevelVectorProperty*>(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); if (propIsoVector.IsNull()) { mitk::IsoDoseLevelVector::Pointer freeIsoValues = mitk::IsoDoseLevelVector::New(); propIsoVector = mitk::IsoDoseLevelVectorProperty::New(freeIsoValues); isoDoseNode->SetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str(), propIsoVector); } UpdateFreeIsoValues(); //global dose issues //ATM the IsoDoseContours have an own (helper) node which is a child of dose node; Will be fixed with the doseMapper refactoring bool showIsoLine = mitk::GetGlobalIsolineVis(); isoDoseNode->GetBoolProperty(mitk::RTConstants::DOSE_SHOW_ISOLINES_PROPERTY_NAME.c_str(), showIsoLine); m_Controls.checkGlobalVisIsoLine->setChecked(showIsoLine); } bool showColorWash = mitk::GetGlobalColorwashVis(); m_selectedNode->GetBoolProperty(mitk::RTConstants::DOSE_SHOW_COLORWASH_PROPERTY_NAME.c_str(),showColorWash); m_Controls.checkGlobalVisColorWash->setChecked(showColorWash); float referenceDose = 0.0; m_selectedNode->GetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(),referenceDose); m_Controls.spinReferenceDose->setValue(referenceDose); mitk::IsoDoseLevelSetProperty::Pointer propIsoSet = dynamic_cast<mitk::IsoDoseLevelSetProperty* >(m_selectedNode->GetProperty(mitk::RTConstants::DOSE_ISO_LEVELS_PROPERTY_NAME.c_str())); if (propIsoSet) { this->m_LevelSetModel->setIsoDoseLevelSet(propIsoSet->GetValue()); } } } void RTDoseVisualizer::NodeRemoved(const mitk::DataNode* node) { /**@TODO This removal seems to be needed because of the current dose rendering approach (additional sub node for iso dose lines). As soon as we have a better and sound single node rendering mechanism for doses. This method should be removed.*/ bool isdose = m_isDosePredicate->CheckNode(node); if (isdose) { mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(node, m_isIsoPredicate); auto iterChildNodes = childNodes->begin(); while (iterChildNodes != childNodes->end()) { this->GetDataStorage()->Remove((*iterChildNodes)); ++iterChildNodes; } } } void RTDoseVisualizer::NodeChanged(const mitk::DataNode *node) { /**@TODO This event seems to be needed because of the current dose rendering approach (additional sub node for iso dose lines). As soon as we have a better and sound single node rendering mechanism for doses. This method should be removed.*/ bool isdose = m_isDosePredicate->CheckNode(node); if(isdose) { bool isvisible = true; if(node->GetBoolProperty("visible", isvisible)) { mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(node, m_isIsoPredicate); mitk::DataStorage::SetOfObjects::const_iterator iterChildNodes = childNodes->begin(); while (iterChildNodes != childNodes->end()) { (*iterChildNodes)->SetVisibility(isvisible); ++iterChildNodes; } } } } void RTDoseVisualizer::UpdateByPreferences() { m_Presets = mitk::LoadPresetsMap(); m_internalUpdate = true; m_Controls.comboPresets->clear(); this->m_selectedPresetName = mitk::GetSelectedPresetName(); m_Controls.checkGlobalVisIsoLine->setChecked(mitk::GetGlobalIsolineVis()); m_Controls.checkGlobalVisColorWash->setChecked(mitk::GetGlobalColorwashVis()); if(m_Presets.empty()) return; int index = 0; int selectedIndex = -1; for (mitk::PresetMapType::const_iterator pos = m_Presets.begin(); pos != m_Presets.end(); ++pos, ++index) { m_Controls.comboPresets->addItem(QString(pos->first.c_str())); if (this->m_selectedPresetName == pos->first) { selectedIndex = index; } } if (selectedIndex == -1) { selectedIndex = 0; MITK_WARN << "Error. Iso dose level preset specified in preferences does not exist. Preset name: "<<this->m_selectedPresetName; this->m_selectedPresetName = m_Presets.begin()->first; mitk::SetSelectedPresetName(this->m_selectedPresetName); MITK_INFO << "Changed selected iso dose level preset to first existing preset. New preset name: "<<this->m_selectedPresetName; } m_Controls.comboPresets->setCurrentIndex(selectedIndex); this->m_LevelSetModel->setIsoDoseLevelSet(this->m_Presets[this->m_selectedPresetName]); mitk::DoseValueAbs referenceDose = 0.0; bool globalSync = mitk::GetReferenceDoseValue(referenceDose); if (globalSync || this->m_selectedNode.IsNull()) { m_Controls.spinReferenceDose->setValue(referenceDose); } bool displayAbsoluteDose = mitk::GetDoseDisplayAbsolute(); m_Controls.radioAbsDose->setChecked(displayAbsoluteDose); m_Controls.radioRelDose->setChecked(!displayAbsoluteDose); this->m_LevelSetModel->setShowAbsoluteDose(displayAbsoluteDose); m_internalUpdate = false; } void RTDoseVisualizer::OnCurrentPresetChanged(const QString& presetName) { if (! m_internalUpdate) { mitk::SetSelectedPresetName(presetName.toStdString()); this->UpdateByPreferences(); this->ActualizeIsoLevelsForAllDoseDataNodes(); this->UpdateBySelectedNode(); } } void RTDoseVisualizer::ActualizeIsoLevelsForAllDoseDataNodes() { std::string presetName = mitk::GetSelectedPresetName(); mitk::PresetMapType presetMap = mitk::LoadPresetsMap(); mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetSubset(m_isDoseOrIsoPredicate); if(presetMap.empty()) return; mitk::IsoDoseLevelSet* selectedPreset = presetMap[presetName]; if (!selectedPreset) { mitkThrow() << "Error. Cannot actualize iso dose level preset. Selected preset does not exist. Preset name: "<<presetName; } for(mitk::DataStorage::SetOfObjects::const_iterator pos = nodes->begin(); pos != nodes->end(); ++pos) { mitk::IsoDoseLevelSet::Pointer clonedPreset = selectedPreset->Clone(); mitk::IsoDoseLevelSetProperty::Pointer propIsoSet = mitk::IsoDoseLevelSetProperty::New(clonedPreset); (*pos)->SetProperty(mitk::RTConstants::DOSE_ISO_LEVELS_PROPERTY_NAME.c_str(),propIsoSet); } } void RTDoseVisualizer::ActualizeReferenceDoseForAllDoseDataNodes() { mitk::DoseValueAbs value = 0; bool sync = mitk::GetReferenceDoseValue(value); if (sync) { mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetSubset(m_isDoseOrIsoPredicate); for(mitk::DataStorage::SetOfObjects::const_iterator pos = nodes->begin(); pos != nodes->end(); ++pos) { (*pos)->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); /**@TODO: ATM the IsoDoseContours have an own (helper) node which is a child of dose node; Will be fixed with the doseMapper refactoring*/ mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(*pos); mitk::DataStorage::SetOfObjects::const_iterator iterChildNodes = childNodes->begin(); while (iterChildNodes != childNodes->end()) { (*iterChildNodes)->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); ++iterChildNodes; } } } } void RTDoseVisualizer::ActualizeDisplayStyleForAllDoseDataNodes() { /** @TODO Klären ob diese präsentations info global oder auch per node gespeichert wird*/ } void RTDoseVisualizer::OnHandleCTKEventReferenceDoseChanged(const ctkEvent&) { mitk::DoseValueAbs referenceDose = 0.0; mitk::GetReferenceDoseValue(referenceDose); this->m_Controls.spinReferenceDose->setValue(referenceDose); } void RTDoseVisualizer::OnHandleCTKEventGlobalVisChanged(const ctkEvent&) { this->m_Controls.checkGlobalVisIsoLine->setChecked(mitk::GetGlobalIsolineVis()); this->m_Controls.checkGlobalVisColorWash->setChecked(mitk::GetGlobalColorwashVis()); } void RTDoseVisualizer::OnHandleCTKEventPresetsChanged(const ctkEvent&) { std::string currentPresetName = mitk::GetSelectedPresetName(); this->OnCurrentPresetChanged(QString::fromStdString(currentPresetName)); } /**@TODO ATM the IsoDoseContours have an own (helper) node which is a child of dose node; Will be fixed with the doseMapper refactoring*/ mitk::DataNode::Pointer RTDoseVisualizer::GetIsoDoseNode(mitk::DataNode::Pointer doseNode) const { mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(doseNode, m_isIsoPredicate); if (childNodes->empty()) { return nullptr; } else { return (*childNodes->begin()); } } diff --git a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.h b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.h index 2181adbeb5..edeee71c45 100644 --- a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.h +++ b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.h @@ -1,169 +1,169 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef RTDoseVisualizer_h #define RTDoseVisualizer_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include "ui_RTDoseVisualizerControls.h" #include <mitkIsoDoseLevelCollections.h> #include <mitkImage.h> #include <mitkNodePredicateBase.h> #include "mitkDoseVisPreferenceHelper.h" // Shader #include <mitkCoreServices.h> #include <vtkSmartPointer.h> #include <mitkRenderingModeProperty.h> #include <vtkContourFilter.h> #include <mitkIRenderWindowPart.h> /*forward declarations*/ class QmitkIsoDoseLevelSetModel; class QmitkDoseColorDelegate; class QmitkDoseValueDelegate; class QmitkDoseVisualStyleDelegate; class ctkEvent; /** \brief RTDoseVisualizer \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ class RTDoseVisualizer : public QmitkAbstractView { Q_OBJECT public: RTDoseVisualizer(); ~RTDoseVisualizer() override; static const std::string VIEW_ID; static const std::string ISO_LINE_NODE_NAME; void OnSliceChanged(itk::Object *sender, const itk::EventObject &e); protected slots: void OnAddFreeValueClicked(); void OnRemoveFreeValueClicked(); void OnUsePrescribedDoseClicked(); void OnDataChangedInIsoLevelSetView(); void OnAbsDoseToggled(bool); void OnGlobalVisColorWashToggled(bool); void OnGlobalVisIsoLineToggled(bool); void OnShowContextMenuIsoSet(const QPoint&); void OnCurrentPresetChanged(const QString&); void OnReferenceDoseChanged(double); void OnHandleCTKEventReferenceDoseChanged(const ctkEvent& event); void OnHandleCTKEventPresetsChanged(const ctkEvent& event); void OnHandleCTKEventGlobalVisChanged(const ctkEvent& event); void ActualizeFreeIsoLine(); protected: void CreateQtPartControl(QWidget *parent) override; void SetFocus() override; void OnSelectionChanged( berry::IWorkbenchPart::Pointer source, const QList<mitk::DataNode::Pointer>& nodes ) override; void PrepareDoseNode(mitk::DataNode* doseNode) const; - /** Update the transfer funtion property for the color wash*/ + /** Update the transfer function property for the color wash*/ void UpdateColorWashTransferFunction(); /** Method updates the list widget according to the current free iso values.*/ void UpdateFreeIsoValues(); /** Update the members according to the currently selected node */ void UpdateBySelectedNode(); /** Update the member widgets according to the information stored in the application preferences*/ void UpdateByPreferences(); - /**helper function that iterates throug all data nodes and sets there iso level set property + /**helper function that iterates through all data nodes and sets there iso level set property according to the selected preset. @TODO: should be moved outside the class, to be available for other classes at well.*/ void ActualizeIsoLevelsForAllDoseDataNodes(); - /**helper function that iterates throug all data nodes and sets there reference dose value + /**helper function that iterates through all data nodes and sets there reference dose value according to the preference. @TODO: should be moved outside the class, to be available for other classes at well.*/ void ActualizeReferenceDoseForAllDoseDataNodes(); /**helper function that iterates through all data nodes and sets there dose display style (relative/absolute) according to the preference. @TODO: should be moved outside the class, to be available for other classes at well.*/ void ActualizeDisplayStyleForAllDoseDataNodes(); void NodeRemoved(const mitk::DataNode* node) override; void NodeChanged(const mitk::DataNode *node) override; Ui::RTDoseVisualizerControls m_Controls; mitk::DataNode::Pointer m_selectedNode; unsigned int m_freeIsoValuesCount; mitk::PresetMapType m_Presets; std::string m_selectedPresetName; /** Prescribed Dose of the selected data.*/ mitk::DoseValueAbs m_PrescribedDose_Data; QmitkIsoDoseLevelSetModel* m_LevelSetModel; QmitkDoseColorDelegate* m_DoseColorDelegate; QmitkDoseValueDelegate* m_DoseValueDelegate; QmitkDoseVisualStyleDelegate* m_DoseVisualDelegate; bool m_internalUpdate; /**Predicate for dose nodes (excluding iso line nodes)*/ mitk::NodePredicateBase::Pointer m_isDosePredicate; /**Predicate for dose nodes and all iso line nodes*/ mitk::NodePredicateBase::Pointer m_isDoseOrIsoPredicate; /**Predicate for iso line nodes*/ mitk::NodePredicateBase::Pointer m_isIsoPredicate; private: mitk::DataNode::Pointer GetIsoDoseNode(mitk::DataNode::Pointer doseNode) const; }; #endif // RTDoseVisualizer_h diff --git a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTUIPreferencePageControls.ui b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTUIPreferencePageControls.ui index efd18081ca..b38f0d5c3c 100644 --- a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTUIPreferencePageControls.ui +++ b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTUIPreferencePageControls.ui @@ -1,86 +1,86 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>RTUIPreferencePageControls</class> <widget class="QWidget" name="RTUIPreferencePageControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>403</width> <height>438</height> </rect> </property> <property name="windowTitle"> <string>Form</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> - <string>Handling of unkown prescribed dose:</string> + <string>Handling of unknown prescribed dose:</string> </property> <layout class="QGridLayout" name="gridLayout"> <item row="1" column="1"> <widget class="QDoubleSpinBox" name="spinRelativeToMax"> <property name="enabled"> <bool>false</bool> </property> <property name="suffix"> <string> %</string> </property> <property name="maximum"> <double>200.000000000000000</double> </property> <property name="value"> <double>80.000000000000000</double> </property> </widget> </item> <item row="0" column="0"> <widget class="QRadioButton" name="radioDefault"> <property name="text"> <string>set to default value:</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QRadioButton" name="radioRelativeToMax"> <property name="text"> <string>set relative to max dose:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QDoubleSpinBox" name="spinDefault"> <property name="suffix"> <string> Gy</string> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> <property name="value"> <double>50.000000000000000</double> </property> </widget> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.ext/resources/icons/tango/scalable/mimetypes/image-x-generic.svg b/Plugins/org.mitk.gui.qt.ext/resources/icons/tango/scalable/mimetypes/image-x-generic.svg index 45dd641ae7..bb846d32f2 100644 --- a/Plugins/org.mitk.gui.qt.ext/resources/icons/tango/scalable/mimetypes/image-x-generic.svg +++ b/Plugins/org.mitk.gui.qt.ext/resources/icons/tango/scalable/mimetypes/image-x-generic.svg @@ -1,581 +1,581 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?>  <svg xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" width="48.000000px" height="48.000000px" xml:space="preserve" id="svg16168" sodipodi:version="0.32" inkscape:version="0.46" sodipodi:docname="image-x-generic.svg" sodipodi:docbase="/home/jimmac/src/cvs/tango-icon-theme/scalable/mimetypes" inkscape:output_extension="org.inkscape.output.svg.inkscape"><metadata id="metadata16236"> <rdf:RDF> <cc:Work rdf:about=""> <dc:format>image/svg+xml</dc:format> <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage" /> - <dc:title>Genric Image</dc:title> + <dc:title>Generic Image</dc:title> <dc:creator> <cc:Agent> <dc:title>Jakub Steiner</dc:title> </cc:Agent> </dc:creator> <dc:subject> <rdf:Bag><rdf:li>image</rdf:li><rdf:li>picture</rdf:li><rdf:li>snapshot</rdf:li><rdf:li>photo</rdf:li></rdf:Bag> </dc:subject> <cc:license rdf:resource="http://creativecommons.org/licenses/publicdomain/" /> </cc:Work> <cc:License rdf:about="http://creativecommons.org/licenses/publicdomain/"><cc:permits rdf:resource="http://creativecommons.org/ns#Reproduction" /><cc:permits rdf:resource="http://creativecommons.org/ns#Distribution" /><cc:permits rdf:resource="http://creativecommons.org/ns#DerivativeWorks" /></cc:License></rdf:RDF> </metadata> <defs id="defs16234"><inkscape:perspective sodipodi:type="inkscape:persp3d" inkscape:vp_x="0 : 24 : 1" inkscape:vp_y="0 : 1000 : 0" inkscape:vp_z="48 : 24 : 1" inkscape:persp3d-origin="24 : 16 : 1" id="perspective80" /><radialGradient inkscape:collect="always" xlink:href="#linearGradient5060" id="radialGradient6719" gradientUnits="userSpaceOnUse" gradientTransform="matrix(-2.774389,0,0,1.969706,112.7623,-872.8854)" cx="605.71429" cy="486.64789" fx="605.71429" fy="486.64789" r="117.14286" /><linearGradient inkscape:collect="always" id="linearGradient5060"><stop style="stop-color:black;stop-opacity:1;" offset="0" id="stop5062" /><stop style="stop-color:black;stop-opacity:0;" offset="1" id="stop5064" /></linearGradient><radialGradient inkscape:collect="always" xlink:href="#linearGradient5060" id="radialGradient6717" gradientUnits="userSpaceOnUse" gradientTransform="matrix(2.774389,0,0,1.969706,-1891.633,-872.8854)" cx="605.71429" cy="486.64789" fx="605.71429" fy="486.64789" r="117.14286" /><linearGradient id="linearGradient5048"><stop style="stop-color:black;stop-opacity:0;" offset="0" id="stop5050" /><stop id="stop5056" offset="0.5" style="stop-color:black;stop-opacity:1;" /><stop style="stop-color:black;stop-opacity:0;" offset="1" id="stop5052" /></linearGradient><linearGradient inkscape:collect="always" xlink:href="#linearGradient5048" id="linearGradient6715" gradientUnits="userSpaceOnUse" gradientTransform="matrix(2.774389,0,0,1.969706,-1892.179,-872.8854)" x1="302.85715" y1="366.64789" x2="302.85715" y2="609.50507" /><linearGradient id="linearGradient8171"><stop style="stop-color:#bbbdba;stop-opacity:1;" offset="0" id="stop8173" /><stop style="stop-color:#70746e;stop-opacity:1;" offset="1" id="stop8175" /></linearGradient><linearGradient inkscape:collect="always" id="linearGradient8155"><stop style="stop-color:#ffffff;stop-opacity:1;" offset="0" id="stop8157" /><stop style="stop-color:#ffffff;stop-opacity:0;" offset="1" id="stop8159" /></linearGradient><linearGradient id="linearGradient2224"><stop style="stop-color:#7c7c7c;stop-opacity:1;" offset="0" id="stop2226" /><stop style="stop-color:#b8b8b8;stop-opacity:1;" offset="1" id="stop2228" /></linearGradient><linearGradient inkscape:collect="always" id="linearGradient2251"><stop style="stop-color:#ffffff;stop-opacity:1;" offset="0" id="stop2253" /><stop style="stop-color:#ffffff;stop-opacity:0;" offset="1" id="stop2255" /></linearGradient><linearGradient id="linearGradient7648" gradientUnits="userSpaceOnUse" x1="21.9326" y1="24.6274" x2="21.9326" y2="7.1091" style="stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667"> <stop offset="0" style="stop-color:#8595bc;stop-opacity:1;" id="stop7650" /> <stop offset="1" style="stop-color:#041a3b;stop-opacity:1;" id="stop7652" /> </linearGradient><linearGradient id="linearGradient2392"><stop id="stop2394" offset="0.0000000" style="stop-color:#715b26;stop-opacity:1.0000000;" /><stop id="stop2396" offset="1.0000000" style="stop-color:#312710;stop-opacity:1.0000000;" /></linearGradient><linearGradient inkscape:collect="always" id="linearGradient12129"><stop style="stop-color:#000000;stop-opacity:1;" offset="0" id="stop12131" /><stop style="stop-color:#000000;stop-opacity:0;" offset="1" id="stop12133" /></linearGradient> <linearGradient style="stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" y2="36.0328" x2="31.0813" y1="3.7319" x1="12.4873" gradientUnits="userSpaceOnUse" id="aigrd1"> <stop id="stop16177" style="stop-color:#D2D2D2;stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" offset="0" /> <stop id="stop16179" style="stop-color:#EDEDED;stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" offset="1" /> </linearGradient> <linearGradient style="stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" y2="22.5769" x2="21.9168" y1="30.3413" x1="21.877" gradientUnits="userSpaceOnUse" id="aigrd2"> <stop id="stop16184" style="stop-color:#5e4f07;stop-opacity:1.0000000;" offset="0.0000000" /> <stop id="stop16186" style="stop-color:#348a31;stop-opacity:1.0000000;" offset="1.0000000" /> </linearGradient> <linearGradient style="stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" y2="7.1091" x2="21.9326" y1="24.6274" x1="21.9326" gradientUnits="userSpaceOnUse" id="aigrd3"> <stop id="stop16199" style="stop-color:#D0D6E5;stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" offset="0" /> <stop id="stop16201" style="stop-color:#093A80;stroke-dasharray:none;stroke-miterlimit:4.0000000;stroke-width:1.2166667" offset="1" /> </linearGradient> <radialGradient inkscape:collect="always" xlink:href="#linearGradient12129" id="radialGradient12135" cx="24.218407" cy="41.636040" fx="24.218407" fy="41.636040" r="22.097088" gradientTransform="matrix(1.000000,0.000000,0.000000,0.184000,0.000000,33.97501)" gradientUnits="userSpaceOnUse" /><linearGradient inkscape:collect="always" xlink:href="#linearGradient7648" id="linearGradient7671" gradientUnits="userSpaceOnUse" gradientTransform="matrix(1.098989,0.000000,0.000000,-0.797757,-1.953865,37.32400)" x1="21.9326" y1="24.627399" x2="21.9326" y2="7.1090999" /><linearGradient inkscape:collect="always" xlink:href="#aigrd3" id="linearGradient7673" gradientUnits="userSpaceOnUse" gradientTransform="matrix(1.098989,0.000000,0.000000,1.106697,-1.953865,-4.922453)" x1="21.9326" y1="24.6274" x2="21.9326" y2="7.1091" /><linearGradient inkscape:collect="always" xlink:href="#aigrd1" id="linearGradient8148" gradientUnits="userSpaceOnUse" gradientTransform="matrix(1.434003,0.000000,0.000000,0.990087,52.32167,2.838918)" x1="12.4873" y1="3.7319" x2="31.0813" y2="36.0328" /><radialGradient inkscape:collect="always" xlink:href="#linearGradient8155" id="radialGradient8161" cx="12.700491" cy="10.404876" fx="12.700491" fy="10.404876" r="19.96875" gradientTransform="matrix(1.710531,-5.396358e-24,2.470345e-24,1.124849,-11.56833,1.802582)" gradientUnits="userSpaceOnUse" /><linearGradient inkscape:collect="always" xlink:href="#linearGradient2251" id="linearGradient8166" gradientUnits="userSpaceOnUse" gradientTransform="translate(5.147570,-3.409792)" x1="33.396004" y1="36.921333" x2="34.170048" y2="38.070381" /><linearGradient inkscape:collect="always" xlink:href="#linearGradient2224" id="linearGradient8169" gradientUnits="userSpaceOnUse" gradientTransform="translate(5.147570,-3.034792)" x1="35.996582" y1="40.458221" x2="33.664921" y2="37.770721" /><linearGradient inkscape:collect="always" xlink:href="#linearGradient8171" id="linearGradient8177" x1="42.1875" y1="31" x2="45" y2="39.984692" gradientUnits="userSpaceOnUse" /></defs> <sodipodi:namedview inkscape:window-height="818" inkscape:window-width="1238" inkscape:pageshadow="2" inkscape:pageopacity="0.0" borderopacity="0.07058824" bordercolor="#666666" pagecolor="#ffffff" id="base" inkscape:zoom="1" inkscape:cx="49.378608" inkscape:cy="-24.095483" inkscape:window-x="0" inkscape:window-y="30" inkscape:current-layer="svg16168" showgrid="false" inkscape:showpageshadow="false" /> <g style="display:inline" transform="matrix(2.175112e-2,0,0,2.493263e-2,42.41049,33.81117)" id="g6707"><rect style="opacity:0.40206185;color:black;fill:url(#linearGradient6715);fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:1;stroke-linecap:round;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" id="rect6709" width="1339.6335" height="478.35718" x="-1559.2523" y="-150.69685" /><path style="opacity:0.40206185;color:black;fill:url(#radialGradient6717);fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:1;stroke-linecap:round;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" d="M -219.61876,-150.68038 C -219.61876,-150.68038 -219.61876,327.65041 -219.61876,327.65041 C -76.744594,328.55086 125.78146,220.48075 125.78138,88.454235 C 125.78138,-43.572302 -33.655436,-150.68036 -219.61876,-150.68038 z " id="path6711" sodipodi:nodetypes="cccc" /><path sodipodi:nodetypes="cccc" id="path6713" d="M -1559.2523,-150.68038 C -1559.2523,-150.68038 -1559.2523,327.65041 -1559.2523,327.65041 C -1702.1265,328.55086 -1904.6525,220.48075 -1904.6525,88.454235 C -1904.6525,-43.572302 -1745.2157,-150.68036 -1559.2523,-150.68038 z " style="opacity:0.40206185;color:black;fill:url(#radialGradient6719);fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:1;stroke-linecap:round;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" /></g><path style="color:#000000;fill:url(#linearGradient8148);fill-opacity:1;fill-rule:nonzero;stroke:#bbbfbb;stroke-width:0.99999994;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" d="M 2.7177715,6.4547749 L 43.379544,6.4547749 C 44.002793,6.4547749 44.504543,6.9565247 44.504543,7.5797745 L 44.504543,31.480581 C 44.504543,32.103831 36.047842,39.499872 35.424593,39.499872 L 2.7177715,39.499872 C 2.0945221,39.499872 1.5927727,38.998122 1.5927727,38.374872 L 1.5927727,7.5797745 C 1.5927727,6.9565247 2.0945221,6.4547749 2.7177715,6.4547749 z " id="rect7603" sodipodi:nodetypes="ccccccccc" /> <g id="g7654" transform="matrix(1.054774,0.000000,0.000000,1.049989,-0.814647,4.485012)"><path id="path7644" d="M 5.512695,30 L 39.643234,30 L 39.643234,19.627375 L 5.512695,19.627375 L 5.512695,30 z " style="fill:url(#linearGradient7671);fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:1.2166667;stroke-miterlimit:4" /><path style="fill:url(#linearGradient7673);fill-rule:nonzero;stroke:none;stroke-width:1.2166667;stroke-miterlimit:4" d="M 5.512695,5.237844 L 39.643234,5.237844 L 39.643234,19.627375 L 5.512695,19.627375 L 5.512695,5.237844 z " id="path16203" /><g id="g16205" style="fill-rule:nonzero;stroke:#000000;stroke-width:1.15611064;stroke-miterlimit:4" transform="matrix(1.189217,0.000000,0.000000,1.189217,-3.525355,-6.535408)"> <g id="g16207"> <path style="opacity:0.04999994;fill:#e8f52f;stroke:none" d="M 18.4,15.4 C 18.4,17.6 16.6,19.5 14.3,19.5 C 12.1,19.5 10.2,17.7 10.2,15.4 C 10.2,13.2 12,11.3 14.3,11.3 C 16.5,11.3 18.4,13.1 18.4,15.4 z " id="path16209" /> <path style="opacity:0.20829994;fill:#ecf751;stroke:none" d="M 18,15.4 C 18,17.4 16.4,19.1 14.3,19.1 C 12.3,19.1 10.6,17.5 10.6,15.4 C 10.6,13.4 12.2,11.7 14.3,11.7 C 16.3,11.7 18,13.3 18,15.4 L 18,15.4 z " id="path16211" /> <path style="opacity:0.36669994;fill:#f0f972;stroke:none" d="M 17.6,15.4 C 17.6,17.2 16.1,18.7 14.3,18.7 C 12.5,18.7 11,17.2 11,15.4 C 11,13.6 12.5,12.1 14.3,12.1 C 16.1,12.1 17.6,13.6 17.6,15.4 L 17.6,15.4 z " id="path16213" /> <path style="opacity:0.525;fill:#f4fa95;stroke:none" d="M 17.2,15.4 C 17.2,17 15.9,18.3 14.3,18.3 C 12.7,18.3 11.4,17 11.4,15.4 C 11.4,13.8 12.7,12.5 14.3,12.5 C 15.9,12.5 17.2,13.8 17.2,15.4 z " id="path16215" /> <path style="opacity:0.6833;fill:#f7fcb7;stroke:none" d="M 16.8,15.4 C 16.8,16.8 15.7,17.9 14.3,17.9 C 12.9,17.9 11.8,16.8 11.8,15.4 C 11.8,14 12.9,12.9 14.3,12.9 C 15.7,12.9 16.8,14 16.8,15.4 L 16.8,15.4 z " id="path16217" /> <path style="opacity:0.8417;fill:#fbfddb;stroke:none" d="M 16.4,15.4 C 16.4,16.6 15.4,17.5 14.3,17.5 C 13.2,17.5 12.2,16.5 12.2,15.4 C 12.2,14.3 13.2,13.3 14.3,13.3 C 15.4,13.3 16.4,14.3 16.4,15.4 z " id="path16219" /> <path style="fill:#ffffff;stroke:none" d="M 16,15.4 C 16,16.4 15.2,17.2 14.2,17.2 C 13.2,17.2 12.4,16.4 12.4,15.4 C 12.4,14.4 13.2,13.6 14.2,13.6 C 15.2,13.6 16,14.4 16,15.4 L 16,15.4 z " id="path16221" /> </g> </g><path style="opacity:0.3;fill-rule:nonzero;stroke:none;stroke-width:1.2166667;stroke-miterlimit:4" d="M 25.015859,21.649044 L 33.697148,21.649044 L 35.362052,22.124732 L 32.507931,22.124732 C 32.507931,22.124732 35.362052,22.362574 36.789115,24.146401 C 38.216174,25.811305 35.12421,27.832976 35.12421,27.832976 C 35.12421,27.832976 35.12421,27.832976 35.12421,27.832976 C 35.005288,27.47621 34.291756,24.622087 32.864696,23.43287 C 31.794399,22.481496 30.605182,22.243652 30.605182,22.243652 L 25.015859,22.243652 L 25.015859,21.767966 L 25.015859,21.649044 z " id="path16223" /><path style="opacity:0.3;fill-rule:nonzero;stroke:none;stroke-width:1.2166667;stroke-miterlimit:4" d="M 30.724106,22.362574 L 25.729391,22.362574 L 35.005288,27.595131 L 30.724106,22.362574 L 30.724106,22.362574 z " id="path16225" /><path style="fill:#515151;fill-rule:nonzero;stroke:none;stroke-width:1.2166667;stroke-miterlimit:4" d="M 25.015859,21.767966 L 33.697148,21.767966 L 35.005288,20.935513 L 32.151167,20.935513 C 32.151167,20.935513 34.767443,20.459827 35.12421,17.486782 C 35.480973,14.513739 31.080869,11.183931 31.080869,11.183931 C 31.080869,11.183931 31.080869,11.183931 31.080869,11.302853 C 31.19979,12.016383 32.389007,17.011096 31.556557,18.913846 C 31.19979,20.578747 30.129495,20.935513 30.129495,20.935513 L 24.659094,20.935513 L 24.896938,21.767966 L 25.015859,21.767966 z " id="path16227" /><path style="fill:#515151;fill-rule:nonzero;stroke:none;stroke-width:1.2166667;stroke-miterlimit:4" d="M 30.248418,20.459827 L 25.253704,20.459827 L 31.19979,11.421773 L 30.248418,20.459827 z " id="path16229" /></g><path style="color:#000000;fill:none;fill-opacity:1;fill-rule:nonzero;stroke:#ffffff;stroke-width:0.99999976;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" d="M 2.8042317,7.4528585 L 43.233985,7.4528585 C 43.384366,7.4528585 43.505431,7.5739234 43.505431,7.7243045 L 43.505431,31.422651 C 43.505431,32.368527 36.401687,38.5 36.251306,38.5 L 2.8042317,38.5 C 2.6538507,38.5 2.5327858,38.378935 2.5327858,38.228554 L 2.5327858,7.7243045 C 2.5327858,7.5739234 2.6538507,7.4528585 2.8042317,7.4528585 z " id="rect7675" sodipodi:nodetypes="ccccccccc" /><rect style="opacity:0.84659095;color:#000000;fill:none;fill-opacity:1;fill-rule:nonzero;stroke:#4f4f4f;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" id="rect8163" width="35.0625" height="25.0625" x="5.5" y="10.5" /><path style="color:#000000;fill:url(#linearGradient8169);fill-opacity:1.0;fill-rule:evenodd;stroke:url(#linearGradient8177);stroke-width:1.00000024;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" d="M 35.206652,39.468763 C 37.23707,39.798661 44.795445,34.938834 44.491063,30.970919 C 42.927801,33.394016 39.732541,32.257657 35.623783,32.416667 C 35.623783,32.416667 36.019152,38.968763 35.206652,39.468763 z " id="path2210" sodipodi:nodetypes="cccc" /><path sodipodi:nodetypes="cccc" id="path2247" d="M 36.657089,37.277261 C 38.026868,36.593432 41.085338,35.130796 42.384719,33.249792 C 40.788625,33.929847 39.436909,33.459288 36.682385,33.440197 C 36.682385,33.440197 36.844707,36.502291 36.657089,37.277261 z " style="opacity:0.36931817;color:#000000;fill:none;fill-opacity:1;fill-rule:evenodd;stroke:url(#linearGradient8166);stroke-width:0.99999982;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" /><path style="opacity:0.30113636;color:#000000;fill:url(#radialGradient8161);fill-opacity:1.0;fill-rule:nonzero;stroke:none;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;marker:none;marker-start:none;marker-mid:none;marker-end:none;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;visibility:visible;display:inline;overflow:visible" d="M 3.0625,8 L 3.0625,30.0625 C 25.388579,30.950861 27.884634,17 43,17 L 43,8 L 3.0625,8 z " id="rect8150" sodipodi:nodetypes="ccccc" /></svg> \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.ext/src/QmitkOpenStdMultiWidgetEditorAction.h b/Plugins/org.mitk.gui.qt.ext/src/QmitkOpenStdMultiWidgetEditorAction.h index abb00fc229..4566f7f45d 100644 --- a/Plugins/org.mitk.gui.qt.ext/src/QmitkOpenStdMultiWidgetEditorAction.h +++ b/Plugins/org.mitk.gui.qt.ext/src/QmitkOpenStdMultiWidgetEditorAction.h @@ -1,50 +1,50 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkOpenStdMultiWidgetEditorAction_h #define QmitkOpenStdMultiWidgetEditorAction_h #ifdef __MINGW32__ -// We need to inlclude winbase.h here in order to declare +// We need to include winbase.h here in order to declare // atomic intrinsics like InterlockedIncrement correctly. -// Otherwhise, they would be declared wrong within qatomic_windows.h . +// Otherwise, they would be declared wrong within qatomic_windows.h . #include <windows.h> #endif #include <QAction> #include <QIcon> #include <org_mitk_gui_qt_ext_Export.h> #include <berryIWorkbenchWindow.h> class MITK_QT_COMMON_EXT_EXPORT QmitkOpenStdMultiWidgetEditorAction : public QAction { Q_OBJECT public: QmitkOpenStdMultiWidgetEditorAction(berry::IWorkbenchWindow::Pointer window); QmitkOpenStdMultiWidgetEditorAction(const QIcon& icon, berry::IWorkbenchWindow::Pointer window); protected slots: void Run(); private: void init(berry::IWorkbenchWindow::Pointer window); berry::IWorkbenchWindow::Pointer m_Window; }; #endif diff --git a/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkExtWorkbenchWindowAdvisorHack.h b/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkExtWorkbenchWindowAdvisorHack.h index a237a8d02e..c5c190b5fa 100644 --- a/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkExtWorkbenchWindowAdvisorHack.h +++ b/Plugins/org.mitk.gui.qt.ext/src/internal/QmitkExtWorkbenchWindowAdvisorHack.h @@ -1,60 +1,60 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkExtWorkbenchWindowAdvisorHack_h #define QmitkExtWorkbenchWindowAdvisorHack_h #include <QObject> class ctkPluginContext; class QmitkPreferencesDialog; class QmitkExtWorkbenchWindowAdvisorHack : public QObject { Q_OBJECT public slots: void onUndo(); void onRedo(); void onImageNavigator(); void onViewNavigator(); void onEditPreferences(); void onQuit(); void onResetPerspective(); void onClosePerspective(); void onNewWindow(); void onIntro(); /** - * @brief This slot is called if the user klicks the menu item "help->context help" or presses F1. + * @brief This slot is called if the user clicks the menu item "help->context help" or presses F1. * The help page is shown in a workbench editor. */ void onHelp(); void onHelpOpenHelpPerspective(); /** * @brief This slot is called if the user clicks in help menu the about button */ void onAbout(); public: QmitkExtWorkbenchWindowAdvisorHack(); ~QmitkExtWorkbenchWindowAdvisorHack() override; static QmitkExtWorkbenchWindowAdvisorHack* undohack; }; #endif diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox index 7ecdc6d7f9..7993e936b0 100644 --- a/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/documentation/UserManual/Manual.dox @@ -1,70 +1,76 @@ /** \page org_mitk_views_fit_genericfitting The Model Fit Generic Fitting View \imageMacro{fit_generic_doc.svg,"Icon of the Generic Fitting View",3.0} \tableofcontents \section FIT_GENERIC_Introduction Introduction This views offers a generic fitting component for time resolved image data. \section FIT_GENERIC__Contact Contact information If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \subsection FIT_GENERIC__Cite Citation information If you use the view for your research please cite our work as reference:\n\n Debus C and Floca R, Ingrisch M, Kompan I, Maier-Hein K, Abdollahi A, Nolden M, MITK-ModelFit: generic open-source framework for model fits and their exploration in medical imaging – design, implementation and application on the example of DCE-MRI. https://doi.org/10.1186/s12859-018-2588-1 (BMC Bioinformatics 2019 20:31) \section FIT_GENERIC__Data_and_ROI_Selection Time series and mask selection \imageMacro{modelfit_generic_maskAndFittingStrategy.png, "Time series and mask selection.", 10} In principle, every model can be fitted on the entire image. However, for model configuration reasons and computational time cost, this is often not advisable. Therefore, apart from the image to be fitted (Selected Time Series), a ROI segmentation can be defined (Selected Mask), within which model fitting is performed. The view currently offers Pixel based and/or ROI based averaged fits of time-varying curves. The ROI based fitting option becomes enabled, if a mask is selected. \section FIT_GENERIC_General_models Supported models -Currently the following models are available for fitting: -- Linear model : y = offset + slope*x -- Generic parameter model : A simple formula can be manually provided and will be parsed for fitting. -- T2 decay model : y = A*exp(-t/B) +The supported models are generic model which can represent any kind of data values y with generic units of y on any kind of data grid x with generic units of x. +When using these model for fitting to your data, be aware that you have to keep track of the quantities and units. +Currently the following models are available: +- Linear Model : y(x) = y-intercept + slope*x +- Generic parameter Model : A simple formula can be manually provided and will be parsed for fitting. +- Exponential Decay Model : y(x) = y-intercept * exp(-x/λ) +- Exponential Decay Offset Model: y(x) = y-intercept * exp(-x/λ) + baseline +- Exponential Saturation Model : if x<onset: y(x) = baseline, else: y(x) = baseline + (y_final-baseline) * (1 - exp(-rate*(x-onset))) +- Two Step Linear Model : if x < x_changepoint: y(x) = y-intercept + slope1*x, else: y(x) = y-intercept1 + slope2*x +- Three Step Linear Model : if x < x_changepoint1: y(x) = baseline, else if x_changepoint1 <= x <= x_changepoint2: y(x) = y-intercept1 + slope1*x, else if x>x_changepoint2: y(x) = y-intercept2 + slope2*x , \section FIT_GENERIC_Settings Model settings \subsection FIT_GENERIC_Settings_model Model specific settings Selecting one of the \ref FIT_GENERIC_General_models "supported models" will open below tabs for further configuration of the model. - The Generic parameter model required as input a formula to be parsed and the number parameters to fit. In the following image, detailed formula information is given. \imageMacro{modelfit_generic_genericParamModelSettings.png, "Formula info for the generic parameter model", 10} \subsection FIT_GENERIC_Settings_start Start parameter In cases of noisy data it can be useful to define the initial starting values of the parameter estimates, at which optimization starts, in order to prevent optimization results in local optima. Each model has default scalar values (applied to every voxel) for initial values of each parameter, however these can be adjusted. Moreover, initial values can also be defined locally for each individual voxel via starting value images. To load a starting value image, change the Type from scalar to image. This can be done by double-clicking on the type cell. In the Value column, selection of a starting value image will be available. \subsection FIT_GENERIC_Settings_constraint Constraints settings To limit the fitting search space and to exclude unphysical/illogical results for model parameter estimates, constraints to individual parameters as well as combinations can be imposed. Each model has default constraints, however, new ones can be defined or removed by the + and – buttons in the table. The first column specifies the parameter(s) involved in the constraint (if multiple parameters are selected, their sum will be used) by selection in the drop down menu. The second column Type defines whether the constraint defines an upper or lower boundary. Value defines the actual constraint value, that should not be crossed, and Width allows for a certain tolerance width. \section FIT_GENERIC_Fitting Executing a fit In order to distinguish results from different model fits to the data, a Fitting name can be defined. As default, the name of the model and the fitting strategy (pixel/ROI) are given. This name will then be appended by the respective parameter name.\n\n For development purposes and evaluation of the fits, the option Generate debug parameter images is available. Enabling this option will result in additional parameter maps displaying the status of the optimizer at fit termination. In the following definitions, an evaluation describes the process of cost function calculation and evaluation by the optimizer for a given parameter set. - Stop condition: Reasons for the fit termination, i.e. criterion reached, maximum number of iterations,... - Optimization time: The overall time from fitting start to termination. - Number of iterations: The number of iterations from fitting start to termination. After all necessary configurations are set, the button Start Modelling is enabled, which starts the fitting routine. Progress can be seen in the message box on the bottom. Resulting parameter maps will afterwards be added to the Data Manager as sub-nodes of the analyzed 4D image. */ diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/src/internal/GenericDataFittingView.cpp b/Plugins/org.mitk.gui.qt.fit.genericfitting/src/internal/GenericDataFittingView.cpp index b22c7e827b..51f148467d 100644 --- a/Plugins/org.mitk.gui.qt.fit.genericfitting/src/internal/GenericDataFittingView.cpp +++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/src/internal/GenericDataFittingView.cpp @@ -1,680 +1,718 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "GenericDataFittingView.h" #include "mitkWorkbenchUtil.h" #include <mitkLinearModelFactory.h> #include <mitkLinearModelParameterizer.h> #include <mitkGenericParamModelFactory.h> #include <mitkGenericParamModelParameterizer.h> -#include <mitkT2DecayModelFactory.h> -#include <mitkT2DecayModelParameterizer.h> +#include <mitkExponentialDecayModelFactory.h> +#include <mitkExponentialDecayModelParameterizer.h> #include <mitkExponentialSaturationModel.h> #include <mitkExponentialSaturationModelFactory.h> #include <mitkExponentialSaturationModelParameterizer.h> +#include "mitkTwoStepLinearModelFactory.h" +#include "mitkTwoStepLinearModelParameterizer.h" +#include "mitkThreeStepLinearModelFactory.h" +#include "mitkThreeStepLinearModelParameterizer.h" #include <mitkValueBasedParameterizationDelegate.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateOr.h> #include <mitkPixelBasedParameterFitImageGenerator.h> #include <mitkROIBasedParameterFitImageGenerator.h> #include <mitkLevenbergMarquardtModelFitFunctor.h> #include <mitkSumOfSquaredDifferencesFitCostFunction.h> #include <mitkNormalizedSumOfSquaredDifferencesFitCostFunction.h> #include <mitkSimpleBarrierConstraintChecker.h> #include <mitkModelFitResultHelper.h> #include <mitkImageTimeSelector.h> #include <mitkMaskedDynamicImageStatisticsGenerator.h> #include <mitkExtractTimeGrid.h> #include <QMessageBox> #include <QThreadPool> #include <QmitkDataStorageComboBox.h> // Includes for image casting between ITK and MITK #include <mitkImage.h> #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include <itkImage.h> #include <itkImageRegionIterator.h> #include <iostream> const std::string GenericDataFittingView::VIEW_ID = "org.mitk.views.fit.genericfitting"; void GenericDataFittingView::SetFocus() { m_Controls.btnModelling->setFocus(); } void GenericDataFittingView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_Controls.btnModelling->setEnabled(false); this->InitModelComboBox(); connect(m_Controls.btnModelling, SIGNAL(clicked()), this, SLOT(OnModellingButtonClicked())); connect(m_Controls.comboModel, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int))); connect(m_Controls.radioPixelBased, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); - //Gerneric setting + //Generic setting m_Controls.groupGeneric->hide(); m_Controls.labelFormulaInfo->hide(); connect(m_Controls.editFormula, SIGNAL(textChanged(const QString&)), this, SLOT(UpdateGUIControls())); connect(m_Controls.checkFormulaInfo, SIGNAL(toggled(bool)), m_Controls.labelFormulaInfo, SLOT(setVisible(bool))); connect(m_Controls.nrOfParams, SIGNAL(valueChanged(int)), this, SLOT(OnNrOfParamsChanged())); //Model fit configuration m_Controls.groupBox_FitConfiguration->hide(); m_Controls.checkBox_Constraints->setEnabled(false); m_Controls.constraintManager->setEnabled(false); m_Controls.initialValuesManager->setEnabled(false); m_Controls.initialValuesManager->setDataStorage(this->GetDataStorage()); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.initialValuesManager, SIGNAL(initialValuesChanged(void)), this, SLOT(UpdateGUIControls())); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), m_Controls.initialValuesManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setVisible(bool))); UpdateGUIControls(); } void GenericDataFittingView::UpdateGUIControls() { m_Controls.lineFitName->setPlaceholderText(QString::fromStdString(this->GetDefaultFitName())); m_Controls.lineFitName->setEnabled(!m_FittingInProgress); m_Controls.checkBox_Constraints->setEnabled(m_modelConstraints.IsNotNull()); bool isGenericFactory = dynamic_cast<mitk::GenericParamModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; m_Controls.groupGeneric->setVisible(isGenericFactory); m_Controls.groupBox_FitConfiguration->setVisible(m_selectedModelFactory); m_Controls.groupBox->setEnabled(!m_FittingInProgress); m_Controls.comboModel->setEnabled(!m_FittingInProgress); m_Controls.groupGeneric->setEnabled(!m_FittingInProgress); m_Controls.groupBox_FitConfiguration->setEnabled(!m_FittingInProgress); m_Controls.radioROIbased->setEnabled(m_selectedMask.IsNotNull()); m_Controls.btnModelling->setEnabled(m_selectedImage.IsNotNull() && m_selectedModelFactory.IsNotNull() && !m_FittingInProgress && CheckModelSettings()); } std::string GenericDataFittingView::GetFitName() const { std::string fitName = m_Controls.lineFitName->text().toStdString(); if (fitName.empty()) { fitName = m_Controls.lineFitName->placeholderText().toStdString(); } return fitName; } std::string GenericDataFittingView::GetDefaultFitName() const { std::string defaultName = "undefined model"; if (this->m_selectedModelFactory.IsNotNull()) { defaultName = this->m_selectedModelFactory->GetClassID(); } if (this->m_Controls.radioPixelBased->isChecked()) { defaultName += "_pixel"; } else { defaultName += "_roi"; } return defaultName; } void GenericDataFittingView::OnNrOfParamsChanged() { PrepareFitConfiguration(); UpdateGUIControls(); } void GenericDataFittingView::OnModellSet(int index) { m_selectedModelFactory = nullptr; if (index > 0) { if (static_cast<ModelFactoryStackType::size_type>(index) <= m_FactoryStack.size() ) { m_selectedModelFactory = m_FactoryStack[index - 1]; } else { MITK_WARN << "Invalid model index. Index outside of the factory stack. Factory stack size: "<< m_FactoryStack.size() << "; invalid index: "<< index; } } - if (m_selectedModelFactory) { this->m_modelConstraints = dynamic_cast<mitk::SimpleBarrierConstraintChecker*> (m_selectedModelFactory->CreateDefaultConstraints().GetPointer()); + if (this->m_modelConstraints.IsNull()) + { + this->m_modelConstraints = mitk::SimpleBarrierConstraintChecker::New(); + } + m_Controls.initialValuesManager->setInitialValues(m_selectedModelFactory->GetParameterNames(), m_selectedModelFactory->GetDefaultInitialParameterization()); m_Controls.constraintManager->setChecker(this->m_modelConstraints, this->m_selectedModelFactory->GetParameterNames()); } UpdateGUIControls(); } bool GenericDataFittingView::IsGenericParamFactorySelected() const { return dynamic_cast<mitk::GenericParamModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; } void GenericDataFittingView::PrepareFitConfiguration() { if (m_selectedModelFactory) { mitk::ModelBase::ParameterNamesType paramNames = m_selectedModelFactory->GetParameterNames(); unsigned int nrOfPools = this->m_Controls.nrOfParams->value(); //init values if (this->IsGenericParamFactorySelected()) { mitk::modelFit::ModelFitInfo::Pointer fitInfo = mitk::modelFit::ModelFitInfo::New(); fitInfo->staticParamMap.Add(mitk::GenericParamModel::NAME_STATIC_PARAMETER_number, { static_cast<double>(nrOfPools) }); auto parameterizer = m_selectedModelFactory->CreateParameterizer(fitInfo); paramNames = parameterizer->GetParameterNames(); m_Controls.initialValuesManager->setInitialValues(paramNames, parameterizer->GetDefaultInitialParameterization()); } else { m_Controls.initialValuesManager->setInitialValues(paramNames, this->m_selectedModelFactory->GetDefaultInitialParameterization()); } //constraints this->m_modelConstraints = dynamic_cast<mitk::SimpleBarrierConstraintChecker*> (m_selectedModelFactory->CreateDefaultConstraints().GetPointer()); if (this->m_modelConstraints.IsNull()) { this->m_modelConstraints = mitk::SimpleBarrierConstraintChecker::New(); } m_Controls.constraintManager->setChecker(this->m_modelConstraints, paramNames); } }; void GenericDataFittingView::OnModellingButtonClicked() { //check if all static parameters set if (m_selectedModelFactory.IsNotNull() && CheckModelSettings()) { mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr; mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr; bool isLinearFactory = dynamic_cast<mitk::LinearModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isGenericFactory = dynamic_cast<mitk::GenericParamModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool isT2DecayFactory = dynamic_cast<mitk::T2DecayModelFactory*> + bool isExponentialDecayFactory = dynamic_cast<mitk::ExponentialDecayModelFactory*> + (m_selectedModelFactory.GetPointer()) != nullptr; + bool isTwoStepLinearFactory = dynamic_cast<mitk::TwoStepLinearModelFactory*> + (m_selectedModelFactory.GetPointer()) != nullptr; + bool isThreeStepLinearFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isExponentialSaturationFactory = dynamic_cast<mitk::ExponentialSaturationModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; if (isLinearFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::LinearModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::LinearModelParameterizer>(fitSession, generator); } } else if (isGenericFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::GenericParamModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::GenericParamModelParameterizer>(fitSession, generator); } } - else if (isT2DecayFactory) + else if (isExponentialDecayFactory) + { + if (this->m_Controls.radioPixelBased->isChecked()) + { + GenerateModelFit_PixelBased<mitk::ExponentialDecayModelParameterizer>(fitSession, generator); + } + else + { + GenerateModelFit_ROIBased<mitk::ExponentialDecayModelParameterizer>(fitSession, generator); + } + } + else if (isTwoStepLinearFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { - GenerateModelFit_PixelBased<mitk::T2DecayModelParameterizer>(fitSession, generator); + GenerateModelFit_PixelBased<mitk::TwoStepLinearModelParameterizer>(fitSession, generator); } else { - GenerateModelFit_ROIBased<mitk::T2DecayModelParameterizer>(fitSession, generator); + GenerateModelFit_ROIBased<mitk::TwoStepLinearModelParameterizer>(fitSession, generator); + } + } + else if (isThreeStepLinearFactory) + { + if (this->m_Controls.radioPixelBased->isChecked()) + { + GenerateModelFit_PixelBased<mitk::ThreeStepLinearModelParameterizer>(fitSession, generator); + } + else + { + GenerateModelFit_ROIBased<mitk::ThreeStepLinearModelParameterizer>(fitSession, generator); } } else if (isExponentialSaturationFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::ExponentialSaturationModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::ExponentialSaturationModelParameterizer>(fitSession, generator); } } //add other models with else if if (generator.IsNotNull() && fitSession.IsNotNull()) { m_FittingInProgress = true; UpdateGUIControls(); DoFit(fitSession, generator); } else { QMessageBox box; box.setText("Fitting error!"); box.setInformativeText("Could not establish fitting job. Error when setting ab generator, model parameterizer or session info."); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } else { QMessageBox box; box.setText("Static parameters for model are not set!"); box.setInformativeText("Some static parameters, that are needed for calculation are not set and equal to zero. Modeling not possible"); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } void GenericDataFittingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList<mitk::DataNode::Pointer>& selectedNodes) { m_selectedNode = nullptr; m_selectedImage = nullptr; m_selectedMaskNode = nullptr; m_selectedMask = nullptr; m_Controls.masklabel->setText("No (valid) mask selected."); m_Controls.timeserieslabel->setText("No (valid) series selected."); QList<mitk::DataNode::Pointer> nodes = selectedNodes; mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image"); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isLegacyMask = mitk::NodePredicateAnd::New(isImage, isBinary); mitk::NodePredicateOr::Pointer maskPredicate = mitk::NodePredicateOr::New(isLegacyMask, isLabelSet); if (nodes.size() > 0 && isImage->CheckNode(nodes.front())) { this->m_selectedNode = nodes.front(); this->m_selectedImage = dynamic_cast<mitk::Image*>(this->m_selectedNode->GetData()); m_Controls.timeserieslabel->setText((this->m_selectedNode->GetName()).c_str()); nodes.pop_front(); } if (nodes.size() > 0 && maskPredicate->CheckNode(nodes.front())) { this->m_selectedMaskNode = nodes.front(); this->m_selectedMask = dynamic_cast<mitk::Image*>(this->m_selectedMaskNode->GetData()); if (this->m_selectedMask->GetTimeSteps() > 1) { MITK_INFO << "Selected mask has multiple timesteps. Only use first timestep to mask model fit. Mask name: " << m_selectedMaskNode->GetName(); mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedMask = maskedImageTimeSelector->GetOutput(); } m_Controls.masklabel->setText((this->m_selectedMaskNode->GetName()).c_str()); } if (m_selectedMask.IsNull()) { this->m_Controls.radioPixelBased->setChecked(true); } UpdateGUIControls(); } bool GenericDataFittingView::CheckModelSettings() const { bool ok = true; - //check wether any model is set at all. Otherwise exit with false + //check whether any model is set at all. Otherwise exit with false if (m_selectedModelFactory.IsNotNull()) { bool isGenericFactory = dynamic_cast<mitk::GenericParamModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; if (isGenericFactory) { ok = !m_Controls.editFormula->text().isEmpty(); } } else { ok = false; } if (this->m_Controls.radioButton_StartParameters->isChecked() && !this->m_Controls.initialValuesManager->hasValidInitialValues()) { std::string warning = "Warning. Invalid start parameters. At least one parameter has an invalid image setting as source."; MITK_ERROR << warning; m_Controls.infoBox->append(QString("") + QString::fromStdString(warning) + QString("")); ok = false; }; return ok; } void GenericDataFittingView::ConfigureInitialParametersOfParameterizer(mitk::ModelParameterizerBase* parameterizer) const { if (m_Controls.radioButton_StartParameters->isChecked()) { //use user defined initial parameters mitk::ValueBasedParameterizationDelegate::Pointer paramDelegate = mitk::ValueBasedParameterizationDelegate::New(); paramDelegate->SetInitialParameterization(m_Controls.initialValuesManager->getInitialValues()); parameterizer->SetInitialParameterizationDelegate(paramDelegate); } mitk::GenericParamModelParameterizer* genericParameterizer = dynamic_cast<mitk::GenericParamModelParameterizer*>(parameterizer); if (genericParameterizer) { genericParameterizer->SetFunctionString(m_Controls.editFormula->text().toStdString()); } } template <typename TParameterizer> void GenericDataFittingView::GenerateModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); auto genericParameterizer = dynamic_cast<mitk::GenericParamModelParameterizer*>(modelParameterizer.GetPointer()); if (genericParameterizer) { genericParameterizer->SetNumberOfParameters(this->m_Controls.nrOfParams->value()); } this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = m_selectedMask->GetUID(); } fitGenerator->SetDynamicImage(this->m_selectedImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); } template <typename TParameterizer> void GenericDataFittingView::GenerateModelFit_ROIBased( mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); auto genericParameterizer = dynamic_cast<mitk::GenericParamModelParameterizer*>(modelParameterizer.GetPointer()); if (genericParameterizer) { genericParameterizer->SetNumberOfParameters(this->m_Controls.nrOfParams->value()); } this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(m_selectedImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage)); generator = fitGenerator.GetPointer(); std::string roiUID = this->m_selectedMask->GetUID(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } void GenericDataFittingView::DoFit(const mitk::modelFit::ModelFitInfo* fitSession, mitk::ParameterFitImageGeneratorBase* generator) { QString message = "Fitting Data Set . . ."; m_Controls.infoBox->append(message); ///////////////////////// //create job and put it into the thread pool ParameterFitBackgroundJob* pJob = new ParameterFitBackgroundJob(generator, fitSession, this->m_selectedNode); pJob->setAutoDelete(true); connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnJobError(QString))); connect(pJob, SIGNAL(Finished()), this, SLOT(OnJobFinished())); connect(pJob, SIGNAL(ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), this, SLOT(OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), Qt::BlockingQueuedConnection); connect(pJob, SIGNAL(JobProgress(double)), this, SLOT(OnJobProgress(double))); connect(pJob, SIGNAL(JobStatusChanged(QString)), this, SLOT(OnJobStatusChanged(QString))); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); } GenericDataFittingView::GenericDataFittingView() : m_FittingInProgress(false) { m_selectedImage = nullptr; m_selectedMask = nullptr; mitk::ModelFactoryBase::Pointer factory = mitk::LinearModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::GenericParamModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); - factory = mitk::T2DecayModelFactory::New().GetPointer(); + factory = mitk::ExponentialDecayModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::ExponentialSaturationModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); + factory = mitk::TwoStepLinearModelFactory::New().GetPointer(); + m_FactoryStack.push_back(factory); + factory = mitk::ThreeStepLinearModelFactory::New().GetPointer(); + m_FactoryStack.push_back(factory); this->m_IsNotABinaryImagePredicate = mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType<mitk::Image>::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true))), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); this->m_IsBinaryImagePredicate = mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType<mitk::Image>::New(), mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); } void GenericDataFittingView::OnJobFinished() { this->m_Controls.infoBox->append(QString("Fitting finished")); this->m_FittingInProgress = false; this->UpdateGUIControls(); }; void GenericDataFittingView::OnJobError(QString err) { MITK_ERROR << err.toStdString().c_str(); m_Controls.infoBox->append(QString("") + err + QString("")); }; void GenericDataFittingView::OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results, const ParameterFitBackgroundJob* pJob) { //Store the resulting parameter fit image via convenience helper function in data storage //(handles the correct generation of the nodes and their properties) mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), results, pJob->GetParentNode()); }; void GenericDataFittingView::OnJobProgress(double progress) { QString report = QString("Progress. ") + QString::number(progress); this->m_Controls.infoBox->append(report); }; void GenericDataFittingView::OnJobStatusChanged(QString info) { this->m_Controls.infoBox->append(info); } void GenericDataFittingView::InitModelComboBox() const { this->m_Controls.comboModel->clear(); this->m_Controls.comboModel->addItem(tr("No model selected")); for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin(); pos != m_FactoryStack.end(); ++pos) { this->m_Controls.comboModel->addItem(QString::fromStdString((*pos)->GetClassID())); } this->m_Controls.comboModel->setCurrentIndex(0); }; mitk::ModelFitFunctorBase::Pointer GenericDataFittingView::CreateDefaultFitFunctor( const mitk::ModelParameterizerBase* parameterizer) const { mitk::LevenbergMarquardtModelFitFunctor::Pointer fitFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::Pointer chi2 = mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("Chi^2", chi2); if (m_Controls.checkBox_Constraints->isChecked()) { fitFunctor->SetConstraintChecker(m_modelConstraints); } mitk::ModelBase::Pointer refModel = parameterizer->GenerateParameterizedModel(); ::itk::LevenbergMarquardtOptimizer::ScalesType scales; scales.SetSize(refModel->GetNumberOfParameters()); scales.Fill(1.0); fitFunctor->SetScales(scales); fitFunctor->SetDebugParameterMaps(m_Controls.checkDebug->isChecked()); return fitFunctor.GetPointer(); } diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorView.cpp b/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorView.cpp index 50ae633df5..bb5465eb1b 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorView.cpp +++ b/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorView.cpp @@ -1,918 +1,918 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "ModelFitInspectorView.h" // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> #include <berryIWorkbenchPage.h> // mitk #include <QmitkRenderWindow.h> // Qt #include <QMessageBox> #include <QFileDialog> #include <QTableWidget> #include <qwt_plot_marker.h> #include <QmitkPlotWidget.h> #include <mitkNodePredicateFunction.h> #include <mitkScalarListLookupTableProperty.h> #include <mitkModelFitConstants.h> #include <mitkExtractTimeGrid.h> #include <mitkModelGenerator.h> #include <mitkModelFitException.h> #include <mitkModelFitParameterValueExtraction.h> #include <mitkModelFitResultRelationRule.h> #include <mitkModelFitPlotDataHelper.h> #include <mitkTimeGridHelper.h> #include <mitkTimeNavigationController.h> const std::string ModelFitInspectorView::VIEW_ID = "org.mitk.views.fit.inspector"; const unsigned int ModelFitInspectorView::INTERPOLATION_STEPS = 10; const std::string DEFAULT_X_AXIS = "Time [s]"; ModelFitInspectorView::ModelFitInspectorView() : m_renderWindowPart(nullptr), m_internalUpdateFlag(false), m_currentFit(nullptr), m_currentModelParameterizer(nullptr), m_currentModelProviderService(nullptr), m_currentSelectedTimeStep(0), m_currentSelectedNode(nullptr) { m_currentSelectedPosition.Fill(0.0); m_modelfitList.clear(); } ModelFitInspectorView::~ModelFitInspectorView() { } void ModelFitInspectorView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_renderWindowPart != renderWindowPart) { m_renderWindowPart = renderWindowPart; } this->m_SliceChangeListener.RenderWindowPartActivated(renderWindowPart); } void ModelFitInspectorView::RenderWindowPartDeactivated( mitk::IRenderWindowPart* renderWindowPart) { m_renderWindowPart = nullptr; this->m_SliceChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void ModelFitInspectorView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_SelectionServiceConnector = std::make_unique<QmitkSelectionServiceConnector>(); m_SelectionServiceConnector->AddPostSelectionListener(this->GetSite()->GetWorkbenchWindow()->GetSelectionService()); m_Controls.inputNodeSelector->SetDataStorage(GetDataStorage()); m_Controls.inputNodeSelector->SetEmptyInfo(QString("Please select input data to be viewed.")); m_Controls.inputNodeSelector->SetInvalidInfo(QString("No input data is selected")); m_Controls.inputNodeSelector->SetPopUpTitel(QString("Choose 3D+t input data that should be viewed!")); m_Controls.inputNodeSelector->SetSelectionIsOptional(false); m_Controls.inputNodeSelector->SetSelectOnlyVisibleNodes(true); auto predicate = mitk::NodePredicateFunction::New([](const mitk::DataNode *node) { bool isModelFitNode = node->GetData() && node->GetData()->GetProperty(mitk::ModelFitConstants::FIT_UID_PROPERTY_NAME().c_str()).IsNotNull(); return isModelFitNode || (node && node->GetData() && node->GetData()->GetTimeSteps() > 1); }); m_Controls.inputNodeSelector->SetNodePredicate(predicate); connect(m_SelectionServiceConnector.get(), &QmitkSelectionServiceConnector::ServiceSelectionChanged, m_Controls.inputNodeSelector, &QmitkSingleNodeSelectionWidget::SetCurrentSelection); connect(m_Controls.inputNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &ModelFitInspectorView::OnInputChanged); this->m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); connect(m_Controls.cmbFit, SIGNAL(currentIndexChanged(int)), this, SLOT(OnFitSelectionChanged(int))); connect(m_Controls.radioScaleFixed, SIGNAL(toggled(bool)), m_Controls.sbFixMin, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed, SIGNAL(toggled(bool)), m_Controls.sbFixMax, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed, SIGNAL(toggled(bool)), m_Controls.labelFixMin, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed, SIGNAL(toggled(bool)), m_Controls.labelFixMax, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed, SIGNAL(toggled(bool)), m_Controls.btnScaleToData, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed, SIGNAL(toggled(bool)), this, SLOT(OnScaleFixedYChecked(bool))); connect(m_Controls.btnScaleToData, SIGNAL(clicked()), this, SLOT(OnScaleToDataYClicked())); connect(m_Controls.sbFixMax, SIGNAL(valueChanged(double)), this, SLOT(OnFixedScalingYChanged(double))); connect(m_Controls.sbFixMin, SIGNAL(valueChanged(double)), this, SLOT(OnFixedScalingYChanged(double))); connect(m_Controls.radioScaleFixed_x, SIGNAL(toggled(bool)), m_Controls.sbFixMin_x, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed_x, SIGNAL(toggled(bool)), m_Controls.sbFixMax_x, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed_x, SIGNAL(toggled(bool)), m_Controls.labelFixMin_x, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed_x, SIGNAL(toggled(bool)), m_Controls.labelFixMax_x, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed_x, SIGNAL(toggled(bool)), m_Controls.btnScaleToData_x, SLOT(setEnabled(bool))); connect(m_Controls.radioScaleFixed_x, SIGNAL(toggled(bool)), this, SLOT(OnScaleFixedXChecked(bool))); connect(m_Controls.btnScaleToData_x, SIGNAL(clicked()), this, SLOT(OnScaleToDataXClicked())); connect(m_Controls.sbFixMax_x, SIGNAL(valueChanged(double)), this, SLOT(OnFixedScalingXChanged(double))); connect(m_Controls.sbFixMin_x, SIGNAL(valueChanged(double)), this, SLOT(OnFixedScalingXChanged(double))); connect(m_Controls.btnFullPlot, SIGNAL(clicked(bool)), this, SLOT(OnFullPlotClicked(bool))); this->EnsureBookmarkPointSet(); m_Controls.inspectionPositionWidget->SetPositionBookmarkNode(m_PositionBookmarksNode.Lock()); connect(m_Controls.inspectionPositionWidget, SIGNAL(PositionBookmarksChanged()), this, SLOT(OnPositionBookmarksChanged())); // For some reason this needs to be called to set the plot widget's minimum width to an // acceptable level (since Qwt 6). // Otherwise it tries to keep both axes equal in length, resulting in a minimum width of // 400-500px which is way too much. m_Controls.widgetPlot->GetPlot()->updateAxes(); m_Controls.cmbFit->clear(); mitk::IRenderWindowPart* renderWindowPart = GetRenderWindowPart(); RenderWindowPartActivated(renderWindowPart); } void ModelFitInspectorView::SetFocus() { } void ModelFitInspectorView::NodeRemoved(const mitk::DataNode* node) { if (node == this->m_currentSelectedNode) { QmitkSingleNodeSelectionWidget::NodeList emptylist; this->m_Controls.inputNodeSelector->SetCurrentSelection(emptylist); } } void ModelFitInspectorView::OnScaleFixedYChecked(bool checked) { m_Controls.widgetPlot->GetPlot()->setAxisAutoScale(QwtPlot::yLeft, !checked); if (checked) { OnScaleToDataYClicked(); } m_Controls.widgetPlot->GetPlot()->replot(); }; void ModelFitInspectorView::OnScaleFixedXChecked(bool checked) { m_Controls.widgetPlot->GetPlot()->setAxisAutoScale(QwtPlot::xBottom, !checked); if (checked) { OnScaleToDataXClicked(); } m_Controls.widgetPlot->GetPlot()->replot(); }; void ModelFitInspectorView::OnScaleToDataYClicked() { auto minmax = this->m_PlotCurves.GetYMinMax(); auto min = minmax.first - std::abs(minmax.first) * 0.01; auto max = minmax.second + std::abs(minmax.second) * 0.01; m_Controls.sbFixMin->setValue(min); m_Controls.sbFixMax->setValue(max); }; void ModelFitInspectorView::OnScaleToDataXClicked() { auto minmax = this->m_PlotCurves.GetXMinMax(); auto min = minmax.first - std::abs(minmax.first) * 0.01; auto max = minmax.second + std::abs(minmax.second) * 0.01; m_Controls.sbFixMin_x->setValue(min); m_Controls.sbFixMax_x->setValue(max); }; void ModelFitInspectorView::OnFixedScalingYChanged(double /*value*/) { m_Controls.widgetPlot->GetPlot()->setAxisScale(QwtPlot::yLeft, m_Controls.sbFixMin->value(), m_Controls.sbFixMax->value()); m_Controls.widgetPlot->GetPlot()->replot(); }; void ModelFitInspectorView::OnFixedScalingXChanged(double /*value*/) { m_Controls.widgetPlot->GetPlot()->setAxisScale(QwtPlot::xBottom, m_Controls.sbFixMin_x->value(), m_Controls.sbFixMax_x->value()); m_Controls.widgetPlot->GetPlot()->replot(); }; void ModelFitInspectorView::OnFullPlotClicked(bool checked) { m_Controls.tabWidget->setVisible(!checked); }; int ModelFitInspectorView::ActualizeFitSelectionWidget() { mitk::modelFit::ModelFitInfo::UIDType selectedFitUD = ""; bool isModelFitNode = false; if (this->m_Controls.inputNodeSelector->GetSelectedNode().IsNotNull()) { isModelFitNode = this->m_Controls.inputNodeSelector->GetSelectedNode()->GetData()->GetPropertyList()->GetStringProperty( mitk::ModelFitConstants::FIT_UID_PROPERTY_NAME().c_str(), selectedFitUD); } mitk::DataStorage::Pointer storage = this->GetDataStorage(); mitk::modelFit::NodeUIDSetType fitUIDs = mitk::modelFit::GetFitUIDsOfNode( this->m_currentSelectedNode, storage); this->m_modelfitList.clear(); this->m_Controls.cmbFit->clear(); for (const auto & fitUID : fitUIDs) { mitk::modelFit::ModelFitInfo::ConstPointer info = mitk::modelFit::CreateFitInfoFromNode(fitUID, storage).GetPointer(); if (info.IsNotNull()) { this->m_modelfitList.insert(std::make_pair(info->uid, info)); std::ostringstream nameStrm; if (info->fitName.empty()) { nameStrm << info->uid; } else { nameStrm << info->fitName; } nameStrm << " (" << info->modelName << ")"; QVariant data(info->uid.c_str()); m_Controls.cmbFit->addItem(QString::fromStdString(nameStrm.str()), data); } else { MITK_ERROR << "Was not able to extract model fit information from storage. Node properties in storage may be invalid. Failed fit UID:" << fitUID; } } int cmbIndex = 0; if (m_modelfitList.empty()) { cmbIndex = -1; }; if (isModelFitNode) { //model was selected, thus select this one in combobox QVariant data(selectedFitUD.c_str()); cmbIndex = m_Controls.cmbFit->findData(data); if (cmbIndex == -1) { MITK_WARN << - "Model fit Inspector in invalid state. Selected fit seems to be not avaible in plugin selection. Failed fit UID:" + "Model fit Inspector in invalid state. Selected fit seems to be not available in plugin selection. Failed fit UID:" << selectedFitUD; } }; m_Controls.cmbFit->setCurrentIndex(cmbIndex); return cmbIndex; } void ModelFitInspectorView::OnInputChanged(const QList<mitk::DataNode::Pointer>& nodes) { if (nodes.size() > 0) { if (nodes.front() != this->m_currentSelectedNode) { m_internalUpdateFlag = true; this->m_currentSelectedNode = nodes.front(); mitk::modelFit::ModelFitInfo::UIDType selectedFitUD = ""; bool isModelFitNode = this->m_currentSelectedNode->GetData()->GetPropertyList()->GetStringProperty( mitk::ModelFitConstants::FIT_UID_PROPERTY_NAME().c_str(), selectedFitUD); if (isModelFitNode) { this->m_currentSelectedNode = this->GetInputNode(this->m_currentSelectedNode); if (this->m_currentSelectedNode.IsNull()) { MITK_WARN << "Model fit Inspector in invalid state. Input image for selected fit cannot be found in data storage. Failed fit UID:" << selectedFitUD; } } auto cmbIndex = ActualizeFitSelectionWidget(); m_internalUpdateFlag = false; m_selectedNodeTime.Modified(); if (cmbIndex == -1) { //only raw 4D data selected. Just update plots for current position m_currentFit = nullptr; m_currentFitTime.Modified(); OnSliceChanged(); m_Controls.plotDataWidget->SetXName(DEFAULT_X_AXIS); } else { //refresh fit selection (and implicitly update plots) OnFitSelectionChanged(cmbIndex); } } } else { if (this->m_currentSelectedNode.IsNotNull()) { m_internalUpdateFlag = true; this->m_currentSelectedNode = nullptr; this->m_currentFit = nullptr; this->m_modelfitList.clear(); this->m_Controls.cmbFit->clear(); m_internalUpdateFlag = false; m_selectedNodeTime.Modified(); OnFitSelectionChanged(0); RefreshPlotData(); m_Controls.plotDataWidget->SetPlotData(&(this->m_PlotCurves)); m_Controls.fitParametersWidget->setFits(QmitkFitParameterModel::FitVectorType()); RenderPlot(); } } } mitk::DataNode::ConstPointer ModelFitInspectorView::GetInputNode(mitk::DataNode::ConstPointer node) { if (node.IsNotNull()) { std::string selectedFitUD = ""; auto rule = mitk::ModelFitResultRelationRule::New(); auto predicate = rule->GetDestinationsDetector(node); mitk::DataStorage::SetOfObjects::ConstPointer parentNodeList = GetDataStorage()->GetSubset(predicate); if (parentNodeList->size() > 0) { return parentNodeList->front().GetPointer(); } } return mitk::DataNode::ConstPointer(); } void ModelFitInspectorView::ValidateAndSetCurrentPosition() { const mitk::Point3D currentSelectedPosition = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetSelectedPosition(nullptr); const unsigned int currentSelectedTimestep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimeStep(); if (m_currentSelectedPosition != currentSelectedPosition || m_currentSelectedTimeStep != currentSelectedTimestep || m_selectedNodeTime > m_currentPositionTime) { //the current position has been changed or the selected node has been changed since the last position validation -> check position m_currentSelectedPosition = currentSelectedPosition; m_currentSelectedTimeStep = currentSelectedTimestep; m_currentPositionTime.Modified(); m_validSelectedPosition = false; auto inputImage = this->GetCurrentInputImage(); if (inputImage.IsNull()) { return; } mitk::BaseGeometry::ConstPointer geometry = inputImage->GetTimeGeometry()->GetGeometryForTimeStep( m_currentSelectedTimeStep).GetPointer(); // check for invalid time step if (geometry.IsNull()) { geometry = inputImage->GetTimeGeometry()->GetGeometryForTimeStep(0); } if (geometry.IsNull()) { return; } m_validSelectedPosition = geometry->IsInside(m_currentSelectedPosition); } } mitk::Image::ConstPointer ModelFitInspectorView::GetCurrentInputImage() const { mitk::Image::ConstPointer result = nullptr; if (this->m_currentFit.IsNotNull()) { result = m_currentFit->inputImage; } else if (this->m_currentSelectedNode.IsNotNull()) { result = dynamic_cast<mitk::Image*>(this->m_currentSelectedNode->GetData()); if (result.IsNotNull() && result->GetTimeSteps() <= 1) { //if the image is not dynamic, we can't use it. result = nullptr; } } return result; }; const mitk::ModelBase::TimeGridType ModelFitInspectorView::GetCurrentTimeGrid() const { if (m_currentModelProviderService && m_currentFit.IsNotNull()) { return m_currentModelProviderService->GetVariableGrid(m_currentFit); } else { //fall back if there is no model provider we assume to use the normal time grid. return ExtractTimeGrid(GetCurrentInputImage()); } }; void ModelFitInspectorView::OnSliceChanged() { ValidateAndSetCurrentPosition(); m_Controls.widgetPlot->setEnabled(m_validSelectedPosition); if (m_currentSelectedNode.IsNotNull()) { m_Controls.inspectionPositionWidget->SetCurrentPosition(m_currentSelectedPosition); if (RefreshPlotData()) { RenderPlot(); m_Controls.plotDataWidget->SetPlotData(&m_PlotCurves); RenderFitInfo(); } } } void ModelFitInspectorView::OnPositionBookmarksChanged() { if (RefreshPlotData()) { RenderPlot(); m_Controls.plotDataWidget->SetPlotData(&m_PlotCurves); RenderFitInfo(); } } void ModelFitInspectorView::OnFitSelectionChanged(int index) { if (!m_internalUpdateFlag) { MITK_DEBUG << "selected fit index: " << index; std::string uid = ""; if (m_Controls.cmbFit->count() > index) { uid = m_Controls.cmbFit->itemData(index).toString().toStdString(); } mitk::modelFit::ModelFitInfo::ConstPointer newFit = nullptr; ModelFitInfoListType::iterator finding = m_modelfitList.find(uid); if (finding != m_modelfitList.end()) { newFit = finding->second; } if (m_currentFit != newFit) { m_currentModelParameterizer = nullptr; m_currentModelProviderService = nullptr; if (newFit.IsNotNull()) { m_currentModelParameterizer = mitk::ModelGenerator::GenerateModelParameterizer(*newFit); m_currentModelProviderService = mitk::ModelGenerator::GetProviderService(newFit->functionClassID); } m_currentFit = newFit; m_currentFitTime.Modified(); auto name = m_currentFit->xAxisName; if (!m_currentFit->xAxisUnit.empty()) { name += " [" + m_currentFit->xAxisUnit + "]"; } m_Controls.plotDataWidget->SetXName(name); OnSliceChanged(); } } } mitk::PlotDataCurveCollection::Pointer ModelFitInspectorView::RefreshPlotDataCurveCollection(const mitk::Point3D& position, const mitk::Image* input, const mitk::modelFit::ModelFitInfo* fitInfo, const mitk::ModelBase::TimeGridType& timeGrid, mitk::ModelParameterizerBase* parameterizer) { mitk::PlotDataCurveCollection::Pointer result = mitk::PlotDataCurveCollection::New(); //sample curve if (input) { result->InsertElement(mitk::MODEL_FIT_PLOT_SAMPLE_NAME(), GenerateImageSamplePlotData(position, input, timeGrid)); } //model signal curve if (fitInfo) { // Interpolate time grid (x values) so the curve looks smooth const mitk::ModelBase::TimeGridType interpolatedTimeGrid = mitk::GenerateSupersampledTimeGrid(timeGrid, INTERPOLATION_STEPS); auto hires_curve = mitk::GenerateModelSignalPlotData(position, fitInfo, interpolatedTimeGrid, parameterizer); result->InsertElement(mitk::MODEL_FIT_PLOT_INTERPOLATED_SIGNAL_NAME(), hires_curve); auto curve = mitk::GenerateModelSignalPlotData(position, fitInfo, timeGrid, parameterizer); result->InsertElement(mitk::MODEL_FIT_PLOT_SIGNAL_NAME(), curve); } return result; }; bool ModelFitInspectorView::RefreshPlotData() { bool changed = false; if (m_currentSelectedNode.IsNull()) { this->m_PlotCurves = mitk::ModelFitPlotData(); changed = m_selectedNodeTime > m_lastRefreshTime; m_lastRefreshTime.Modified(); } else { assert(GetRenderWindowPart() != NULL); const mitk::Image* input = GetCurrentInputImage(); const mitk::ModelBase::TimeGridType timeGrid = GetCurrentTimeGrid(); if (m_currentFitTime > m_lastRefreshTime || m_currentPositionTime > m_lastRefreshTime) { if (m_validSelectedPosition) { m_PlotCurves.currentPositionPlots = RefreshPlotDataCurveCollection(m_currentSelectedPosition,input,m_currentFit, timeGrid, m_currentModelParameterizer); } else { m_PlotCurves.currentPositionPlots = mitk::PlotDataCurveCollection::New(); } changed = true; } auto bookmarks = m_PositionBookmarks.Lock(); if (bookmarks.IsNotNull()) { if (m_currentFitTime > m_lastRefreshTime || bookmarks->GetMTime() > m_lastRefreshTime) { m_PlotCurves.positionalPlots.clear(); auto endIter = bookmarks->End(); for (auto iter = bookmarks->Begin(); iter != endIter; iter++) { auto collection = RefreshPlotDataCurveCollection(iter.Value(), input, m_currentFit, timeGrid, m_currentModelParameterizer); m_PlotCurves.positionalPlots.emplace(iter.Index(), std::make_pair(iter.Value(), collection)); } changed = true; } } else { m_PlotCurves.positionalPlots.clear(); } // input data curve if (m_currentFitTime > m_lastRefreshTime) { m_PlotCurves.staticPlots->clear(); if (m_currentFit.IsNotNull()) { m_PlotCurves.staticPlots = GenerateAdditionalModelFitPlotData(m_currentSelectedPosition, m_currentFit, timeGrid); } changed = true; } m_lastRefreshTime.Modified(); } return changed; } void ModelFitInspectorView::RenderFitInfo() { assert(m_renderWindowPart != nullptr); // configure fit information if (m_currentFit.IsNull()) { m_Controls.lFitType->setText(""); m_Controls.lFitUID->setText(""); m_Controls.lModelName->setText(""); m_Controls.lModelType->setText(""); } else { m_Controls.lFitType->setText(QString::fromStdString(m_currentFit->fitType)); m_Controls.lFitUID->setText(QString::fromStdString(m_currentFit->uid)); m_Controls.lModelName->setText(QString::fromStdString(m_currentFit->modelName)); m_Controls.lModelType->setText(QString::fromStdString(m_currentFit->modelType)); } // print results std::stringstream infoOutput; m_Controls.fitParametersWidget->setVisible(false); m_Controls.groupSettings->setVisible(false); if (m_currentFit.IsNull()) { infoOutput << "No fit selected. Only raw image data is plotted."; } else if (!m_validSelectedPosition) { infoOutput << "Current position is outside of the input image of the selected fit.\nInspector is deactivated."; } else { m_Controls.fitParametersWidget->setVisible(true); m_Controls.fitParametersWidget->setFits({ m_currentFit }); m_Controls.fitParametersWidget->setPositionBookmarks(m_PositionBookmarks.Lock()); m_Controls.fitParametersWidget->setCurrentPosition(m_currentSelectedPosition); } // configure data table m_Controls.tableInputData->clearContents(); if (m_currentFit.IsNull()) { infoOutput << "No fit selected. Only raw image data is plotted."; } else { m_Controls.groupSettings->setVisible(true); m_Controls.tableInputData->setRowCount(m_PlotCurves.staticPlots->size()); unsigned int rowIndex = 0; for (mitk::PlotDataCurveCollection::const_iterator pos = m_PlotCurves.staticPlots->begin(); pos != m_PlotCurves.staticPlots->end(); ++pos, ++rowIndex) { QColor dataColor; if (pos->first == "ROI") { dataColor = QColor(0, 190, 0); } else { //Use HSV schema of QColor to calculate a different color depending on the //number of already existing free iso lines. dataColor.setHsv(((rowIndex + 1) * 85) % 360, 255, 255); } QTableWidgetItem* newItem = new QTableWidgetItem(QString::fromStdString(pos->first)); m_Controls.tableInputData->setItem(rowIndex, 0, newItem); newItem = new QTableWidgetItem(); newItem->setBackgroundColor(dataColor); m_Controls.tableInputData->setItem(rowIndex, 1, newItem); } } m_Controls.lInfo->setText(QString::fromStdString(infoOutput.str())); } void ModelFitInspectorView::RenderPlotCurve(const mitk::PlotDataCurveCollection* curveCollection, const QColor& sampleColor, const QColor& signalColor, const std::string& posString) { auto sampleCurve = mitk::ModelFitPlotData::GetSamplePlot(curveCollection); if (sampleCurve) { std::string name = mitk::MODEL_FIT_PLOT_SAMPLE_NAME() + posString; unsigned int curveId = m_Controls.widgetPlot->InsertCurve(name.c_str()); m_Controls.widgetPlot->SetCurveData(curveId, sampleCurve->GetValues()); m_Controls.widgetPlot->SetCurvePen(curveId, QPen(Qt::NoPen)); // QwtSymbol needs to passed as a real pointer from MITK v2013.09.0 on // (QwtPlotCurve deletes it on destruction and assignment). QwtSymbol* dataSymbol = new QwtSymbol(QwtSymbol::Diamond, sampleColor, sampleColor, QSize(8, 8)); m_Controls.widgetPlot->SetCurveSymbol(curveId, dataSymbol); // Again, there is no way to set a curve's legend attributes via QmitkPlotWidget so this // gets unnecessarily complicated. QwtPlotCurve* measurementCurve = dynamic_cast<QwtPlotCurve*>(m_Controls.widgetPlot-> GetPlot()->itemList(QwtPlotItem::Rtti_PlotCurve).back()); measurementCurve->setLegendAttribute(QwtPlotCurve::LegendShowSymbol); measurementCurve->setLegendIconSize(QSize(8, 8)); } //draw model curve auto signalCurve = mitk::ModelFitPlotData::GetInterpolatedSignalPlot(curveCollection); if (signalCurve) { std::string name = mitk::MODEL_FIT_PLOT_SIGNAL_NAME() + posString; QPen pen; pen.setColor(signalColor); pen.setWidth(2); unsigned int curveId = m_Controls.widgetPlot->InsertCurve(name.c_str()); m_Controls.widgetPlot->SetCurveData(curveId, signalCurve->GetValues()); m_Controls.widgetPlot->SetCurvePen(curveId, pen); // Manually set the legend attribute to use the symbol as the legend icon and alter its // size. Otherwise it would revert to default which is drawing a square which is the color // of the curve's pen, so in this case none which defaults to black. // Unfortunately, QmitkPlotWidget offers no way to set the legend attribute and icon size so // this looks a bit hacky. QwtPlotCurve* fitCurve = dynamic_cast<QwtPlotCurve*>(m_Controls.widgetPlot->GetPlot()-> itemList(QwtPlotItem::Rtti_PlotCurve).back()); fitCurve->setLegendAttribute(QwtPlotCurve::LegendShowLine); } } void ModelFitInspectorView::RenderPlot() { m_Controls.widgetPlot->Clear(); std::string xAxis = DEFAULT_X_AXIS; std::string yAxis = "Intensity"; std::string plotTitle = "Raw data plot: no data"; if (m_currentSelectedNode.IsNotNull()) { plotTitle = "Raw data plot: " + m_currentSelectedNode->GetName(); } if (m_currentFit.IsNotNull()) { plotTitle = m_currentFit->modelName.c_str(); xAxis = m_currentFit->xAxisName; if (!m_currentFit->xAxisUnit.empty()) { xAxis += " [" + m_currentFit->xAxisUnit + "]"; } yAxis = m_currentFit->yAxisName; if (!m_currentFit->yAxisUnit.empty()) { yAxis += " [" + m_currentFit->yAxisUnit + "]"; } } m_Controls.widgetPlot->SetAxisTitle(QwtPlot::xBottom, xAxis.c_str()); m_Controls.widgetPlot->SetAxisTitle(QwtPlot::yLeft, yAxis.c_str()); m_Controls.widgetPlot->SetPlotTitle(plotTitle.c_str()); // Draw static curves unsigned int colorIndex = 0; for (mitk::PlotDataCurveCollection::const_iterator pos = m_PlotCurves.staticPlots->begin(); pos != m_PlotCurves.staticPlots->end(); ++pos) { QColor dataColor; unsigned int curveId = m_Controls.widgetPlot->InsertCurve(pos->first.c_str()); m_Controls.widgetPlot->SetCurveData(curveId, pos->second->GetValues()); if (pos->first == "ROI") { dataColor = QColor(0, 190, 0); QPen pen; pen.setColor(dataColor); pen.setStyle(Qt::SolidLine); m_Controls.widgetPlot->SetCurvePen(curveId, pen); } else { //Use HSV schema of QColor to calculate a different color depending on the //number of already existing curves. dataColor.setHsv((++colorIndex * 85) % 360, 255, 150); m_Controls.widgetPlot->SetCurvePen(curveId, QPen(Qt::NoPen)); } // QwtSymbol needs to passed as a real pointer from MITK v2013.09.0 on // (QwtPlotCurve deletes it on destruction and assignment). QwtSymbol* dataSymbol = new QwtSymbol(QwtSymbol::Triangle, dataColor, dataColor, QSize(8, 8)); m_Controls.widgetPlot->SetCurveSymbol(curveId, dataSymbol); // Again, there is no way to set a curve's legend attributes via QmitkPlotWidget so this // gets unnecessarily complicated. QwtPlotCurve* measurementCurve = dynamic_cast<QwtPlotCurve*>(m_Controls.widgetPlot-> GetPlot()->itemList(QwtPlotItem::Rtti_PlotCurve).back()); measurementCurve->setLegendAttribute(QwtPlotCurve::LegendShowSymbol); measurementCurve->setLegendIconSize(QSize(8, 8)); } // Draw positional curves for (const auto& posIter : this->m_PlotCurves.positionalPlots) { QColor dataColor; dataColor.setHsv((++colorIndex * 85) % 360, 255, 150); this->RenderPlotCurve(posIter.second.second, dataColor, dataColor, " @ "+mitk::ModelFitPlotData::GetPositionalCollectionName(posIter)); } // Draw current pos curve this->RenderPlotCurve(m_PlotCurves.currentPositionPlots, QColor(Qt::red), QColor(Qt::black), ""); QwtLegend* legend = new QwtLegend(); legend->setFrameShape(QFrame::Box); legend->setFrameShadow(QFrame::Sunken); legend->setLineWidth(1); m_Controls.widgetPlot->SetLegend(legend, QwtPlot::BottomLegend); m_Controls.widgetPlot->Replot(); } void ModelFitInspectorView::EnsureBookmarkPointSet() { if (m_PositionBookmarks.IsExpired() || m_PositionBookmarksNode.IsExpired()) { const char* nodeName = "org.mitk.gui.qt.fit.inspector.positions"; mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode(nodeName); if (!node) { node = mitk::DataNode::New(); node->SetName(nodeName); node->SetBoolProperty("helper object", true); this->GetDataStorage()->Add(node); } m_PositionBookmarksNode = node; mitk::PointSet::Pointer pointSet = dynamic_cast<mitk::PointSet*>(node->GetData()); if (pointSet.IsNull()) { pointSet = mitk::PointSet::New(); node->SetData(pointSet); } m_PositionBookmarks = pointSet; } } diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorViewControls.ui b/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorViewControls.ui index 28f81f5577..691f3784be 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorViewControls.ui +++ b/Plugins/org.mitk.gui.qt.fit.inspector/src/internal/ModelFitInspectorViewControls.ui @@ -1,762 +1,762 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>ModelFitInspectorViewControls</class> <widget class="QWidget" name="ModelFitInspectorViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>721</width> <height>865</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout" stretch="0,4,0,0,0"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <layout class="QFormLayout" name="formLayout_2"> <property name="horizontalSpacing"> <number>6</number> </property> <property name="verticalSpacing"> <number>6</number> </property> <item row="2" column="0"> <widget class="QLabel" name="lblFit"> <property name="text"> <string>Modelfit:</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QComboBox" name="cmbFit"/> </item> <item row="1" column="1"> <widget class="QmitkSingleNodeSelectionWidget" name="inputNodeSelector" native="true"/> </item> <item row="1" column="0"> <widget class="QLabel" name="lblInput"> <property name="text"> <string>Input</string> </property> </widget> </item> </layout> </item> <item> <widget class="QmitkPlotWidget" name="widgetPlot" native="true"> <property name="enabled"> <bool>true</bool> </property> <property name="sizePolicy"> <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>400</height> </size> </property> </widget> </item> <item> <widget class="QLabel" name="lInfo"> <property name="text"> <string/> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_3"> <item> <spacer name="horizontalSpacer_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="btnFullPlot"> <property name="text"> <string>Full screen plot</string> </property> <property name="checkable"> <bool>true</bool> </property> <property name="flat"> <bool>false</bool> </property> </widget> </item> </layout> </item> <item> <widget class="QTabWidget" name="tabWidget"> <property name="enabled"> <bool>true</bool> </property> <property name="currentIndex"> <number>0</number> </property> <widget class="QWidget" name="tabInfo"> <attribute name="title"> <string>Fit info</string> </attribute> <layout class="QFormLayout" name="formLayout"> <item row="0" column="0"> <widget class="QLabel" name="label_3"> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="text"> <string>Fit type</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="lFitType"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string/> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_4"> <property name="text"> <string>Fit uid:</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QLabel" name="lFitUID"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string/> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label"> <property name="text"> <string>Model name:</string> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_2"> <property name="text"> <string>Model type:</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QLabel" name="lModelName"> <property name="text"> <string/> </property> </widget> </item> <item row="3" column="1"> <widget class="QLabel" name="lModelType"> <property name="text"> <string/> </property> </widget> </item> </layout> </widget> <widget class="QWidget" name="tabResults"> <attribute name="title"> <string>Fit parameter</string> </attribute> <attribute name="toolTip"> <string>Parameter used for the fit.</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_4"> <property name="spacing"> <number>3</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QmitkFitParameterWidget" name="fitParametersWidget" native="true"/> </item> </layout> </widget> <widget class="QWidget" name="tabBookmarks"> <attribute name="title"> <string>Inspection positions</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_3"> <property name="spacing"> <number>3</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QmitkInspectionPositionWidget" name="inspectionPositionWidget" native="true"/> </item> </layout> </widget> <widget class="QWidget" name="tabSettings"> <attribute name="title"> <string>View settings</string> </attribute> <attribute name="toolTip"> <string>Settings for the visualization of fittings</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_5"> <property name="spacing"> <number>3</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QGroupBox" name="groupBox_x"> <property name="title"> <string>X-axis scaling:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_8"> <item> <widget class="QRadioButton" name="radioScaleAuto_x"> <property name="enabled"> <bool>true</bool> </property> <property name="text"> <string>automatic</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioScaleFixed_x"> <property name="enabled"> <bool>true</bool> </property> <property name="text"> <string>fixed</string> </property> <property name="checked"> <bool>false</bool> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <item> <widget class="QLabel" name="labelFixMin_x"> <property name="enabled"> <bool>false</bool> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string>min:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="sbFixMin_x"> <property name="enabled"> <bool>false</bool> </property> <property name="minimum"> <double>-9999.000000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> <item> <spacer name="horizontalSpacer_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="labelFixMax_x"> <property name="enabled"> <bool>false</bool> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string>max:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="sbFixMax_x"> <property name="enabled"> <bool>false</bool> </property> <property name="minimum"> <double>-9999.000000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> <item> <spacer name="horizontalSpacer_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="btnScaleToData_x"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> <string>Sets the min and max to the current range of data +-10%</string> </property> <property name="text"> <string>Scale to data</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_y"> <property name="title"> <string>Y-axis scaling:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <widget class="QRadioButton" name="radioScaleAuto"> <property name="enabled"> <bool>true</bool> </property> <property name="text"> <string>automatic</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioScaleFixed"> <property name="enabled"> <bool>true</bool> </property> <property name="text"> <string>fixed</string> </property> <property name="checked"> <bool>false</bool> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QLabel" name="labelFixMin"> <property name="enabled"> <bool>false</bool> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string>min:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="sbFixMin"> <property name="enabled"> <bool>false</bool> </property> <property name="minimum"> <double>-9999.000000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> <item> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="labelFixMax"> <property name="enabled"> <bool>false</bool> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string>max:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="sbFixMax"> <property name="enabled"> <bool>false</bool> </property> <property name="minimum"> <double>-9999.000000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> <item> <spacer name="horizontalSpacer_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="btnScaleToData"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> <string>Sets the min and max to the current range of data +-10%</string> </property> <property name="text"> <string>Scale to data</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupSettings"> <property name="title"> <string>Additional input data visibility:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QTableWidget" name="tableInputData"> <property name="font"> <pointsize>8</pointsize> </property> <attribute name="horizontalHeaderDefaultSectionSize"> <number>150</number> </attribute> <attribute name="horizontalHeaderHighlightSections"> <bool>false</bool> </attribute> <attribute name="horizontalHeaderStretchLastSection"> <bool>true</bool> </attribute> <attribute name="verticalHeaderVisible"> <bool>false</bool> </attribute> <attribute name="verticalHeaderDefaultSectionSize"> <number>20</number> </attribute> <attribute name="verticalHeaderMinimumSectionSize"> <number>20</number> </attribute> <column> <property name="text"> <string>Name</string> </property> <property name="toolTip"> <string extracomment="Name of the data"/> </property> </column> <column> <property name="text"> <string>Color</string> </property> <property name="toolTip"> <string extracomment="Visibility of the data in diagram"/> </property> </column> </widget> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tabData"> <attribute name="title"> <string>Plot data export</string> </attribute> <attribute name="toolTip"> - <string>Display and export option for the current data samples, model signals and additinal fitting informations of the plot.</string> + <string>Display and export option for the current data samples, model signals and additional fitting information of the plot.</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_7"> <property name="spacing"> <number>3</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QmitkFitPlotDataWidget" name="plotDataWidget" native="true"> <property name="minimumSize"> <size> <width>80</width> <height>0</height> </size> </property> </widget> </item> </layout> </widget> </widget> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkPlotWidget</class> <extends>QWidget</extends> <header>QmitkPlotWidget.h</header> </customwidget> <customwidget> <class>QmitkFitParameterWidget</class> <extends>QWidget</extends> <header>QmitkFitParameterWidget.h</header> </customwidget> <customwidget> <class>QmitkInspectionPositionWidget</class> <extends>QWidget</extends> <header>QmitkInspectionPositionWidget.h</header> </customwidget> <customwidget> <class>QmitkFitPlotDataWidget</class> <extends>QWidget</extends> <header>QmitkFitPlotDataWidget.h</header> </customwidget> </customwidgets> <resources/> <connections> <connection> <sender>radioScaleFixed</sender> <signal>clicked(bool)</signal> <receiver>sbFixMin</receiver> <slot>setEnabled(bool)</slot> <hints> <hint type="sourcelabel"> <x>66</x> <y>528</y> </hint> <hint type="destinationlabel"> <x>86</x> <y>559</y> </hint> </hints> </connection> <connection> <sender>radioScaleFixed</sender> <signal>clicked(bool)</signal> <receiver>sbFixMax</receiver> <slot>setEnabled(bool)</slot> <hints> <hint type="sourcelabel"> <x>208</x> <y>535</y> </hint> <hint type="destinationlabel"> <x>195</x> <y>559</y> </hint> </hints> </connection> <connection> <sender>radioScaleFixed</sender> <signal>clicked(bool)</signal> <receiver>btnScaleToData</receiver> <slot>setEnabled(bool)</slot> <hints> <hint type="sourcelabel"> <x>299</x> <y>530</y> </hint> <hint type="destinationlabel"> <x>292</x> <y>557</y> </hint> </hints> </connection> </connections> </ui> diff --git a/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationWorkbenchWindowAdvisorHack.h b/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationWorkbenchWindowAdvisorHack.h index e77da14cc8..56cff93fcf 100644 --- a/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationWorkbenchWindowAdvisorHack.h +++ b/Plugins/org.mitk.gui.qt.flowapplication/src/internal/QmitkFlowApplicationWorkbenchWindowAdvisorHack.h @@ -1,59 +1,59 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkFlowApplicationWorkbenchWindowAdvisorHack_h #define QmitkFlowApplicationWorkbenchWindowAdvisorHack_h #include <QObject> class ctkPluginContext; class QmitkPreferencesDialog; /** This class is a "hack" due to the currently missing command framework. It is a direct clone of QmitkExtWorkbenchWindowAdvisorHack.*/ class QmitkFlowApplicationWorkbenchWindowAdvisorHack : public QObject { Q_OBJECT public slots: void onUndo(); void onRedo(); void onImageNavigator(); void onEditPreferences(); void onQuit(); void onResetPerspective(); void onClosePerspective(); void onIntro(); /** - * @brief This slot is called if the user klicks the menu item "help->context help" or presses F1. + * @brief This slot is called if the user clicks the menu item "help->context help" or presses F1. * The help page is shown in a workbench editor. */ void onHelp(); void onHelpOpenHelpPerspective(); /** * @brief This slot is called if the user clicks in help menu the about button */ void onAbout(); public: QmitkFlowApplicationWorkbenchWindowAdvisorHack(); ~QmitkFlowApplicationWorkbenchWindowAdvisorHack() override; static QmitkFlowApplicationWorkbenchWindowAdvisorHack* undohack; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp index 7ca288ff21..31b08445a6 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.cpp @@ -1,1152 +1,1152 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include <algorithm> // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkIGTTrackingDataEvaluationView.h" // Qt #include <QMessageBox> #include <qfiledialog.h> #include <qstringlist.h> // MITK #include "mitkNavigationDataCSVSequentialPlayer.h" #include <mitkNavigationDataRecorderDeprecated.h> #include <mitkQuaternionAveraging.h> #include <mitkTransform.h> #include <mitkStaticIGTHelperFunctions.h> #include <mitkNodePredicateDataType.h> //ITK #include <itksys/SystemTools.hxx> //VNL #include <vnl/vnl_vector.h> //vtk headers #include <vtkPoints.h> #include <vtkSmartPointer.h> #include <vtkLandmarkTransform.h> const std::string QmitkIGTTrackingDataEvaluationView::VIEW_ID = "org.mitk.views.igttrackingdataevaluation"; QmitkIGTTrackingDataEvaluationView::QmitkIGTTrackingDataEvaluationView() : m_Controls(nullptr) , m_scalingfactor(1) { m_CSVtoXMLInputFilenameVector = std::vector<std::string>(); m_CSVtoXMLOutputFilenameVector = std::vector<std::string>(); } QmitkIGTTrackingDataEvaluationView::~QmitkIGTTrackingDataEvaluationView() { } void QmitkIGTTrackingDataEvaluationView::CreateQtPartControl(QWidget *parent) { // build up qt view, unless already done if (!m_Controls) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkIGTTrackingDataEvaluationViewControls; m_Controls->setupUi(parent); connect(m_Controls->m_LoadInputFileList, SIGNAL(clicked()), this, SLOT(OnLoadFileList())); connect(m_Controls->m_StartEvaluation, SIGNAL(clicked()), this, SLOT(OnEvaluateData())); connect(m_Controls->m_AddToCurrentList, SIGNAL(clicked()), this, SLOT(OnAddToCurrentList())); connect(m_Controls->m_GeneratePointSetOfMeanPositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSet())); connect(m_Controls->m_GenerateRotationLines, SIGNAL(clicked()), this, SLOT(OnGenerateRotationLines())); connect(m_Controls->m_GeneratePointSet, SIGNAL(clicked()), this, SLOT(OnGenerateGroundTruthPointSet())); connect(m_Controls->m_Convert, SIGNAL(clicked()), this, SLOT(OnConvertCSVtoXMLFile())); connect(m_Controls->m_loadCSVtoXMLInputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadInputList())); connect(m_Controls->m_loadCSVtoXMLOutputList, SIGNAL(clicked()), this, SLOT(OnCSVtoXMLLoadOutputList())); connect(m_Controls->m_OrientationCalculationGenerateReference, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcRef())); connect(m_Controls->m_OrientationCalculationWriteOrientationsToFile, SIGNAL(clicked()), this, SLOT(OnOrientationCalculation_CalcOrientandWriteToFile())); connect(m_Controls->m_GeneratePointSetsOfSinglePositions, SIGNAL(clicked()), this, SLOT(OnGeneratePointSetsOfSinglePositions())); connect(m_Controls->m_StartEvaluationAll, SIGNAL(clicked()), this, SLOT(OnEvaluateDataAll())); connect(m_Controls->m_GridMatching, SIGNAL(clicked()), this, SLOT(OnPerfomGridMatching())); connect(m_Controls->m_ComputeRotation, SIGNAL(clicked()), this, SLOT(OnComputeRotation())); //initialize data storage combo boxes m_Controls->m_ReferencePointSetComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ReferencePointSetComboBox->SetAutoSelectNewItems(true); m_Controls->m_ReferencePointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); m_Controls->m_MeasurementPointSetComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MeasurementPointSetComboBox->SetAutoSelectNewItems(true); m_Controls->m_MeasurementPointSetComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); } } void QmitkIGTTrackingDataEvaluationView::OnComputeRotation() { //Get all data from UI auto EvaluationDataCollection = GetAllDataFromUIList(); //Compute mean Quaternions auto OrientationVector = GetMeanOrientationsOfAllData(EvaluationDataCollection); //Compute Rotations itk::Vector<double> rotationVec; //adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = m_Controls->m_rotVecX->value(); //X rotationVec[1] = m_Controls->m_rotVecY->value(); //Y rotationVec[2] = m_Controls->m_rotVecZ->value(); //Z std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> allOrientationErrors; for (std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError>::size_type i = 0; i < OrientationVector.size() - 1; ++i) { double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(OrientationVector.at(i), OrientationVector.at(i+1), rotationVec); double AngularError = fabs(AngleBetweenTwoQuaternions - 11.25); std::stringstream description; description << "Rotation Error ROT" << (i + 1) << " / ROT" << (i + 2); allOrientationErrors.push_back({ AngularError, description.str() }); MITK_INFO << description.str() << ": " << AngularError; } //compute statistics std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> orientationErrorStatistics; orientationErrorStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(allOrientationErrors); MITK_INFO << "## Rotation error statistics: ##"; for (auto stat : orientationErrorStatistics) { MITK_INFO << stat.description << ": " << stat.distanceError; } //write results to file allOrientationErrors.insert(allOrientationErrors.end(), orientationErrorStatistics.begin(), orientationErrorStatistics.end()); allOrientationErrors.push_back({rotationVec[0],"Rot Vector [x]"}); allOrientationErrors.push_back({rotationVec[1], "Rot Vector [y]"}); allOrientationErrors.push_back({rotationVec[2], "Rot Vector [z]"}); std::stringstream filenameOrientationStat; filenameOrientationStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".orientationStatistics.csv"; MITK_INFO << "Writing output to file " << filenameOrientationStat.str(); writeToFile(filenameOrientationStat.str(), allOrientationErrors); } void QmitkIGTTrackingDataEvaluationView::OnPerfomGridMatching() { mitk::PointSet::Pointer reference = dynamic_cast<mitk::PointSet*>(m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()); mitk::PointSet::Pointer measurement = dynamic_cast<mitk::PointSet*>(m_Controls->m_MeasurementPointSetComboBox->GetSelectedNode()->GetData()); //convert point sets to vtk poly data vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New(); vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New(); for (int i = 0; i<reference->GetSize(); i++) { double point[3] = { reference->GetPoint(i)[0], reference->GetPoint(i)[1], reference->GetPoint(i)[2] }; sourcePoints->InsertNextPoint(point); double point_targets[3] = { measurement->GetPoint(i)[0], measurement->GetPoint(i)[1], measurement->GetPoint(i)[2] }; targetPoints->InsertNextPoint(point_targets); } //compute transform vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); //compute FRE of transform double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(reference, measurement, transform); MITK_INFO << "FRE after grid matching: " + QString::number(FRE) + " mm"; //convert from vtk to itk data types itk::Matrix<float, 3, 3> rotationFloat = itk::Matrix<float, 3, 3>(); itk::Vector<float, 3> translationFloat = itk::Vector<float, 3>(); itk::Matrix<double, 3, 3> rotationDouble = itk::Matrix<double, 3, 3>(); itk::Vector<double, 3> translationDouble = itk::Vector<double, 3>(); vtkSmartPointer<vtkMatrix4x4> m = transform->GetMatrix(); for (int k = 0; k<3; k++) for (int l = 0; l<3; l++) { rotationFloat[k][l] = m->GetElement(k, l); rotationDouble[k][l] = m->GetElement(k, l); } for (int k = 0; k<3; k++) { translationFloat[k] = m->GetElement(k, 3); translationDouble[k] = m->GetElement(k, 3); } //create affine transform 3D mitk::AffineTransform3D::Pointer mitkTransform = mitk::AffineTransform3D::New(); mitkTransform->SetMatrix(rotationDouble); mitkTransform->SetOffset(translationDouble); mitk::NavigationData::Pointer transformNavigationData = mitk::NavigationData::New(mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(mitkTransform); m_Controls->m_ReferencePointSetComboBox->GetSelectedNode()->GetData()->GetGeometry()->Modified(); //write to file std::stringstream filename; filename << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".GridMatchingResult.csv"; MITK_INFO << "Writing output to file " << filename.str(); std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> FRE_Error; FRE_Error.push_back({ FRE, "FRE after grid matching [mm]" }); writeToFile(filename.str(), FRE_Error); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcRef() { if (m_FilenameVector.size() != 3) { MessageBox("Need exactly three points as reference, aborting!"); return; } //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector[i]); //check if the stream is valid and skip file if not //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); //update pipline until number of samples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); //store mean position as reference switch (i) { case 0: m_RefPoint1 = myEvaluationFilter->GetPositionMean(0); break; case 1: m_RefPoint2 = myEvaluationFilter->GetPositionMean(0); break; case 2: m_RefPoint3 = myEvaluationFilter->GetPositionMean(0); break; } } MessageBox("Created Reference!"); } void QmitkIGTTrackingDataEvaluationView::OnOrientationCalculation_CalcOrientandWriteToFile() { //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //open file header QString outputname = QString(m_FilenameVector.at(i).c_str()) + "_orientationFile.csv"; m_CurrentWriteFile.open(outputname.toStdString().c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } //write header to file m_CurrentWriteFile << "Nr;Calypso_Time;Valid_Reference;MeasureTool_Measurement-Tool[x];MeasureTool_Measurement-Tool[y];MeasureTool_Measurement-Tool[z];MeasureTool_Measurement-Tool[qx];MeasureTool_Measurement-Tool[qy];MeasureTool_Measurement-Tool[qz];MeasureTool_Measurement-Tool[qr]\n"; //update pipeline until number of samples is reached int step = 0; mitk::Point3D point1, point2, point3; mitk::Quaternion current_orientation; for (int j = 0; !myPlayer->IsAtEnd(); j++) { myPlayer->Update(); mitk::NavigationData::Pointer currentNavData = myPlayer->GetOutput(0); switch (step) { case 0: step++; point1 = currentNavData->GetPosition(); break; case 1: step++; point2 = currentNavData->GetPosition(); break; case 2: step = 0; point3 = currentNavData->GetPosition(); //compute transform from reference to current points if (point1[0] == 0 && point1[1] == 0 && point1[2] == 0 && point2[0] == 0 && point2[1] == 0 && point2[2] == 0 && point3[0] == 0 && point3[1] == 0 && point3[2] == 0 ) current_orientation.fill(0); else { vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New(); double sourcepoint1[3] = { point1[0], point1[1], point1[2] }; double sourcepoint2[3] = { point2[0], point2[1], point2[2] }; double sourcepoint3[3] = { point3[0], point3[1], point3[2] }; sourcePoints->InsertNextPoint(sourcepoint1); sourcePoints->InsertNextPoint(sourcepoint2); sourcePoints->InsertNextPoint(sourcepoint3); vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New(); double targetpoint1[3] = { m_RefPoint1[0], m_RefPoint1[1], m_RefPoint1[2] }; double targetpoint2[3] = { m_RefPoint2[0], m_RefPoint2[1], m_RefPoint2[2] }; double targetpoint3[3] = { m_RefPoint3[0], m_RefPoint3[1], m_RefPoint3[2] }; targetPoints->InsertNextPoint(targetpoint1); targetPoints->InsertNextPoint(targetpoint2); targetPoints->InsertNextPoint(targetpoint3); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->Modified(); transform->Update(); mitk::Transform::Pointer newTransform = mitk::Transform::New(); newTransform->SetMatrix(transform->GetMatrix()); current_orientation = newTransform->GetOrientation(); //add pointset with the three positions if ((j > 15) && (j < 18)) { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); mitk::PointSet::Pointer newPointSet = mitk::PointSet::New(); newPointSet->InsertPoint(0, point1); newPointSet->InsertPoint(1, point2); newPointSet->InsertPoint(2, point3); QString name = QString(m_FilenameVector.at(i).c_str()); newNode->SetName(name.toStdString().c_str()); newNode->SetData(newPointSet); newNode->SetFloatProperty("pointsize", 0.1); this->GetDataStorage()->Add(newNode); } } break; } m_CurrentWriteFile <GetTimeStamp() << ";"; //IMPORTANT: change to GetIGTTimeStamp in new version! m_CurrentWriteFile << "true;"; m_CurrentWriteFile << currentNavData->GetPosition()[0] << ";"; m_CurrentWriteFile << currentNavData->GetPosition()[1] << ";"; m_CurrentWriteFile << currentNavData->GetPosition()[2] << ";"; m_CurrentWriteFile << current_orientation.x() << ";"; m_CurrentWriteFile << current_orientation.y() << ";"; m_CurrentWriteFile << current_orientation.z() << ";"; m_CurrentWriteFile << current_orientation.r() << ";"; m_CurrentWriteFile << "\n"; } //close output file m_CurrentWriteFile.close(); } MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::OnAddToCurrentList() { //read in files QStringList files = QFileDialog::getOpenFileNames(nullptr, "Select one or more files to open", "/", "CSV (*.csv)"); if (files.isEmpty()) return; for (int i = 0; i < files.size(); i++) { std::string tmp = files.at(i).toStdString().c_str(); m_FilenameVector.push_back(tmp); } //fill list at GUI m_Controls->m_FileList->clear(); for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_FileList); } } void QmitkIGTTrackingDataEvaluationView::OnLoadFileList() { m_FilenameVector = std::vector<std::string>(); m_FilenameVector.clear(); OnAddToCurrentList(); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateDataAll() { std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> results5cm, results15cm, results30cm, resultsAccum; mitk::HummelProtocolEvaluation::HummelProtocolMeasurementVolume volume; if (m_Controls->m_standardVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::standard; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); mitk::HummelProtocolEvaluation::Evaluate15cmDistances(m_PointSetMeanPositions, volume, results15cm); mitk::HummelProtocolEvaluation::Evaluate30cmDistances(m_PointSetMeanPositions, volume, results30cm); mitk::HummelProtocolEvaluation::EvaluateAccumulatedDistances(m_PointSetMeanPositions, volume, resultsAccum); } else if (m_Controls->m_smallVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::small; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); } else if (m_Controls->m_mediumVolume->isChecked()) { volume = mitk::HummelProtocolEvaluation::medium; mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_PointSetMeanPositions, volume, results5cm); } //write results to file std::stringstream filename5cm; filename5cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results5cm.csv"; MITK_INFO << "Writing output to file " << filename5cm.str(); writeToFile(filename5cm.str(), results5cm); std::stringstream filename15cm; filename15cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results15cm.csv"; MITK_INFO << "Writing output to file " << filename15cm.str(); writeToFile(filename15cm.str(), results15cm); std::stringstream filename30cm; filename30cm << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".results30cm.csv"; MITK_INFO << "Writing output to file " << filename30cm.str(); writeToFile(filename30cm.str(), results30cm); std::stringstream filenameAccum; filenameAccum << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsAccumDist.csv"; MITK_INFO << "Writing output to file " << filenameAccum.str(); writeToFile(filenameAccum.str(), resultsAccum); } void QmitkIGTTrackingDataEvaluationView::OnEvaluateData() { //open output file m_CurrentWriteFile.open(std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str(), std::ios::out); if (m_CurrentWriteFile.bad()) { MessageBox("Error: Can't open output file!"); return; } std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> jitterValues; //write output file header WriteHeader(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++i) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } if (myPlayer->GetNumberOfSnapshots() < m_Controls->m_NumberOfSamples->value()) { MITK_WARN << "Number of snapshots (" << myPlayer->GetNumberOfSnapshots() << ") smaller than number of samples to evaluate (" << m_Controls->m_NumberOfSamples->value() << ") ! Cannot proceed!"; return; } //update pipline until number of samples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) myEvaluationFilter->Update(); //store all jitter values in separate vector for statistics jitterValues.push_back({ myEvaluationFilter->GetPositionErrorRMS(0), "RMS" }); //write result to output file WriteDataSet(myEvaluationFilter, m_FilenameVector.at(i)); } //close output file for single data m_CurrentWriteFile.close(); //compute statistics std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> jitterStatistics = mitk::HummelProtocolEvaluation::ComputeStatistics(jitterValues); MITK_INFO << "## Jitter (RMS) statistics: ##"; for (auto jitterStat : jitterStatistics) {MITK_INFO << jitterStat.description << ": " << jitterStat.distanceError;} //write statistic results to separate file std::stringstream filenameJitterStat; filenameJitterStat << std::string(m_Controls->m_OutputFilename->text().toUtf8()).c_str() << ".resultsJitterStatistics.csv"; MITK_INFO << "Writing output to file " << filenameJitterStat.str(); writeToFile(filenameJitterStat.str(), jitterStatistics); //calculate angles if option is on if (m_Controls->m_settingDifferenceAngles->isChecked() || m_Controls->m_DifferencesSLERP->isChecked()) CalculateDifferenceAngles(); MessageBox("Finished!"); } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSetsOfSinglePositions() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create point set for this file mitk::PointSet::Pointer thisPointSet = mitk::PointSet::New(); //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //update pipline until number of samlples is reached and store every single point for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); j++) { myPlayer->Update(); mitk::Point3D thisPoint = myPlayer->GetOutput()->GetPosition(); thisPoint[0] *= m_scalingfactor; thisPoint[1] *= m_scalingfactor; thisPoint[2] *= m_scalingfactor; thisPointSet->InsertPoint(j, thisPoint); } //add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + QString("PointSet_of_All_Positions_") + QString::number(i); newNode->SetName(name.toStdString()); newNode->SetData(thisPointSet); this->GetDataStorage()->Add(newNode); } } void QmitkIGTTrackingDataEvaluationView::OnGeneratePointSet() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) { myEvaluationFilter->Update(); } //add mean position to point set mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } generatedPointSet->InsertPoint(i, meanPos); } //add point set to data storage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString name = this->m_Controls->m_prefix->text() + "PointSet_of_Mean_Positions"; newNode->SetName(name.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); m_PointSetMeanPositions = generatedPointSet; } void QmitkIGTTrackingDataEvaluationView::OnGenerateRotationLines() { m_scalingfactor = m_Controls->m_ScalingFactor->value(); //start loop and iterate through all files of list for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) { myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); } //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); //create line from mean pos to a second point which lies along the sensor (1,0,0 in tool coordinates for aurora) mitk::Point3D meanPos = myEvaluationFilter->GetPositionMean(0); if (m_scalingfactor != 1) { meanPos[0] *= m_scalingfactor; meanPos[1] *= m_scalingfactor; meanPos[2] *= m_scalingfactor; } mitk::Point3D secondPoint; mitk::Point3D thirdPoint; mitk::Point3D fourthPoint; mitk::FillVector3D(secondPoint, 2, 0, 0); //X vnl_vector<mitk::ScalarType> secondPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * secondPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D secondPointTransformedMITK; mitk::FillVector3D(secondPointTransformedMITK, secondPointTransformed[0], secondPointTransformed[1], secondPointTransformed[2]); mitk::FillVector3D(thirdPoint, 0, 4, 0); //Y vnl_vector<mitk::ScalarType> thirdPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * thirdPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D thirdPointTransformedMITK; mitk::FillVector3D(thirdPointTransformedMITK, thirdPointTransformed[0], thirdPointTransformed[1], thirdPointTransformed[2]); mitk::FillVector3D(fourthPoint, 0, 0, 6); //Z vnl_vector<mitk::ScalarType> fourthPointTransformed = myEvaluationFilter->GetQuaternionMean(0).rotation_matrix_transpose().transpose() * fourthPoint.GetVnlVector() + meanPos.GetVnlVector(); mitk::Point3D fourthPointTransformedMITK; mitk::FillVector3D(fourthPointTransformedMITK, fourthPointTransformed[0], fourthPointTransformed[1], fourthPointTransformed[2]); mitk::PointSet::Pointer rotationLine = mitk::PointSet::New(); rotationLine->InsertPoint(0, secondPointTransformedMITK); rotationLine->InsertPoint(1, meanPos); rotationLine->InsertPoint(2, thirdPointTransformedMITK); rotationLine->InsertPoint(3, meanPos); rotationLine->InsertPoint(4, fourthPointTransformedMITK); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = this->m_Controls->m_prefix->text() + "RotationLineNumber" + QString::number(i); newNode->SetName(nodeName.toStdString()); newNode->SetData(rotationLine); newNode->SetBoolProperty("show contour", true); newNode->SetFloatProperty("pointsize", 0.5); this->GetDataStorage()->Add(newNode); } } void QmitkIGTTrackingDataEvaluationView::OnGenerateGroundTruthPointSet() { mitk::PointSet::Pointer generatedPointSet = mitk::PointSet::New(); int currentPointID = 0; mitk::Point3D currentPoint; mitk::FillVector3D(currentPoint, 0, 0, 0); for (int i = 0; i < m_Controls->m_PointNumber2->value(); i++) { for (int j = 0; j < m_Controls->m_PointNumber1->value(); j++) { generatedPointSet->InsertPoint(currentPointID, currentPoint); currentPointID++; currentPoint[1] += m_Controls->m_PointDistance->value(); } currentPoint[1] = 0; currentPoint[2] += m_Controls->m_PointDistance->value(); } mitk::DataNode::Pointer newNode = mitk::DataNode::New(); QString nodeName = "GroundTruthPointSet_" + QString::number(m_Controls->m_PointNumber1->value()) + "x" + QString::number(m_Controls->m_PointNumber2->value()) + "_(" + QString::number(m_Controls->m_PointDistance->value()) + "mm)"; newNode->SetName(nodeName.toStdString()); newNode->SetData(generatedPointSet); newNode->SetFloatProperty("pointsize", 5); this->GetDataStorage()->Add(newNode); } void QmitkIGTTrackingDataEvaluationView::OnConvertCSVtoXMLFile() { if (m_Controls->m_ConvertSingleFile->isChecked()) { //convert one file int lines = ConvertOneFile(this->m_Controls->m_InputCSV->text().toStdString(), this->m_Controls->m_OutputXML->text().toStdString()); QString result = "Converted one file with" + QString::number(lines) + " data sets"; MessageBox(result.toStdString()); } else //converte file list { if (m_CSVtoXMLInputFilenameVector.empty() || m_CSVtoXMLOutputFilenameVector.empty()) { MessageBox("Error: one list is not loaded!"); return; } else if (m_CSVtoXMLInputFilenameVector.size() != m_CSVtoXMLOutputFilenameVector.size()) { MessageBox("Error: lists do not have the same number of files!"); return; } for (std::size_t i = 0; i < m_CSVtoXMLInputFilenameVector.size(); ++i) { ConvertOneFile(m_CSVtoXMLInputFilenameVector.at(i), m_CSVtoXMLOutputFilenameVector.at(i)); } QString result = "Converted " + QString::number(m_CSVtoXMLInputFilenameVector.size()) + " files from file list!"; MessageBox(result.toStdString()); } } int QmitkIGTTrackingDataEvaluationView::ConvertOneFile(std::string inputFilename, std::string outputFilename) { std::vector<mitk::NavigationData::Pointer> myNavigationDatas = GetNavigationDatasFromFile(inputFilename); mitk::NavigationDataRecorderDeprecated::Pointer myRecorder = mitk::NavigationDataRecorderDeprecated::New(); myRecorder->SetFileName(outputFilename.c_str()); mitk::NavigationData::Pointer input = mitk::NavigationData::New(); if (m_Controls->m_ConvertCSV->isChecked()) myRecorder->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); myRecorder->AddNavigationData(input); myRecorder->StartRecording(); for (std::size_t i = 0; i < myNavigationDatas.size(); ++i) { input->Graft(myNavigationDatas.at(i)); myRecorder->Update(); } myRecorder->StopRecording(); return myNavigationDatas.size(); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadInputList() { //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLInputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLInputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::OnCSVtoXMLLoadOutputList() { //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_CSVtoXMLOutputFilenameVector = this->GetFileContentLineByLine(filename.toStdString()); m_Controls->m_labelCSVtoXMLOutputList->setText("READY"); } void QmitkIGTTrackingDataEvaluationView::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkIGTTrackingDataEvaluationView::WriteHeader() { m_CurrentWriteFile << "Filename;"; m_CurrentWriteFile << "N;"; m_CurrentWriteFile << "N_invalid;"; m_CurrentWriteFile << "Percentage_invalid;"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << "Position_Mean[x];"; m_CurrentWriteFile << "Position_Mean[y];"; m_CurrentWriteFile << "Position_Mean[z];"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << "Position_StandDev[x];"; m_CurrentWriteFile << "Position_StandDev[y];"; m_CurrentWriteFile << "Position_StandDev[z];"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << "Position_SampleStandDev[x];"; m_CurrentWriteFile << "Position_SampleStandDev[y];"; m_CurrentWriteFile << "Position_SampleStandDev[z];"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << "Quaternion_Mean[qx];"; m_CurrentWriteFile << "Quaternion_Mean[qy];"; m_CurrentWriteFile << "Quaternion_Mean[qz];"; m_CurrentWriteFile << "Quaternion_Mean[qr];"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << "Quaternion_StandDev[qx];"; m_CurrentWriteFile << "Quaternion_StandDev[qy];"; m_CurrentWriteFile << "Quaternion_StandDev[qz];"; m_CurrentWriteFile << "Quaternion_StandDev[qr];"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << "PositionError_Mean;"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << "PositionError_StandDev;"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << "PositionError_SampleStandDev;"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << "PositionError_RMS;"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << "PositionError_Median;"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << "PositionError_Max;"; m_CurrentWriteFile << "PositionError_Min;"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << "Euler_tx;"; m_CurrentWriteFile << "Euler_ty;"; m_CurrentWriteFile << "Euler_tz;"; } if (m_Controls->m_settingEulerRMS->isChecked()) { m_CurrentWriteFile << "EulerErrorRMS (rad);"; m_CurrentWriteFile << "EulerErrorRMS (grad);"; } m_CurrentWriteFile << "\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter, std::string dataSetName) { if (myEvaluationFilter->GetNumberOfOutputs() == 0) m_CurrentWriteFile << "Error: no input \n"; else { m_CurrentWriteFile << dataSetName << ";"; m_CurrentWriteFile << myEvaluationFilter->GetNumberOfAnalysedNavigationData(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetNumberOfInvalidSamples(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPercentageOfInvalidSamples(0) << ";"; if (m_Controls->m_settingPosMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionMean(0)[2] << ";"; } if (m_Controls->m_settingPosStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionStandardDeviation(0)[2] << ";"; } if (m_Controls->m_settingPosSampleStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionSampleStandardDeviation(0)[2] << ";"; } if (m_Controls->m_settingQuaternionMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).x() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).y() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).z() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionMean(0).r() << ";"; } if (m_Controls->m_settionQuaternionStabw->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).x() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).y() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).z() << ";"; m_CurrentWriteFile << myEvaluationFilter->GetQuaternionStandardDeviation(0).r() << ";"; } if (m_Controls->m_settingPosErrorMean->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMean(0) << ";"; if (m_Controls->m_settingPosErrorStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorStandardDeviation(0) << ";"; if (m_Controls->m_settingPosErrorSampleStabw->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorSampleStandardDeviation(0) << ";"; if (m_Controls->m_settingPosErrorRMS->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorRMS(0) << ";"; if (m_Controls->m_settingPosErrorMedian->isChecked()) m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMedian(0) << ";"; if (m_Controls->m_settingPosErrorMinMax->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMax(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetPositionErrorMin(0) << ";"; } if (m_Controls->m_settingEulerMean->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[0] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[1] << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesMean(0)[2] << ";"; } if (m_Controls->m_settingEulerRMS->isChecked()) { m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMS(0) << ";"; m_CurrentWriteFile << myEvaluationFilter->GetEulerAnglesRMSDegree(0) << ";"; } m_CurrentWriteFile << "\n"; } } std::vector<mitk::Quaternion> QmitkIGTTrackingDataEvaluationView::GetMeanOrientationsOfAllData(std::vector<mitk::NavigationDataEvaluationFilter::Pointer> allData, bool useSLERP) { std::vector<mitk::Quaternion> returnValue; for (auto dataSet : allData) { if (useSLERP) returnValue.push_back(GetSLERPAverage(dataSet)); else returnValue.push_back(dataSet->GetQuaternionMean(0)); } return returnValue; } std::vector<mitk::NavigationDataEvaluationFilter::Pointer> QmitkIGTTrackingDataEvaluationView::GetAllDataFromUIList() { std::vector<mitk::NavigationDataEvaluationFilter::Pointer> EvaluationDataCollection; //start loop and iterate through all files of list: store the evaluation data for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { //create navigation data player mitk::NavigationDataCSVSequentialPlayer::Pointer myPlayer = ConstructNewNavigationDataPlayer(); myPlayer->SetFiletype(mitk::NavigationDataCSVSequentialPlayer::ManualLoggingCSV); myPlayer->SetFileName(m_FilenameVector.at(i)); //create evaluation filter mitk::NavigationDataEvaluationFilter::Pointer myEvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); //connect pipeline for (unsigned int j = 0; j < myPlayer->GetNumberOfOutputs(); ++j) myEvaluationFilter->SetInput(j, myPlayer->GetOutput(j)); //update pipline until number of samlples is reached for (int j = 0; j < m_Controls->m_NumberOfSamples->value(); ++j) myEvaluationFilter->Update(); myEvaluationFilter->SetInput(nullptr); myPlayer = nullptr; EvaluationDataCollection.push_back(myEvaluationFilter); } return EvaluationDataCollection; } void QmitkIGTTrackingDataEvaluationView::CalculateDifferenceAngles() { //Get all data from UI std::vector<mitk::NavigationDataEvaluationFilter::Pointer> EvaluationDataCollection = GetAllDataFromUIList(); //calculation and writing of output data //open output file m_CurrentAngleDifferencesWriteFile.open(std::string((m_Controls->m_OutputFilename->text() + ".angledifferences.csv").toUtf8()).c_str(), std::ios::out); if (m_CurrentAngleDifferencesWriteFile.bad()) { MessageBox("Error: Can't open output file for angle differences calculation!"); return; } //write header WriteDifferenceAnglesHeader(); //compute angle differences QString pos1 = "invalid"; QString pos2 = "invalid"; //now iterate through all evaluation data and calculate the angles for (std::size_t i = 0; i < m_FilenameVector.size(); ++i) { pos1 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(i))); for (std::size_t j = 0; j < m_FilenameVector.size(); ++j) { pos2 = QString::fromStdString(itksys::SystemTools::GetFilenameWithoutLastExtension(m_FilenameVector.at(j))); mitk::Quaternion q1; mitk::Quaternion q2; if (m_Controls->m_DifferencesSLERP->isChecked()) { //compute slerp average q1 = GetSLERPAverage(EvaluationDataCollection.at(i)); q2 = GetSLERPAverage(EvaluationDataCollection.at(j)); } else { //compute arithmetic average q1 = EvaluationDataCollection.at(i)->GetQuaternionMean(0); q2 = EvaluationDataCollection.at(j)->GetQuaternionMean(0); } itk::Vector<double> rotationVec; //adapt for Aurora 5D tools: [0,0,1000] rotationVec[0] = 10000; //X rotationVec[1] = 0; //Y rotationVec[2] = 0; //Z double AngleBetweenTwoQuaternions = mitk::StaticIGTHelperFunctions::GetAngleBetweenTwoQuaterions(q1, q2, rotationVec); //write data set WriteDifferenceAnglesDataSet(pos1.toStdString(), pos2.toStdString(), i, j, AngleBetweenTwoQuaternions); } } //close output file m_CurrentAngleDifferencesWriteFile.close(); } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesHeader() { m_CurrentAngleDifferencesWriteFile << "Name;Idx1;Idx2;Angle [Degree]\n"; } void QmitkIGTTrackingDataEvaluationView::WriteDifferenceAnglesDataSet(std::string pos1, std::string pos2, int idx1, int idx2, double angle) { m_CurrentAngleDifferencesWriteFile << "Angle between " << pos1 << " and " << pos2 << ";" << idx1 << ";" << idx2 << ";" << angle << "\n"; MITK_INFO << "Angle: " << angle; } std::vector<mitk::NavigationData::Pointer> QmitkIGTTrackingDataEvaluationView::GetNavigationDatasFromFile(std::string filename) { std::vector<mitk::NavigationData::Pointer> returnValue = std::vector<mitk::NavigationData::Pointer>(); std::vector<std::string> fileContentLineByLine = GetFileContentLineByLine(filename); for (std::size_t i = 1; i < fileContentLineByLine.size(); ++i) //skip header so start at 1 { returnValue.push_back(GetNavigationDataOutOfOneLine(fileContentLineByLine.at(i))); } return returnValue; } std::vector<std::string> QmitkIGTTrackingDataEvaluationView::GetFileContentLineByLine(std::string filename) { std::vector<std::string> readData = std::vector<std::string>(); //save old locale char * oldLocale; oldLocale = setlocale(LC_ALL, nullptr); //define own locale std::locale C("C"); setlocale(LC_ALL, "C"); //read file std::ifstream file; file.open(filename.c_str(), std::ios::in); if (file.good()) { //read out file file.seekg(0L, std::ios::beg); // move to begin of file while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line if (buffer.size() > 0) readData.push_back(buffer); } } file.close(); //switch back to old locale setlocale(LC_ALL, oldLocale); return readData; } mitk::NavigationData::Pointer QmitkIGTTrackingDataEvaluationView::GetNavigationDataOutOfOneLine(std::string line) { mitk::NavigationData::Pointer returnValue = mitk::NavigationData::New(); QString myLine = QString(line.c_str()); QStringList myLineList = myLine.split(';'); mitk::Point3D position; mitk::Quaternion orientation; bool valid = false; if (myLineList.at(2).toStdString() == "1") valid = true; position[0] = myLineList.at(3).toDouble(); position[1] = myLineList.at(4).toDouble(); position[2] = myLineList.at(5).toDouble(); orientation[0] = myLineList.at(6).toDouble(); orientation[1] = myLineList.at(7).toDouble(); orientation[2] = myLineList.at(8).toDouble(); orientation[3] = myLineList.at(9).toDouble(); returnValue->SetDataValid(valid); returnValue->SetPosition(position); returnValue->SetOrientation(orientation); return returnValue; } mitk::Quaternion QmitkIGTTrackingDataEvaluationView::GetSLERPAverage(mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter) { mitk::Quaternion average; - //build a vector of quaternions from the evaulation filter (caution always takes the first (0) input of the filter + //build a vector of quaternions from the evaluation filter (caution always takes the first (0) input of the filter std::vector<mitk::Quaternion> quaternions = std::vector<mitk::Quaternion>(); for (int i = 0; i < evaluationFilter->GetNumberOfAnalysedNavigationData(0); i++) { mitk::Quaternion currentq = evaluationFilter->GetLoggedOrientation(i, 0); quaternions.push_back(currentq); } //compute the slerp average using the quaternion averaging class mitk::QuaternionAveraging::Pointer myAverager = mitk::QuaternionAveraging::New(); average = myAverager->CalcAverage(quaternions); return average; } void QmitkIGTTrackingDataEvaluationView::writeToFile(std::string filename, std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> values) { std::fstream currentFile; currentFile.open(filename.c_str(), std::ios::out); if (currentFile.bad()) { MITK_WARN << "Cannot open file, aborting!"; return; } currentFile << "Description" << ";" << "Error[mm]" << "\n"; for (auto currentError : values) { currentFile << currentError.description << ";" << currentError.distanceError << "\n"; } currentFile.close(); } mitk::NavigationDataCSVSequentialPlayer::Pointer QmitkIGTTrackingDataEvaluationView::ConstructNewNavigationDataPlayer() { bool rightHanded = m_Controls->m_RigthHanded->isChecked(); QString separator = m_Controls->m_SeparatorSign->text(); QChar sepaSign = separator.at(0); //char separatorSign; char separatorSign = sepaSign.toLatin1(); //std::string separatorSign = m_Controls->m_SeparatorSign->text().toStdString(); int sampleCount = m_Controls->m_SampleCount->value(); bool headerRow = m_Controls->m_HeaderRow->isChecked(); int xPos = m_Controls->m_XPos->value(); int yPos = m_Controls->m_YPos->value(); int zPos = m_Controls->m_ZPos->value(); bool useQuats = m_Controls->m_UseQuats->isChecked(); int qx = m_Controls->m_Qx->value(); int qy = m_Controls->m_Qy->value(); int qz = m_Controls->m_Qz->value(); int qr = m_Controls->m_Qr->value(); int azimuth = m_Controls->m_Azimuth->value(); int elevation = m_Controls->m_Elevation->value(); int roll = m_Controls->m_Roll->value(); bool eulersInRad = m_Controls->m_Radiants->isChecked(); //need to find the biggest column number to determine the minimal number of columns the .csv file has to have int allInts[] = {xPos, yPos, zPos, qx, qy, qr, azimuth, elevation, roll}; int minNumberOfColumns = (*std::max_element(allInts, allInts+9)+1); //size needs to be +1 because columns start at 0 but size at 1 mitk::NavigationDataCSVSequentialPlayer::Pointer navDataPlayer = mitk::NavigationDataCSVSequentialPlayer::New(); navDataPlayer->SetOptions(rightHanded, separatorSign, sampleCount, headerRow, xPos, yPos, zPos, useQuats, qx, qy, qz, qr, azimuth, elevation, roll, eulersInRad, minNumberOfColumns); return navDataPlayer; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h index 634b99190e..0c9453a938 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationView.h @@ -1,128 +1,128 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkIGTTrackingDataEvaluationView_h #define QmitkIGTTrackingDataEvaluationView_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include "ui_QmitkIGTTrackingDataEvaluationViewControls.h" #include "mitkHummelProtocolEvaluation.h" #include <mitkNavigationDataEvaluationFilter.h> #include "mitkNavigationDataCSVSequentialPlayer.h" /*! \brief QmitkIGTTrackingDataEvaluationView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. */ class QmitkIGTTrackingDataEvaluationView : public QmitkAbstractView { Q_OBJECT public: static const std::string VIEW_ID; QmitkIGTTrackingDataEvaluationView(); ~QmitkIGTTrackingDataEvaluationView() override; void CreateQtPartControl(QWidget *parent) override; void SetFocus() override {} protected slots: void OnLoadFileList(); void OnAddToCurrentList(); void OnEvaluateData(); void OnEvaluateDataAll(); void OnGeneratePointSet(); void OnGeneratePointSetsOfSinglePositions(); void OnGenerateRotationLines(); void OnGenerateGroundTruthPointSet(); void OnConvertCSVtoXMLFile(); void OnCSVtoXMLLoadInputList(); void OnCSVtoXMLLoadOutputList(); void OnPerfomGridMatching(); void OnComputeRotation(); - /** Reads in exactly three position files als reference. */ + /** Reads in exactly three position files as reference. */ void OnOrientationCalculation_CalcRef(); - /** Uses always three positions (1,2,3: first orientation; 4,5,6: second orientation; and so on) in every file to calcualte a orientation. */ + /** Uses always three positions (1,2,3: first orientation; 4,5,6: second orientation; and so on) in every file to calculate a orientation. */ void OnOrientationCalculation_CalcOrientandWriteToFile(); protected: Ui::QmitkIGTTrackingDataEvaluationViewControls* m_Controls; std::vector<std::string> m_FilenameVector; void MessageBox(std::string s); std::fstream m_CurrentWriteFile; void WriteHeader(); void WriteDataSet(mitk::NavigationDataEvaluationFilter::Pointer evaluationFilter, std::string dataSetName); //members for orientation calculation mitk::Point3D m_RefPoint1; mitk::Point3D m_RefPoint2; mitk::Point3D m_RefPoint3; double m_scalingfactor; //scaling factor for visualization, 1 by default - //angle diffrences: seperated file + //angle differences: separated file std::fstream m_CurrentAngleDifferencesWriteFile; void CalculateDifferenceAngles(); void WriteDifferenceAnglesHeader(); void WriteDifferenceAnglesDataSet(std::string pos1, std::string pos2, int idx1, int idx2, double angle); void writeToFile(std::string filename, std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> values); //different help methods to read a csv logging file std::vector<mitk::NavigationData::Pointer> GetNavigationDatasFromFile(std::string filename); std::vector<std::string> GetFileContentLineByLine(std::string filename); mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line); //help method to sonstruct the NavigationDataCSVSequentialPlayer filled with all the options from the UI mitk::NavigationDataCSVSequentialPlayer::Pointer ConstructNewNavigationDataPlayer(); //CSV to XML members std::vector<std::string> m_CSVtoXMLInputFilenameVector; std::vector<std::string> m_CSVtoXMLOutputFilenameVector; //returns the number of converted lines int ConvertOneFile(std::string inputFilename, std::string outputFilename); /** @brief calculates the angle in the plane perpendicular to the rotation axis of the two quaterions. */ double GetAngleBetweenTwoQuaterions(mitk::Quaternion a, mitk::Quaternion b); /** @brief calculates the slerp average of a set of quaternions which is stored in the navigation data evaluation filter */ mitk::Quaternion GetSLERPAverage(mitk::NavigationDataEvaluationFilter::Pointer); /** @brief Stores the mean positions of all evaluated data */ mitk::PointSet::Pointer m_PointSetMeanPositions; /** @return returns the mean orientation of all given data */ std::vector<mitk::Quaternion> GetMeanOrientationsOfAllData(std::vector<mitk::NavigationDataEvaluationFilter::Pointer> allData, bool useSLERP = false); /** @return returns all data read from the data list as NavigationDataEvaluationFilters */ std::vector<mitk::NavigationDataEvaluationFilter::Pointer> GetAllDataFromUIList(); }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui index 2dd08f80f3..05b3634caa 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingDataEvaluationViewControls.ui @@ -1,1780 +1,1780 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkIGTTrackingDataEvaluationViewControls</class> <widget class="QWidget" name="QmitkIGTTrackingDataEvaluationViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>448</width> <height>955</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QTabWidget" name="tabWidget"> <property name="currentIndex"> <number>0</number> </property> <widget class="QWidget" name="tab"> <attribute name="title"> <string>Evaluation</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QLabel" name="label"> <property name="text"> <string>Input File List (recorded NavigationData / *.csv):</string> </property> </widget> </item> <item> <widget class="QListWidget" name="m_FileList"/> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_LoadInputFileList"> <property name="minimumSize"> <size> <width>120</width> <height>0</height> </size> </property> <property name="text"> <string>Load New List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_6"> <item> <spacer name="horizontalSpacer_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_AddToCurrentList"> <property name="minimumSize"> <size> <width>120</width> <height>0</height> </size> </property> <property name="text"> <string>Add To Current List</string> </property> </widget> </item> </layout> </item> <item> <widget class="Line" name="line_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_17"> <property name="text"> <string>(1) - VISUALIZATION - of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_17"> <item> <widget class="QLabel" name="label_18"> <property name="text"> <string>Prefix for Data Nodes:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_prefix"/> </item> </layout> </item> <item> <widget class="QPushButton" name="m_GeneratePointSetOfMeanPositions"> <property name="text"> <string>Generate PointSet of Mean Positions</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_GeneratePointSetsOfSinglePositions"> <property name="text"> <string>Generate PointSets of Single Positions</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_GenerateRotationLines"> <property name="text"> <string>Generate Lines for Rotation</string> </property> </widget> </item> <item> <widget class="Line" name="line_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_19"> <property name="text"> <string>(3) - JITTER - Evaluation per file / data set:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <item> <widget class="QLabel" name="label_2"> <property name="text"> <string>Result CSV Filename:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_OutputFilename"> <property name="text"> <string>D:/tmp/output.csv</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_3"> <item> <spacer name="horizontalSpacer_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_StartEvaluation"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>COMPUTE RESULTS PER DATA SET</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="Line" name="line_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_20"> <property name="text"> <string>(3) - ACCURACY - Evaluation of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_16"> <item> <spacer name="horizontalSpacer_16"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_StartEvaluationAll"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>COMPUTE RESULTS OF ALL DATA</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_17"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="Line" name="line_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_21"> <property name="text"> <string>(4) - GRID MATCHING - Evaluation of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_19"> <item> <widget class="QLabel" name="label_22"> <property name="text"> <string>Reference PointSet:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_20"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QmitkDataStorageComboBox" name="m_ReferencePointSetComboBox"> <property name="minimumSize"> <size> <width>150</width> <height>0</height> </size> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_20"> <item> <widget class="QLabel" name="label_23"> <property name="text"> <string>Measurement PointSet:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_21"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QmitkDataStorageComboBox" name="m_MeasurementPointSetComboBox"> <property name="minimumSize"> <size> <width>150</width> <height>0</height> </size> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_18"> <item> <spacer name="horizontalSpacer_18"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_GridMatching"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> - <string>PERFOM GRID MATCHING</string> + <string>PERFORM GRID MATCHING</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_19"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="Line" name="line_7"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_24"> <property name="text"> <string>(5) - ROTATION - Evaluation of all data sets:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_21"> <item> <spacer name="horizontalSpacer_22"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_ComputeRotation"> <property name="minimumSize"> <size> <width>220</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>200</width> <height>50</height> </size> </property> <property name="text"> <string>COMPUTE ROTATION ERRORS</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_23"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <spacer name="spacer1"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Expanding</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>220</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tab_2"> <attribute name="title"> <string>Settings</string> </attribute> <layout class="QGridLayout" name="gridLayout_5"> <item row="0" column="0"> <widget class="QToolBox" name="toolBox"> <widget class="QWidget" name="page_5"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>409</width> <height>768</height> </rect> </property> <attribute name="label"> <string>General</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_4"> <item> <widget class="QGroupBox" name="GeneralOptions"> <property name="title"> <string/> </property> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <item> <widget class="QLabel" name="label_16"> <property name="text"> <string>Scaling Factor for Visualization:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_15"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>38</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QDoubleSpinBox" name="m_ScalingFactor"> <property name="minimum"> <double>1.000000000000000</double> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <item> <widget class="QLabel" name="label_3"> <property name="text"> <string>Number of samples to analyze:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>60</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_NumberOfSamples"> <property name="maximum"> <number>1000000</number> </property> <property name="value"> <number>150</number> </property> </widget> </item> </layout> </item> <item> <widget class="Line" name="line_8"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_15"> <property name="text"> <string>Tracking Volume:</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_standardVolume"> <property name="text"> <string>Standard Volume (10 X 9 Positions)</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_mediumVolume"> <property name="text"> <string>Medium Volume (5 X 5 Positions)</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_smallVolume"> <property name="text"> <string>Small Volume (3 X 4 Positions)</string> </property> </widget> </item> <item> <widget class="Line" name="line_9"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_40"> <property name="text"> <string>Rotation Evaluation:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_26"> <item> <widget class="QLabel" name="label_41"> <property name="text"> <string>Rotation Vector:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_28"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_42"> <property name="text"> <string>X</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_rotVecX"> <property name="maximum"> <number>99999</number> </property> </widget> </item> <item> <spacer name="horizontalSpacer_27"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_43"> <property name="text"> <string>Y</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_rotVecY"> <property name="maximum"> <number>99999</number> </property> </widget> </item> <item> <spacer name="horizontalSpacer_26"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_44"> <property name="text"> <string>Z</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_rotVecZ"> <property name="maximum"> <number>99999</number> </property> <property name="value"> <number>10000</number> </property> </widget> </item> </layout> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> </item> </layout> </widget> <widget class="QWidget" name="page"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>286</width> <height>746</height> </rect> </property> <attribute name="label"> <string>.csv file input options</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_13"> <item> <widget class="QGroupBox" name="m_FileOptionsBox"> <property name="title"> <string>File Options:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_12"> <item> <layout class="QHBoxLayout" name="horizontalLayout_23"> <item> <widget class="QLabel" name="label_26"> <property name="text"> <string>Separator in the csv file: </string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_25"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>60</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLineEdit" name="m_SeparatorSign"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string>;</string> </property> <property name="maxLength"> <number>1</number> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_25"> <item> <widget class="QLabel" name="label_25"> <property name="text"> - <string>Use every n-th smaple n:</string> + <string>Use every n-th sample n:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_24"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_SampleCount"> <property name="value"> <number>1</number> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="m_HeaderRow"> <property name="text"> <string>The csv file has a header row</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="CoordinateType"> <property name="title"> <string>Type of Coordinate System:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_19"> <item> <layout class="QHBoxLayout" name="horizontalLayout_24"> <item> <widget class="QRadioButton" name="m_LeftHanded"> <property name="text"> <string>Left handed </string> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_RigthHanded"> <property name="text"> <string>Right handed</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="PositionAndOrientationOptions"> <property name="title"> <string>Position and Orientation Options:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_11"> <item> <layout class="QGridLayout" name="gridLayout"> <item row="2" column="0"> <widget class="QLabel" name="label_28"> <property name="text"> <string>Y</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QSpinBox" name="m_YPos"> <property name="value"> <number>4</number> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_29"> <property name="text"> <string>Z</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_ZPos"> <property name="value"> <number>5</number> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_27"> <property name="text"> <string>X</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="m_XPos"> <property name="value"> <number>3</number> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_4"> <property name="text"> <string>Coordinate:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="label_5"> <property name="text"> - <string>Colum number:</string> + <string>Column number:</string> </property> </widget> </item> </layout> </item> <item> <widget class="QRadioButton" name="m_UseQuats"> <property name="text"> <string>Use Quaternions for Orientation</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout_2"> <item row="4" column="0"> <widget class="QLabel" name="label_35"> <property name="text"> <string>Qr</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_Qz"> <property name="value"> <number>8</number> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label_33"> <property name="text"> <string>Qy</string> </property> </widget> </item> <item row="4" column="1"> <widget class="QSpinBox" name="m_Qr"> <property name="value"> <number>9</number> </property> </widget> </item> <item row="2" column="1"> <widget class="QSpinBox" name="m_Qy"> <property name="value"> <number>7</number> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="m_Qx"> <property name="value"> <number>6</number> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_32"> <property name="text"> <string>Qx</string> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_34"> <property name="text"> <string>Qz</string> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_6"> <property name="text"> <string>Quaternion component:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="label_36"> <property name="text"> <string>Column number:</string> </property> </widget> </item> </layout> </item> <item> <widget class="QRadioButton" name="m_UseEuler"> <property name="text"> <string>Use Euler Angles for Orientation</string> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout_3"> <item row="0" column="1"> <widget class="QLabel" name="label_30"> <property name="text"> <string>Column number:</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_37"> <property name="text"> <string>Azimuth</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QSpinBox" name="m_Elevation"> <property name="minimum"> <number>-1</number> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_39"> <property name="text"> <string>Roll</string> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_7"> <property name="text"> <string>Angle:</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_Roll"> <property name="minimum"> <number>-1</number> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label_38"> <property name="text"> <string>Elevation</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="m_Azimuth"> <property name="minimum"> <number>-1</number> </property> </widget> </item> </layout> </item> <item> <widget class="QWidget" name="EulerUnity" native="true"> <layout class="QVBoxLayout" name="verticalLayout_18"> <item> <widget class="QLabel" name="label_31"> <property name="text"> <string>Unity for Euler Angles:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_22"> <item> <widget class="QRadioButton" name="m_Radiants"> <property name="text"> <string>Radiants</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_Degrees"> <property name="text"> <string>Degrees</string> </property> <property name="checked"> <bool>false</bool> </property> </widget> </item> </layout> </item> </layout> </widget> </item> </layout> </widget> </item> </layout> </widget> <widget class="QWidget" name="toolBoxPage1"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>343</width> <height>607</height> </rect> </property> <attribute name="label"> <string>Output per data set</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_17"> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> <string>Position</string> </property> <layout class="QVBoxLayout" name="verticalLayout_14"> <item> <widget class="QCheckBox" name="m_settingPosMean"> <property name="text"> <string>Mean (x,y,z)</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosStabw"> <property name="text"> <string>Standard Deviation (x,y,z)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosSampleStabw"> <property name="text"> <string>Sample Standard Deviation (x,y,z)</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_6"> <property name="title"> <string>Orientation</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QCheckBox" name="m_settingQuaternionMean"> <property name="text"> <string>Quaternion Mean (qx,qy,qz,qr)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_QuaternionMeanSlerp"> <property name="text"> <string>Quaternion Mean (SLERP)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settionQuaternionStabw"> <property name="text"> <string>Quaternion Standard Deviation (qx,qy,qz,qr)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingEulerMean"> <property name="text"> <string>Euler Mean (tx,ty,tz)</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingDifferenceAngles"> <property name="text"> <string>Difference Angles to all other Positions</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_DifferencesSLERP"> <property name="text"> <string>Difference Angles to all other Positions (SLERP)</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_7"> <property name="title"> <string>Position Error</string> </property> <layout class="QVBoxLayout" name="verticalLayout_15"> <item> <widget class="QCheckBox" name="m_settingPosErrorMean"> <property name="text"> <string>Mean</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorStabw"> <property name="text"> <string>Standard Deviation</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorSampleStabw"> <property name="text"> <string>Sample Standard Deviation</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorRMS"> <property name="text"> <string>RMS</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorMedian"> <property name="text"> <string>Median</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_settingPosErrorMinMax"> <property name="text"> <string>Min/Max</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_8"> <property name="title"> <string>Orientation Error</string> </property> <layout class="QVBoxLayout" name="verticalLayout_16"> <item> <widget class="QCheckBox" name="m_settingEulerRMS"> <property name="text"> <string>Euler RMS</string> </property> </widget> </item> </layout> </widget> </item> </layout> </widget> </widget> </item> </layout> </widget> <widget class="QWidget" name="tab_3"> <attribute name="title"> <string>Tools</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_10"> <item> <widget class="QGroupBox" name="groupBox_2"> <property name="title"> <string>Point Set Ground Truth Generator</string> </property> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <layout class="QHBoxLayout" name="horizontalLayout_8"> <item> <widget class="QLabel" name="label_8"> <property name="text"> <string>Generate</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_PointNumber1"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>999</number> </property> <property name="value"> <number>10</number> </property> </widget> </item> <item> <widget class="QLabel" name="label_9"> <property name="text"> <string>X</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_PointNumber2"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>999</number> </property> <property name="value"> <number>9</number> </property> </widget> </item> <item> <widget class="QLabel" name="label_10"> <property name="text"> <string>Point Set</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_7"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_7"> <item> <widget class="QLabel" name="label_11"> <property name="text"> <string>Inter Point Distance (in mm):</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_8"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_PointDistance"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>99999</number> </property> <property name="value"> <number>50</number> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_9"> <item> <spacer name="horizontalSpacer_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_GeneratePointSet"> <property name="text"> <string>Generate</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_3"> <property name="title"> <string>Result CSV File to NavigationData Converter</string> </property> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <widget class="QRadioButton" name="m_ConvertSingleFile"> <property name="text"> <string>Convert Single File</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QLabel" name="label_12"> <property name="text"> <string>Input CSV Logging File:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_InputCSV"> <property name="text"> <string>C:/Tools/test.csv</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_13"> <property name="text"> <string>Output Navigation Data File:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_OutputXML"> <property name="text"> <string>C:/Tools/testoutput.xml</string> </property> </widget> </item> <item> <widget class="Line" name="line_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_ConvertFileList"> <property name="text"> <string>Convert File List</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_14"> <property name="text"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> (use text files with a complete filename in every line)</body></html></string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_11"> <item> <widget class="QLabel" name="m_labelCSVtoXMLInputList"> <property name="text"> <string>not loaded</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_10"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_loadCSVtoXMLInputList"> <property name="minimumSize"> <size> <width>100</width> <height>0</height> </size> </property> <property name="text"> <string>Load Input List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_12"> <item> <widget class="QLabel" name="m_labelCSVtoXMLOutputList"> <property name="text"> <string>not loaded</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_11"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_loadCSVtoXMLOutputList"> <property name="minimumSize"> <size> <width>100</width> <height>0</height> </size> </property> <property name="text"> <string>Load Output List</string> </property> </widget> </item> </layout> </item> <item> <widget class="Line" name="line"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_14"> <item> <spacer name="horizontalSpacer_12"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QGroupBox" name="groupBox_4"> <property name="title"> <string>Output Format</string> </property> <layout class="QVBoxLayout" name="verticalLayout_9"> <item> <widget class="QRadioButton" name="m_ConvertXML"> <property name="text"> <string>XML</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_ConvertCSV"> <property name="text"> <string>CSV</string> </property> </widget> </item> </layout> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_10"> <item> <spacer name="horizontalSpacer_9"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_Convert"> <property name="text"> <string>Convert</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_5"> <property name="title"> <string>Orientation Calculation (out of three positions)</string> </property> <layout class="QVBoxLayout" name="verticalLayout_8"> <item> <layout class="QHBoxLayout" name="horizontalLayout_13"> <item> <spacer name="horizontalSpacer_13"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_OrientationCalculationGenerateReference"> <property name="text"> <string>Generate Reference From Current List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_15"> <item> <spacer name="horizontalSpacer_14"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_OrientationCalculationWriteOrientationsToFile"> <property name="text"> <string>Write Orientation Quaternions To File</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>632</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkDataStorageComboBox</class> <extends>QComboBox</extends> <header>QmitkDataStorageComboBox.h</header> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp index 096380482c..275e53428e 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.cpp @@ -1,606 +1,606 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkIGTTrackingSemiAutomaticMeasurementView.h" // Qt #include <QMessageBox> #include <qfiledialog.h> #include <qevent.h> #include <QCheckBox> // MITK #include <mitkNavigationToolStorageDeserializer.h> #include <mitkTrackingDeviceSourceConfigurator.h> #include <mitkLogBackend.h> #include "mitkHummelProtocolEvaluation.h" // POCO #include <Poco/File.h> #include <Poco/Path.h> const std::string QmitkIGTTrackingSemiAutomaticMeasurementView::VIEW_ID = "org.mitk.views.igttrackingsemiautomaticmeasurement"; QmitkIGTTrackingSemiAutomaticMeasurementView::QmitkIGTTrackingSemiAutomaticMeasurementView() : m_Controls(nullptr) { m_NextFile = 0; m_FilenameVector = std::vector<std::string>(); m_Timer = new QTimer(this); m_logging = false; m_referenceValid = true; m_tracking = false; m_EvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); } QmitkIGTTrackingSemiAutomaticMeasurementView::~QmitkIGTTrackingSemiAutomaticMeasurementView() { } void QmitkIGTTrackingSemiAutomaticMeasurementView::CreateResults() { QString LogFileName = m_Controls->m_OutputPath->text() + "_results.log"; mitk::LogBackend::Unregister(); mitk::LogBackend::SetLogFile(LogFileName.toStdString()); mitk::LogBackend::Register(); double RMSmean = 0; for (std::size_t i = 0; i < m_RMSValues.size(); ++i) { MITK_INFO << "RMS at " << this->m_FilenameVector.at(i) << ": " << m_RMSValues.at(i); RMSmean += m_RMSValues.at(i); } RMSmean /= m_RMSValues.size(); MITK_INFO << "RMS mean over " << m_RMSValues.size() << " values: " << RMSmean; mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName("Tracking Results"); newNode->SetData(this->m_MeanPoints); this->GetDataStorage()->Add(newNode); std::vector<mitk::HummelProtocolEvaluation::HummelProtocolDistanceError> results5cmDistances; if (m_Controls->m_mediumVolume->isChecked()) mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_MeanPoints, mitk::HummelProtocolEvaluation::medium, results5cmDistances); else if (m_Controls->m_smallVolume->isChecked()) mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_MeanPoints, mitk::HummelProtocolEvaluation::small, results5cmDistances); else if (m_Controls->m_standardVolume->isChecked()) mitk::HummelProtocolEvaluation::Evaluate5cmDistances(m_MeanPoints, mitk::HummelProtocolEvaluation::standard, results5cmDistances); } void QmitkIGTTrackingSemiAutomaticMeasurementView::CreateQtPartControl(QWidget *parent) { // build up qt view, unless already done if (!m_Controls) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkIGTTrackingSemiAutomaticMeasurementViewControls; m_Controls->setupUi(parent); //buttons connect(m_Controls->m_LoadMeasurementToolStorage, SIGNAL(clicked()), this, SLOT(OnLoadMeasurementStorage())); connect(m_Controls->m_LoadReferenceToolStorage, SIGNAL(clicked()), this, SLOT(OnLoadReferenceStorage())); connect(m_Controls->m_StartTracking, SIGNAL(clicked()), this, SLOT(OnStartTracking())); connect(m_Controls->m_LoadList, SIGNAL(clicked()), this, SLOT(OnMeasurementLoadFile())); connect(m_Controls->m_StartNextMeasurement, SIGNAL(clicked()), this, SLOT(StartNextMeasurement())); connect(m_Controls->m_ReapeatLastMeasurement, SIGNAL(clicked()), this, SLOT(RepeatLastMeasurement())); connect(m_Controls->m_SetReference, SIGNAL(clicked()), this, SLOT(OnSetReference())); connect(m_Controls->m_UseReferenceTrackingSystem, SIGNAL(toggled(bool)), this, SLOT(OnUseReferenceToggled(bool))); connect(m_Controls->m_CreateResults, SIGNAL(clicked()), this, SLOT(CreateResults())); //event filter qApp->installEventFilter(this); //timers connect(m_Timer, SIGNAL(timeout()), this, SLOT(UpdateTimer())); } //initialize some view m_Controls->m_StopTracking->setEnabled(false); } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnUseReferenceToggled(bool state) { if (state) { m_Controls->m_ReferenceBox->setEnabled(true); m_Controls->m_SetReference->setEnabled(true); } else { m_Controls->m_ReferenceBox->setEnabled(false); m_Controls->m_SetReference->setEnabled(false); } } mitk::NavigationToolStorage::Pointer QmitkIGTTrackingSemiAutomaticMeasurementView::ReadStorage(std::string file) { mitk::NavigationToolStorage::Pointer returnValue; //initialize tool storage returnValue = mitk::NavigationToolStorage::New(); //read tool storage from disk mitk::NavigationToolStorageDeserializer::Pointer myDeserializer = mitk::NavigationToolStorageDeserializer::New(GetDataStorage()); returnValue = myDeserializer->Deserialize(file); if (returnValue.IsNull()) { QMessageBox msgBox; msgBox.setText(myDeserializer->GetErrorMessage().c_str()); msgBox.exec(); returnValue = nullptr; } return returnValue; } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnSetReference() { //initialize reference m_ReferenceStartPositions = std::vector<mitk::Point3D>(); m_ReferenceTrackingDeviceSource->Update(); QString Label = "Positions At Start: "; for (unsigned int i = 0; i < m_ReferenceTrackingDeviceSource->GetNumberOfOutputs(); ++i) { mitk::Point3D position = m_ReferenceTrackingDeviceSource->GetOutput(i)->GetPosition(); Label = Label + "Tool" + QString::number(i) + ":[" + QString::number(position[0]) + ":" + QString::number(position[1]) + ":" + QString::number(position[1]) + "] "; m_ReferenceStartPositions.push_back(position); } m_Controls->m_ReferencePosAtStart->setText(Label); } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnLoadMeasurementStorage() { //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Toolfile"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; m_MeasurementStorage = ReadStorage(filename.toStdString()); //update label - Poco::Path myPath = Poco::Path(filename.toStdString()); //use this to seperate filename from path + Poco::Path myPath = Poco::Path(filename.toStdString()); //use this to separate filename from path QString toolLabel = QString("Tool Storage: ") + QString::number(m_MeasurementStorage->GetToolCount()) + " Tools from " + myPath.getFileName().c_str(); m_Controls->m_MeasurementToolStorageLabel->setText(toolLabel); //update status widget m_Controls->m_ToolStatusWidget->RemoveStatusLabels(); m_Controls->m_ToolStatusWidget->PreShowTools(m_MeasurementStorage); } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnLoadReferenceStorage() { //read in filename static QString oldFile; if (oldFile.isNull()) oldFile = "/"; QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Toolfile"), oldFile, tr("All Files (*.*)")); if (filename.isNull()) return; oldFile = filename; m_ReferenceStorage = ReadStorage(filename.toStdString()); //update label - Poco::Path myPath = Poco::Path(filename.toStdString()); //use this to seperate filename from path + Poco::Path myPath = Poco::Path(filename.toStdString()); //use this to separate filename from path QString toolLabel = QString("Tool Storage: ") + QString::number(m_ReferenceStorage->GetToolCount()) + " Tools from " + myPath.getFileName().c_str(); m_Controls->m_ReferenceToolStorageLabel->setText(toolLabel); } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnStartTracking() { //check if everything is ready to start tracking if (m_MeasurementStorage.IsNull()) { MessageBox("Error: No measurement tools loaded yet!"); return; } else if (m_ReferenceStorage.IsNull() && m_Controls->m_UseReferenceTrackingSystem->isChecked()) { - MessageBox("Error: No refernce tools loaded yet!"); + MessageBox("Error: No reference tools loaded yet!"); return; } else if (m_MeasurementStorage->GetToolCount() == 0) { MessageBox("Error: No way to track without tools!"); return; } else if (m_Controls->m_UseReferenceTrackingSystem->isChecked() && (m_ReferenceStorage->GetToolCount() == 0)) { MessageBox("Error: No way to track without tools!"); return; } //build the first IGT pipeline (MEASUREMENT) mitk::TrackingDeviceSourceConfigurator::Pointer myTrackingDeviceSourceFactory1 = mitk::TrackingDeviceSourceConfigurator::New(this->m_MeasurementStorage, this->m_Controls->m_MeasurementTrackingDeviceConfigurationWidget->GetTrackingDevice()); m_MeasurementTrackingDeviceSource = myTrackingDeviceSourceFactory1->CreateTrackingDeviceSource(this->m_MeasurementToolVisualizationFilter); if (m_MeasurementTrackingDeviceSource.IsNull()) { MessageBox(myTrackingDeviceSourceFactory1->GetErrorMessage()); return; } //connect the tool visualization widget for (unsigned int i = 0; i < m_MeasurementTrackingDeviceSource->GetNumberOfOutputs(); ++i) { m_Controls->m_ToolStatusWidget->AddNavigationData(m_MeasurementTrackingDeviceSource->GetOutput(i)); m_EvaluationFilter->SetInput(i, m_MeasurementTrackingDeviceSource->GetOutput(i)); } m_Controls->m_ToolStatusWidget->ShowStatusLabels(); m_Controls->m_ToolStatusWidget->SetShowPositions(true); m_Controls->m_ToolStatusWidget->SetShowQuaternions(true); //build the second IGT pipeline (REFERENCE) if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { mitk::TrackingDeviceSourceConfigurator::Pointer myTrackingDeviceSourceFactory2 = mitk::TrackingDeviceSourceConfigurator::New(this->m_ReferenceStorage, this->m_Controls->m_ReferenceDeviceConfigurationWidget->GetTrackingDevice()); m_ReferenceTrackingDeviceSource = myTrackingDeviceSourceFactory2->CreateTrackingDeviceSource(); if (m_ReferenceTrackingDeviceSource.IsNull()) { MessageBox(myTrackingDeviceSourceFactory2->GetErrorMessage()); return; } } //initialize tracking try { m_MeasurementTrackingDeviceSource->Connect(); m_MeasurementTrackingDeviceSource->StartTracking(); if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { m_ReferenceTrackingDeviceSource->Connect(); m_ReferenceTrackingDeviceSource->StartTracking(); } } catch (...) { MessageBox("Error while starting the tracking device!"); return; } //set reference if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) OnSetReference(); //start timer m_Timer->start(1000 / (m_Controls->m_SamplingRate->value())); m_Controls->m_StartTracking->setEnabled(false); m_Controls->m_StartTracking->setEnabled(true); m_tracking = true; } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnStopTracking() { if (this->m_logging) FinishMeasurement(); m_MeasurementTrackingDeviceSource->Disconnect(); m_MeasurementTrackingDeviceSource->StopTracking(); if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { m_ReferenceTrackingDeviceSource->Disconnect(); m_ReferenceTrackingDeviceSource->StopTracking(); } m_Timer->stop(); m_Controls->m_StartTracking->setEnabled(true); m_Controls->m_StartTracking->setEnabled(false); m_tracking = false; } void QmitkIGTTrackingSemiAutomaticMeasurementView::OnMeasurementLoadFile() { m_FilenameVector = std::vector<std::string>(); m_FilenameVector.clear(); m_NextFile = 0; //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Measurement Filename List"), "/", tr("All Files (*.*)")); if (filename.isNull()) return; //define own locale std::locale C("C"); setlocale(LC_ALL, "C"); //read file std::ifstream file; file.open(filename.toStdString().c_str(), std::ios::in); if (file.good()) { //read out file file.seekg(0L, std::ios::beg); // move to begin of file while (!file.eof()) { std::string buffer; std::getline(file, buffer); // read out file line by line if (buffer.size() > 0) m_FilenameVector.push_back(buffer); } } //fill list at GUI m_Controls->m_MeasurementList->clear(); for (unsigned int i = 0; i < m_FilenameVector.size(); i++) { new QListWidgetItem(tr(m_FilenameVector.at(i).c_str()), m_Controls->m_MeasurementList); } //update label next measurement std::stringstream label; label << "Next Measurement: " << m_FilenameVector.at(0); m_Controls->m_NextMeasurement->setText(label.str().c_str()); //reset results files m_MeanPoints = mitk::PointSet::New(); m_RMSValues = std::vector<double>(); m_EvaluationFilter = mitk::NavigationDataEvaluationFilter::New(); if (m_MeasurementToolVisualizationFilter.IsNotNull()) m_EvaluationFilter->SetInput(0, m_MeasurementToolVisualizationFilter->GetOutput(0)); } void QmitkIGTTrackingSemiAutomaticMeasurementView::UpdateTimer() { if (m_EvaluationFilter.IsNotNull() && m_logging) m_EvaluationFilter->Update(); else m_MeasurementToolVisualizationFilter->Update(); m_Controls->m_ToolStatusWidget->Refresh(); //update reference if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { m_ReferenceTrackingDeviceSource->Update(); QString Label = "Current Positions: "; bool distanceThresholdExceeded = false; for (unsigned int i = 0; i < m_ReferenceTrackingDeviceSource->GetNumberOfOutputs(); ++i) { mitk::Point3D position = m_ReferenceTrackingDeviceSource->GetOutput(i)->GetPosition(); Label = Label + "Tool" + QString::number(i) + ":[" + QString::number(position[0]) + ":" + QString::number(position[1]) + ":" + QString::number(position[1]) + "] "; if (position.EuclideanDistanceTo(m_ReferenceStartPositions.at(i)) > m_Controls->m_ReferenceThreshold->value()) distanceThresholdExceeded = true; } m_Controls->m_ReferenceCurrentPos->setText(Label); if (distanceThresholdExceeded) { m_Controls->m_ReferenceOK->setText("<html><body style=\" font-family:\'MS Shell Dlg 2\'; font-size:28pt; font-weight:400; font-style:normal;\">NOT OK!</body></html>"); m_referenceValid = false; } else { m_Controls->m_ReferenceOK->setText("<html><body style=\" font-family:\'MS Shell Dlg 2\'; font-size:28pt; font-weight:400; font-style:normal;\">OK</body></html>"); m_referenceValid = true; } } //update logging if (m_logging) { //check for missing objects if (m_MeasurementLoggingFilterXML.IsNull() || m_MeasurementLoggingFilterCSV.IsNull() ) { return; } //log/measure m_MeasurementLoggingFilterXML->Update(); m_MeasurementLoggingFilterCSV->Update(); if (m_Controls->m_UseReferenceTrackingSystem->isChecked() && m_ReferenceLoggingFilterXML.IsNotNull() && m_ReferenceLoggingFilterCSV.IsNotNull()) { m_ReferenceLoggingFilterXML->Update(); m_ReferenceLoggingFilterCSV->Update(); } m_loggedFrames++; LogAdditionalCSVFile(); //check if all frames are logged ... if yes finish the measurement if (m_loggedFrames > m_Controls->m_SamplesPerMeasurement->value()) { FinishMeasurement(); } //update logging label QString loggingLabel = "Collected Samples: " + QString::number(m_loggedFrames); m_Controls->m_CollectedSamples->setText(loggingLabel); } } void QmitkIGTTrackingSemiAutomaticMeasurementView::StartNextMeasurement() { if (this->m_NextFile >= static_cast<int>(m_FilenameVector.size())) { MessageBox("Last Measurement reached!"); return; } m_loggedFrames = 0; m_logging = true; //check if directory exists, if not create one Poco::File myPath(std::string(m_Controls->m_OutputPath->text().toUtf8()).c_str()); if (!myPath.exists()) myPath.createDirectory(); QString LogFileName = m_Controls->m_OutputPath->text() + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".log"; mitk::LogBackend::Unregister(); mitk::LogBackend::SetLogFile(LogFileName.toStdString()); mitk::LogBackend::Register(); //initialize logging filters m_MeasurementLoggingFilterXML = mitk::NavigationDataRecorderDeprecated::New(); m_MeasurementLoggingFilterXML->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); m_MeasurementLoggingFilterCSV = mitk::NavigationDataRecorderDeprecated::New(); m_MeasurementLoggingFilterCSV->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); m_MeasurementLoggingFilterXML->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::xml); m_MeasurementLoggingFilterCSV->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); QString MeasurementFilenameXML = m_Controls->m_OutputPath->text() + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".xml"; QString MeasurementFilenameCSV = m_Controls->m_OutputPath->text() + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".csv"; m_MeasurementLoggingFilterXML->SetFileName(MeasurementFilenameXML.toStdString()); m_MeasurementLoggingFilterCSV->SetFileName(MeasurementFilenameCSV.toStdString()); m_MeasurementLoggingFilterXML->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); m_MeasurementLoggingFilterCSV->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { m_ReferenceLoggingFilterXML = mitk::NavigationDataRecorderDeprecated::New(); m_ReferenceLoggingFilterXML->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); m_ReferenceLoggingFilterCSV = mitk::NavigationDataRecorderDeprecated::New(); m_ReferenceLoggingFilterCSV->SetRecordingMode(mitk::NavigationDataRecorderDeprecated::NormalFile); m_ReferenceLoggingFilterXML->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::xml); m_ReferenceLoggingFilterCSV->SetOutputFormat(mitk::NavigationDataRecorderDeprecated::csv); QString ReferenceFilenameXML = m_Controls->m_OutputPath->text() + "Reference_" + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".xml"; QString ReferenceFilenameCSV = m_Controls->m_OutputPath->text() + "Reference_" + QString(m_FilenameVector.at(m_NextFile).c_str()) + ".csv"; m_ReferenceLoggingFilterXML->SetFileName(ReferenceFilenameXML.toStdString()); m_ReferenceLoggingFilterCSV->SetFileName(ReferenceFilenameCSV.toStdString()); m_ReferenceLoggingFilterXML->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); m_ReferenceLoggingFilterCSV->SetRecordCountLimit(m_Controls->m_SamplesPerMeasurement->value()); } //start additional csv logging StartLoggingAdditionalCSVFile(m_FilenameVector.at(m_NextFile)); //connect filter for (unsigned int i = 0; i < m_MeasurementToolVisualizationFilter->GetNumberOfOutputs(); ++i) { m_MeasurementLoggingFilterXML->AddNavigationData(m_MeasurementToolVisualizationFilter->GetOutput(i)); m_MeasurementLoggingFilterCSV->AddNavigationData(m_MeasurementToolVisualizationFilter->GetOutput(i)); } if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) for (unsigned int i = 0; i < m_ReferenceTrackingDeviceSource->GetNumberOfOutputs(); ++i) { m_ReferenceLoggingFilterXML->AddNavigationData(m_ReferenceTrackingDeviceSource->GetOutput(i)); m_ReferenceLoggingFilterCSV->AddNavigationData(m_ReferenceTrackingDeviceSource->GetOutput(i)); } //start filter m_MeasurementLoggingFilterXML->StartRecording(); m_MeasurementLoggingFilterCSV->StartRecording(); if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { m_ReferenceLoggingFilterXML->StartRecording(); m_ReferenceLoggingFilterCSV->StartRecording(); } //disable all buttons DisableAllButtons(); //update label next measurement std::stringstream label; if ((m_NextFile + 1) >= static_cast<int>(m_FilenameVector.size())) label << "Next Measurement: <none>"; else label << "Next Measurement: " << m_FilenameVector.at(m_NextFile + 1); m_Controls->m_NextMeasurement->setText(label.str().c_str()); //update label last measurement std::stringstream label2; label2 << "Last Measurement: " << m_FilenameVector.at(m_NextFile); m_Controls->m_LastMeasurement->setText(label2.str().c_str()); m_NextFile++; } void QmitkIGTTrackingSemiAutomaticMeasurementView::RepeatLastMeasurement() { m_NextFile--; StartNextMeasurement(); } void QmitkIGTTrackingSemiAutomaticMeasurementView::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkIGTTrackingSemiAutomaticMeasurementView::DisableAllButtons() { m_Controls->m_LoadList->setEnabled(false); m_Controls->m_StartNextMeasurement->setEnabled(false); m_Controls->m_ReapeatLastMeasurement->setEnabled(false); m_Controls->m_SamplingRate->setEnabled(false); m_Controls->m_SamplesPerMeasurement->setEnabled(false); m_Controls->m_ReferenceThreshold->setEnabled(false); } void QmitkIGTTrackingSemiAutomaticMeasurementView::EnableAllButtons() { m_Controls->m_LoadList->setEnabled(true); m_Controls->m_StartNextMeasurement->setEnabled(true); m_Controls->m_ReapeatLastMeasurement->setEnabled(true); m_Controls->m_SamplingRate->setEnabled(true); m_Controls->m_SamplesPerMeasurement->setEnabled(true); m_Controls->m_ReferenceThreshold->setEnabled(true); } void QmitkIGTTrackingSemiAutomaticMeasurementView::FinishMeasurement() { m_logging = false; m_MeasurementLoggingFilterXML->StopRecording(); m_MeasurementLoggingFilterCSV->StopRecording(); if (m_Controls->m_UseReferenceTrackingSystem->isChecked()) { m_ReferenceLoggingFilterXML->StopRecording(); m_ReferenceLoggingFilterCSV->StopRecording(); } StopLoggingAdditionalCSVFile(); int id = m_NextFile - 1; mitk::Point3D positionMean = m_EvaluationFilter->GetPositionMean(0); MITK_INFO << "Evaluated " << m_EvaluationFilter->GetNumberOfAnalysedNavigationData(0) << " samples."; double rms = m_EvaluationFilter->GetPositionErrorRMS(0); MITK_INFO << "RMS: " << rms; MITK_INFO << "Position Mean: " << positionMean; m_MeanPoints->SetPoint(id, positionMean); if (static_cast<int>(m_RMSValues.size()) <= id) m_RMSValues.push_back(rms); else m_RMSValues[id] = rms; m_EvaluationFilter->ResetStatistic(); EnableAllButtons(); } void QmitkIGTTrackingSemiAutomaticMeasurementView::StartLoggingAdditionalCSVFile(std::string filePostfix) { //write logfile header QString header = "Nr;MITK_Time;Valid_Reference;"; QString tool = QString("MeasureTool_") + QString(m_MeasurementTrackingDeviceSource->GetOutput(0)->GetName()); header = header + tool + "[x];" + tool + "[y];" + tool + "[z];" + tool + "[qx];" + tool + "[qy];" + tool + "[qz];" + tool + "[qr]\n"; //open logfile and write header m_logFileCSV.open(std::string(m_Controls->m_OutputPath->text().toUtf8()).append("/LogFileCombined").append(filePostfix.c_str()).append(".csv").c_str(), std::ios::out); m_logFileCSV << header.toStdString().c_str(); } void QmitkIGTTrackingSemiAutomaticMeasurementView::LogAdditionalCSVFile() { mitk::Point3D pos = m_MeasurementTrackingDeviceSource->GetOutput(0)->GetPosition(); mitk::Quaternion rot = m_MeasurementTrackingDeviceSource->GetOutput(0)->GetOrientation(); std::string valid = ""; if (m_referenceValid) valid = "true"; else valid = "false"; std::stringstream timestamp; timestamp << m_MeasurementTrackingDeviceSource->GetOutput(0)->GetTimeStamp(); QString dataSet = QString::number(m_loggedFrames) + ";" + QString(timestamp.str().c_str()) + ";" + QString(valid.c_str()) + ";" + QString::number(pos[0]) + ";" + QString::number(pos[1]) + ";" + QString::number(pos[2]) + ";" + QString::number(rot.x()) + ";" + QString::number(rot.y()) + ";" + QString::number(rot.z()) + ";" + QString::number(rot.r()) + "\n"; m_logFileCSV << dataSet.toStdString(); } void QmitkIGTTrackingSemiAutomaticMeasurementView::StopLoggingAdditionalCSVFile() { m_logFileCSV.close(); } bool QmitkIGTTrackingSemiAutomaticMeasurementView::eventFilter(QObject *, QEvent *ev) { if (ev->type() == QEvent::KeyPress) { QKeyEvent *k = (QKeyEvent *)ev; bool down = k->key() == 16777239; if (down && m_tracking && !m_logging) StartNextMeasurement(); } return false; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h index 8e687e471c..2130bafbe9 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementView.h @@ -1,120 +1,120 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkIGTTrackingSemiAutomaticMeasurementView_h #define QmitkIGTTrackingSemiAutomaticMeasurementView_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> //QT #include <QTimer> //MITK #include <mitkNavigationToolStorage.h> #include <mitkTrackingDeviceSource.h> #include <mitkNavigationDataObjectVisualizationFilter.h> #include <mitkNavigationDataRecorderDeprecated.h> #include <mitkNavigationDataEvaluationFilter.h> #include "ui_QmitkIGTTrackingSemiAutomaticMeasurementViewControls.h" /*! \brief QmitkIGTTrackingSemiAutomaticMeasurementView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. */ class QmitkIGTTrackingSemiAutomaticMeasurementView : public QmitkAbstractView { Q_OBJECT public: static const std::string VIEW_ID; QmitkIGTTrackingSemiAutomaticMeasurementView(); ~QmitkIGTTrackingSemiAutomaticMeasurementView() override; void CreateQtPartControl(QWidget *parent) override; void SetFocus() override {} protected slots: void OnLoadMeasurementStorage(); void OnLoadReferenceStorage(); void OnStartTracking(); void OnStopTracking(); void OnMeasurementLoadFile(); void OnSetReference(); void StartNextMeasurement(); void RepeatLastMeasurement(); void UpdateTimer(); void CreateResults(); void OnUseReferenceToggled(bool state); protected: Ui::QmitkIGTTrackingSemiAutomaticMeasurementViewControls* m_Controls; //the tool storages mitk::NavigationToolStorage::Pointer m_MeasurementStorage; mitk::NavigationToolStorage::Pointer m_ReferenceStorage; //members for the filter pipeline mitk::TrackingDeviceSource::Pointer m_MeasurementTrackingDeviceSource; mitk::NavigationDataObjectVisualizationFilter::Pointer m_MeasurementToolVisualizationFilter; mitk::NavigationDataRecorderDeprecated::Pointer m_MeasurementLoggingFilterXML; mitk::NavigationDataRecorderDeprecated::Pointer m_MeasurementLoggingFilterCSV; mitk::TrackingDeviceSource::Pointer m_ReferenceTrackingDeviceSource; mitk::NavigationDataRecorderDeprecated::Pointer m_ReferenceLoggingFilterXML; mitk::NavigationDataRecorderDeprecated::Pointer m_ReferenceLoggingFilterCSV; //members for file name list std::vector<std::string> m_FilenameVector; int m_NextFile; //help methods mitk::NavigationToolStorage::Pointer ReadStorage(std::string file); void MessageBox(std::string s); void DisableAllButtons(); void EnableAllButtons(); void FinishMeasurement(); void StartLoggingAdditionalCSVFile(std::string filePostfix); void LogAdditionalCSVFile(); void StopLoggingAdditionalCSVFile(); //timer QTimer* m_Timer; - //memebers for reference checking + //members for reference checking std::vector<mitk::Point3D> m_ReferenceStartPositions; bool m_referenceValid; //logging members int m_loggedFrames; bool m_logging; std::fstream m_logFileCSV; //event filter for key presses bool eventFilter(QObject *obj, QEvent *ev) override; //results members mitk::PointSet::Pointer m_MeanPoints; std::vector<double> m_RMSValues; mitk::NavigationDataEvaluationFilter::Pointer m_EvaluationFilter; bool m_tracking; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui index b85fd511cb..431fe62b9e 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/QmitkIGTTrackingSemiAutomaticMeasurementViewControls.ui @@ -1,588 +1,588 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkIGTTrackingSemiAutomaticMeasurementViewControls</class> <widget class="QWidget" name="QmitkIGTTrackingSemiAutomaticMeasurementViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>419</width> <height>931</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QTabWidget" name="tabWidget"> <property name="currentIndex"> <number>0</number> </property> <widget class="QWidget" name="tab"> <attribute name="title"> <string>Tracking Initialization</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_4"> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> <string>Measurement Tracking System</string> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QmitkTrackingDeviceConfigurationWidget" name="m_MeasurementTrackingDeviceConfigurationWidget" native="true"/> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <item> <widget class="QLabel" name="m_MeasurementToolStorageLabel"> <property name="text"> <string>Tool Storage: <none></string> </property> </widget> </item> <item> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_LoadMeasurementToolStorage"> <property name="text"> <string>Load Tool Storage</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="m_ReferenceBox"> <property name="title"> <string>Reference Trackingsystem</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QmitkTrackingDeviceConfigurationWidget" name="m_ReferenceDeviceConfigurationWidget" native="true"/> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QLabel" name="m_ReferenceToolStorageLabel"> <property name="text"> <string>Tool Storage: <none></string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_LoadReferenceToolStorage"> <property name="text"> <string>Load Tool Storage</string> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QPushButton" name="m_StartTracking"> <property name="text"> <string>Start Tracking</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_StopTracking"> <property name="text"> <string>Stop Tracking</string> </property> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tab_2"> <attribute name="title"> <string>Measurement</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <widget class="QLabel" name="label"> <property name="text"> <string>Measurement List:</string> </property> </widget> </item> <item> <widget class="QListWidget" name="m_MeasurementList"/> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_3"> <item> <spacer name="horizontalSpacer_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_LoadList"> <property name="text"> <string>Load List</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <item> <widget class="QLabel" name="label_2"> <property name="text"> <string>Output Path:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_OutputPath"> <property name="text"> <string>C:/temp/</string> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="m_LastMeasurement"> <property name="text"> <string>Last Measurement: <none></string> </property> </widget> </item> <item> <widget class="QLabel" name="m_NextMeasurement"> <property name="text"> <string>Next Measurement: <none></string> </property> </widget> </item> <item> <widget class="QLabel" name="m_CollectedSamples"> <property name="text"> <string>Collected Samples: <none></string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_7"> <item> <spacer name="horizontalSpacer_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_StartNextMeasurement"> <property name="minimumSize"> <size> <width>200</width> <height>0</height> </size> </property> <property name="text"> <string>Start Next Measurement</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_8"> <item> <spacer name="horizontalSpacer_7"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_ReapeatLastMeasurement"> <property name="minimumSize"> <size> <width>200</width> <height>0</height> </size> </property> <property name="text"> <string>Repeat Last Measurement</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_10"> <item> <spacer name="horizontalSpacer_9"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_CreateResults"> <property name="minimumSize"> <size> <width>200</width> <height>0</height> </size> </property> <property name="text"> <string>Create Results</string> </property> </widget> </item> </layout> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>281</height> </size> </property> </spacer> </item> <item> <widget class="Line" name="line_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_7"> <property name="text"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Measurement Sensors:</body></html></string> </property> </widget> </item> <item> <widget class="QmitkToolTrackingStatusWidget" name="m_ToolStatusWidget" native="true"/> </item> <item> <widget class="Line" name="line"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item> <widget class="QLabel" name="label_3"> <property name="text"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Reference Sensors:</body></html></string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_SetReference"> <property name="text"> <string>Set Reference</string> </property> </widget> </item> <item> <widget class="QLabel" name="m_ReferencePosAtStart"> <property name="text"> - <string>Reference Postion: <none></string> + <string>Reference Position: <none></string> </property> </widget> </item> <item> <widget class="QLabel" name="m_ReferenceCurrentPos"> <property name="text"> <string>Current Positions: <none></string> </property> </widget> </item> <item> <widget class="QLabel" name="m_ReferenceOK"> <property name="text"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> OK</body></html></string> </property> <property name="alignment"> <set>Qt::AlignCenter</set> </property> </widget> </item> </layout> </widget> <widget class="QWidget" name="tab_3"> <attribute name="title"> <string>Settings</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <item> <widget class="QLabel" name="label_4"> <property name="text"> <string>Sampling Rate (Times Per Second):</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QDoubleSpinBox" name="m_SamplingRate"> <property name="maximum"> <double>999.000000000000000</double> </property> <property name="value"> <double>15.000000000000000</double> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_6"> <item> <widget class="QLabel" name="label_5"> <property name="text"> <string>Samples Per Measurement:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QSpinBox" name="m_SamplesPerMeasurement"> <property name="maximum"> <number>1000</number> </property> <property name="value"> <number>150</number> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_9"> <item> <widget class="QLabel" name="label_6"> <property name="text"> <string>Threshold For Reference Tools:</string> </property> </widget> </item> <item> <spacer name="horizontalSpacer_8"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QDoubleSpinBox" name="m_ReferenceThreshold"> <property name="value"> <double>1.000000000000000</double> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="m_UseReferenceTrackingSystem"> <property name="text"> <string>Use Reference Tracking System</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_2"> <property name="title"> <string>Tracking Volume</string> </property> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <widget class="QRadioButton" name="m_smallVolume"> <property name="text"> <string>Small Volume (3 X 4 Positions)</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_mediumVolume"> <property name="text"> <string>Medium Volume (5 X 5 Positions)</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="m_standardVolume"> <property name="text"> <string>Standard Volume (10 X 9 Positions)</string> </property> </widget> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkToolTrackingStatusWidget</class> <extends>QWidget</extends> <header>QmitkToolTrackingStatusWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkTrackingDeviceConfigurationWidget</class> <extends>QWidget</extends> <header>QmitkTrackingDeviceConfigurationWidget.h</header> <container>1</container> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h index 3c8c7a6f61..14c5fcda60 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkHummelProtocolEvaluation.h @@ -1,92 +1,92 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkHummelProtocolEvaluation_h #define mitkHummelProtocolEvaluation_h #include <mitkPointSet.h> #include <array> namespace mitk { /**Documentation * \brief Static methods for evaluations according to the assessment protocol * for EM trackers published by Hummel et al. 2005 [1]. * * [1] Hummel, J. et al. - Design and application of an assessment protocol for electromagnetic tracking systems. Med Phys 32(7), July 2005 * * \ingroup IGT */ class HummelProtocolEvaluation { public: /** Distance error with description. */ struct HummelProtocolDistanceError {double distanceError; std::string description;}; /** Tracking volumes for evaluation. - * standard: The standard volume of 9 x 10 measurment points as described in [1] + * standard: The standard volume of 9 x 10 measurement points as described in [1] * small: A small volume in the center 3 x 4 measurement points, for smaller field generators [2] * [2] Maier-Hein, L. et al. - Standardized assessment of new electromagnetic field generators in an interventional radiology setting. Med Phys 39(6), June 2012 */ enum HummelProtocolMeasurementVolume { small, medium, standard }; /** Evaluates the 5 cm distances as defined by the Hummel protocol [1,2]. - * @return Returns true if evaluation was successfull, false if not. + * @return Returns true if evaluation was successful, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate5cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Evaluates the 15 cm distances as defined by the Hummel protocol [1,2]. - * @return Returns true if evaluation was successfull, false if not. + * @return Returns true if evaluation was successful, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate15cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Evaluates the 30 cm distances as defined by the Hummel protocol [1,2]. - * @return Returns true if evaluation was successfull, false if not. + * @return Returns true if evaluation was successful, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool Evaluate30cmDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Evaluates the accumulated distances as defined by the Hummel protocol [1,2]. - * @return Returns true if evaluation was successfull, false if not. + * @return Returns true if evaluation was successful, false if not. * @param[out] Results Please give an empty vector. The results will be added to this vector. */ static bool EvaluateAccumulatedDistances(mitk::PointSet::Pointer p, HummelProtocolMeasurementVolume m, std::vector<HummelProtocolDistanceError> &Results); /** Computes statistics (as mean, standard deviation, quantiles, min, max, etc.) on the given values. * The results are stored inside the return value. */ static std::vector<HummelProtocolDistanceError> ComputeStatistics(std::vector<HummelProtocolDistanceError> values); protected: /** Converts a pointset holding all measurement points of the hummel protocol in line-by-line order * to an array representing the hummel board. */ static std::array<std::array<mitk::Point3D, 10> ,9> ParseMatrixStandardVolume(mitk::PointSet::Pointer p); - //It would be really wonderfull if we could replace std::array<std::array<mitk::Point3D, 10> ,9> by mitk::Matrix< mitk::Point3D, 9, 10 > but - //unfortunatly this version does not compile under Linux. To be precise under Linux only matrices like this: mitk::Matriy<double, 9, 10> compile + //It would be really wonderful if we could replace std::array<std::array<mitk::Point3D, 10> ,9> by mitk::Matrix< mitk::Point3D, 9, 10 > but + //unfortunately this version does not compile under Linux. To be precise under Linux only matrices like this: mitk::Matriy<double, 9, 10> compile //even the usage of a double pointer (eg mitk::Matrix<double* , 9, 10>) does not compile. We always got an error message saying: //vnl_c_vector.h:42:49: error: invalid use of incomplete type ‘class vnl_numeric_traits<itk::Point<double, 3u> >’ //Under Windows this error does not appear there everything compiles fine. static std::array<std::array<mitk::Point3D, 5>, 5> ParseMatrixMediumVolume(mitk::PointSet::Pointer p); }; } // namespace mitk #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h index 308fb486f2..31c35eea24 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h +++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h @@ -1,148 +1,148 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkNavigationDataCSVSequentialPlayer_h #define mitkNavigationDataCSVSequentialPlayer_h #include <mitkNavigationDataPlayerBase.h> namespace mitk { /**Documentation * \brief This class is a NavigationDataPlayer which can play CSV formatted * files in sequential order, which means it doesn't care about timestamps and just * outputs the navigationdatas in their sequential order. * * It is thought to interpret custom csv files. To do so please adapt the column * numbers of position and orientation in the internal method GetNavigationDataOutOfOneLine(). * * So far only one (the first) tool is read in as required for the hummel protocol measurements. * * This class can also interpret MITK style csv files (set filetype to NavigationDataCSV), but * you can also use the MITK navigation data player class inside the MITK-IGT module which * is newer and better maintained. * * \ingroup IGT */ class NavigationDataCSVSequentialPlayer : public NavigationDataPlayerBase { public: mitkClassMacro(NavigationDataCSVSequentialPlayer, NavigationDataPlayerBase); itkNewMacro(Self); /** * \brief sets the file name and path (if XMLString is set, this is neglected) */ void SetFileName(const std::string& _FileName); /** - * @brief SetOptions sets the options for reading out the data out of the correct postions of the file. They need to be set before using the player + * @brief SetOptions sets the options for reading out the data out of the correct positions of the file. They need to be set before using the player * @param rightHanded true if the used coordinate System is right handed, false if it is left handed * @param seperatorSign symbol that is used to separate the values in the .csv file * @param sampleCount every n-th sample in the file that should be used * @param headerRow true if the .csv file has a header row otherwise false - * @param xPos number of the colum in the .csv file for the x-coordinates of the position - * @param yPos number of the colum in the .csv file for the y-coordinates of the position - * @param zPos number of the colum in the .csv file for the z-coordinates of the position + * @param xPos number of the column in the .csv file for the x-coordinates of the position + * @param yPos number of the column in the .csv file for the y-coordinates of the position + * @param zPos number of the column in the .csv file for the z-coordinates of the position * @param useQuats true if Quaternions are used to construct the orientation, false if Euler Angles are used * @param qx number of the column in the .csv file for the x component of the quaternion * @param qy number of the column in the .csv file for the y component of the quaternion * @param qz number of the column in the .csv file for the z component of the quaternion * @param qr number of the column in the .csv file for the r component of the quaternion - * @param azimuth number of the colum in the .csv file for Azimuth (Euler Angles). Set < 0 if angle is not defined - * @param elevatino number of the colum in the .csv file for Elevation (Euler Angles) Set < 0 if angle is not defined - * @param roll number of the colum in the .csv file for Roll (Euler Angles) Set < 0 if angle is not defined + * @param azimuth number of the column in the .csv file for Azimuth (Euler Angles). Set < 0 if angle is not defined + * @param elevatino number of the column in the .csv file for Elevation (Euler Angles) Set < 0 if angle is not defined + * @param roll number of the column in the .csv file for Roll (Euler Angles) Set < 0 if angle is not defined * @param eulerInRadiants true if the Euler Angles in the .csv file are in radiants, false if they are in degrees * @param minNumberOfColumns */ void SetOptions(bool rightHanded, char seperatorSign, int sampleCount, bool headerRow, int xPos, int yPos, int zPos, bool useQuats, int qx, int qy, int qz, int qr, int azimuth, int elevatino, int roll, bool eulerInRadiants, int minNumberOfColums); /** * \brief returns the file name and path */ itkGetStringMacro(FileName); enum Filetype { NavigationDataCSV, //for csv files from the MITK navigation data player - ManualLoggingCSV //for custum csv files + ManualLoggingCSV //for custom csv files }; /** * \brief Sets the file type. ManualLoggingCSV is default and is thought for your * custom csv files. You can also set it to NavigationDataCSV, then this * player interprets MITK style csv files. */ itkSetMacro(Filetype, Filetype); /** * \return Returns true if the player reached the end of the file. */ bool IsAtEnd(); /** * \brief Used for pipeline update just to tell the pipeline * that we always have to update */ void UpdateOutputInformation() override; int GetNumberOfSnapshots(); protected: NavigationDataCSVSequentialPlayer(); ~NavigationDataCSVSequentialPlayer() override; /// /// do the work here /// void GenerateData() override; std::string m_FileName; int m_CurrentPos; Filetype m_Filetype; //member for the navigation datas which were read (only one output is supported at the moment) std::vector<mitk::NavigationData::Pointer> m_NavigationDatas; std::vector<mitk::NavigationData::Pointer> GetNavigationDatasFromFile(std::string filename); std::vector<std::string> GetFileContentLineByLine(std::string filename); mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line); void FillOutputEmpty(int number); mitk::NavigationData::Pointer GetEmptyNavigationData(); bool m_RightHanded; //true if the used coordinate System is right handed, false if it is left handed char m_SeparatorSign; //symbol that is used to separate the values in the .csv file int m_SampleCount; //every n-th sample in the file that should be used bool m_HeaderRow; //true if the .csv file has a header row otherwise false - int m_XPos; //number of the colum in the .csv file for the x-coordinates of the position - int m_YPos; //number of the colum in the .csv file for the y-coordinates of the position - int m_ZPos; //number of the colum in the .csv file for the z-coordinates of the position + int m_XPos; //number of the column in the .csv file for the x-coordinates of the position + int m_YPos; //number of the column in the .csv file for the y-coordinates of the position + int m_ZPos; //number of the column in the .csv file for the z-coordinates of the position bool m_UseQuats; //true if Quaternions are used to construct the orientation, false if Euler Angles are used int m_Qx; //number of the column in the .csv file for the x component of the quaternion int m_Qy; //number of the column in the .csv file for the y component of the quaternion int m_Qz; //number of the column in the .csv file for the z component of the quaternion int m_Qr; //number of the column in the .csv file for the r component of the quaternion - int m_Azimuth; //number of the colum in the .csv file for Azimuth (Euler Angles) - int m_Elevation; //number of the colum in the .csv file for Elevation (Euler Angles) - int m_Roll; //number of the colum in the .csv file for Roll (Euler Angles) + int m_Azimuth; //number of the column in the .csv file for Azimuth (Euler Angles) + int m_Elevation; //number of the column in the .csv file for Elevation (Euler Angles) + int m_Roll; //number of the column in the .csv file for Roll (Euler Angles) bool m_EulersInRadiants; // true if the Euler Angles in the .csv file are in radiants, false if they are in degrees int m_MinNumberOfColumns; //minimal number of columns the file has to have (e.g. if you read data from column 8 the file has to have at least 8 columns) }; } // namespace mitk #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetIntersectionFilter.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetIntersectionFilter.h index b29cde2d78..4bf3e852bc 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetIntersectionFilter.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetIntersectionFilter.h @@ -1,90 +1,90 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkUSNavigationTargetIntersectionFilter_h #define mitkUSNavigationTargetIntersectionFilter_h #include "mitkCommon.h" #include "mitkNumericTypes.h" #include "itkObjectFactory.h" #include "vtkSmartPointer.h" #include "vtkPolyData.h" namespace itk { template<class T> class SmartPointer; } namespace mitk { class Surface; class PointSet; /** * \brief Calculates the intersection between a mitk::Surface and a line. * Surface and line have to be set by SetTargetSurface() and SetLine. * CalculateIntersection() can be called then to calculate the intersection. * The results can be got afterwards by GetIsIntersecting(), * GetIntersectionPoint(), GetIntersectionNearestSurfacePointId() and * GetDistanceToIntersection(). */ class USNavigationTargetIntersectionFilter : public itk::Object { public: mitkClassMacroItkParent(USNavigationTargetIntersectionFilter, itk::Object); itkNewMacro(Self); itkSetMacro(TargetSurface, itk::SmartPointer<mitk::Surface>); void SetLine(itk::SmartPointer<mitk::PointSet> line); /** * \return if line and surface are intersecting */ itkGetMacro(IsIntersecting, bool); /** - * \return the position where the intersection occured, the result is not defined if no intersection occured + * \return the position where the intersection occurred, the result is not defined if no intersection occurred */ mitk::Point3D GetIntersectionPoint(); /** - * \return id of the nearest vertex of the target to the interseciont, the result is not defined if no intersection occured + * \return id of the nearest vertex of the target to the interseciont, the result is not defined if no intersection occurred */ int GetIntersectionNearestSurfacePointId(); /** * \return distance between the first line point and the intersection point */ double GetDistanceToIntersection(); /** * \brief Does the intersection calculation. * SetTargetSurface() and SetLine() have to be called before. */ void CalculateIntersection(); protected: USNavigationTargetIntersectionFilter(); ~USNavigationTargetIntersectionFilter() override; itk::SmartPointer<mitk::Surface> m_TargetSurface; vtkSmartPointer<vtkPolyData> m_TargetSurfaceVtk; double m_LinePoint1[3]; double m_LinePoint2[3]; bool m_IsIntersecting; double m_IntersectionPoint[3]; int m_IntersectionCellId; double m_Distance; }; } #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.cpp index 443d255018..7e66bdde6e 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.cpp @@ -1,189 +1,189 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // MITK #include "mitkUSNavigationTargetOcclusionFilter.h" #include "mitkDataNode.h" #include "mitkSurface.h" // VTK #include "vtkSmartPointer.h" #include "vtkPointData.h" #include "vtkPolyData.h" #include "vtkOBBTree.h" #include "vtkFloatArray.h" #include "vtkTransform.h" #include "vtkTransformPolyDataFilter.h" mitk::USNavigationTargetOcclusionFilter::USNavigationTargetOcclusionFilter() : m_StartPositionInput(0) { } mitk::USNavigationTargetOcclusionFilter::~USNavigationTargetOcclusionFilter() { } void mitk::USNavigationTargetOcclusionFilter::SetTargetStructure(itk::SmartPointer<DataNode> targetStructure) { m_TargetStructure = targetStructure; } void mitk::USNavigationTargetOcclusionFilter::SetObstacleStructures(DataStorage::SetOfObjects::ConstPointer obstacleStructures) { m_ObstacleStructures = obstacleStructures; } void mitk::USNavigationTargetOcclusionFilter::SelectStartPositionInput(unsigned int n) { m_StartPositionInput = n; } void mitk::USNavigationTargetOcclusionFilter::GenerateData() { mitk::NavigationDataPassThroughFilter::GenerateData(); // get vtk surface an the points vtkSmartPointer<vtkPolyData> targetSurfaceVtk = this->GetVtkPolyDataOfTarget(); if ( ! targetSurfaceVtk ) { return; } // cannot do anything without a target surface vtkIdType numberOfPoints = targetSurfaceVtk->GetNumberOfPoints(); // create array for scalar values vtkSmartPointer<vtkFloatArray> colors = vtkSmartPointer<vtkFloatArray>::New(); colors->SetNumberOfComponents(1); colors->SetName("USNavigation::Occlusion"); const mitk::NavigationData* nd = this->GetInput(m_StartPositionInput); // set every value to -1 if there is no (valid) navigation data if ( nd == nullptr || ! nd->IsDataValid() ) { float intersection = -1; for ( vtkIdType n = 0; n < numberOfPoints; n++ ) { colors->InsertNextTuple1(intersection); } if ( numberOfPoints > 0 ) { targetSurfaceVtk->GetPointData()->AddArray(colors); targetSurfaceVtk->GetPointData()->Update(); } return; } // initialize values with 0 (no intersection) if there is valid navigation // data and there are some obstacle structures defined else if ( m_ObstacleStructures.IsNull() ) { float intersection = 0; for ( vtkIdType n = 0; n < numberOfPoints; n++ ) { colors->InsertNextTuple1(intersection); } if ( numberOfPoints > 0 ) { targetSurfaceVtk->GetPointData()->AddArray(colors); targetSurfaceVtk->GetPointData()->Update(); } return; } // get the current position from the navigation data mitk::Point3D position = nd->GetPosition(); double point1[3]; point1[0] = position[0]; point1[1] = position[1]; point1[2] = position[2]; // transform vtk polydata according to mitk geometry vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New(); transformFilter->SetInputData(0, targetSurfaceVtk); transformFilter->SetTransform(m_TargetStructure->GetData()->GetGeometry()->GetVtkTransform()); transformFilter->Update(); vtkSmartPointer<vtkPolyData> targetSurfaceVtkTransformed = transformFilter->GetOutput(); std::vector<bool> occlusion(numberOfPoints, false); // calculate occlusion for every obstacle structure for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ObstacleStructures->Begin(); it != m_ObstacleStructures->End(); ++it) { vtkSmartPointer<vtkPolyData> polyData = dynamic_cast<mitk::Surface*>(it->Value()->GetData())->GetVtkPolyData(); - // transform the obstacle strucutre according to the mitk geometry + // transform the obstacle structure according to the mitk geometry vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New(); transformFilter->SetInputData(0, polyData); transformFilter->SetTransform(it->Value()->GetData()->GetGeometry()->GetVtkTransform()); transformFilter->Update(); polyData = transformFilter->GetOutput(); // build an obb tree locator vtkSmartPointer<vtkOBBTree> cellLocator = vtkSmartPointer<vtkOBBTree>::New(); cellLocator->SetDataSet(polyData); cellLocator->BuildLocator(); // test for intersection with every point on the surface for ( vtkIdType n = 0; n < numberOfPoints; n++ ) { vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New(); if ( cellLocator->IntersectWithLine(point1, targetSurfaceVtkTransformed->GetPoint(n), points, nullptr) != 0 ) { occlusion.at(n) = true; } } } if ( numberOfPoints > 0 ) { // set the occlusion values as scalar array to the vtkPolyData float one = 1.0f; float zero = 0.0f; for ( std::vector<bool>::iterator it = occlusion.begin(); it != occlusion.end(); ++it ) { colors->InsertNextTuple1(*it ? one : zero); } targetSurfaceVtk->GetPointData()->AddArray(colors); targetSurfaceVtk->GetPointData()->Update(); } } vtkSmartPointer<vtkPolyData> mitk::USNavigationTargetOcclusionFilter::GetVtkPolyDataOfTarget() { if ( m_TargetStructure.IsNull() ) { MITK_WARN("USNavigationTargetOcclusionFilter") << "Target structure must not be null."; return nullptr; } mitk::Surface::Pointer targetSurface = dynamic_cast<mitk::Surface*>(m_TargetStructure->GetData()); if ( targetSurface.IsNull() ) { MITK_WARN("USNavigationTargetOcclusionFilter") << "A mitk::Surface has to be set to the data node."; return nullptr; } vtkSmartPointer<vtkPolyData> targetSurfaceVtk = targetSurface->GetVtkPolyData(); if( targetSurfaceVtk == nullptr ) { MITK_WARN("USNavigationTargetOcclusionFilter") << "VtkPolyData of the mitk::Surface of the data node must not be null."; return nullptr; } return targetSurfaceVtk; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.h index 9de23a22c5..bc3d042bcb 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Filter/mitkUSNavigationTargetOcclusionFilter.h @@ -1,81 +1,81 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkUSNavigationTargetOcclusionFilter_h #define mitkUSNavigationTargetOcclusionFilter_h #include "mitkNavigationDataPassThroughFilter.h" #include "mitkDataStorage.h" namespace itk { template<class T> class SmartPointer; } class vtkPolyData; template<class T> class vtkSmartPointer; namespace mitk { class DataNode; /** * \brief NavigationData filter calcuting occluded positions on a target surface. * The occlusion caused by obstacle structures is calculated between the current * NavigationData position and a given target surface. */ class USNavigationTargetOcclusionFilter : public NavigationDataPassThroughFilter { public: mitkClassMacro(USNavigationTargetOcclusionFilter, NavigationDataPassThroughFilter); itkNewMacro(Self); /** * \brief Sets the target structure for which the occluded positions should be calculated. - * \param targetStructure DataNode conatining a mitk::Surface + * \param targetStructure DataNode containing a mitk::Surface */ void SetTargetStructure(itk::SmartPointer<DataNode> targetStructure); /** * \brief Sets the obstacle structures which can occlude the target structure. * \param obstacleStructures Set of DataNodes containing a mitk::Surface each */ void SetObstacleStructures(DataStorage::SetOfObjects::ConstPointer obstacleStructures); /** * \brief Sets the index of the input which is used for occlusion calculation. * The occlusion will be calculated between the NavigationData position of * this input and the target structure. */ void SelectStartPositionInput(unsigned int n); protected: USNavigationTargetOcclusionFilter(); ~USNavigationTargetOcclusionFilter() override; void GenerateData() override; /** * \brief Returns the vtk poly data of the target structure. * \return vtkPolyData if the target structure data node contains one, returns null otherwise */ vtkSmartPointer<vtkPolyData> GetVtkPolyDataOfTarget(); DataStorage::SetOfObjects::ConstPointer m_ObstacleStructures; itk::SmartPointer<DataNode> m_TargetStructure; unsigned int m_StartPositionInput; std::vector<bool> m_OccludedPositions; }; } // namespace mitk #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationCombinedModalityPersistence.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationCombinedModalityPersistence.cpp index 344f0f25de..9634e91b55 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationCombinedModalityPersistence.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationCombinedModalityPersistence.cpp @@ -1,209 +1,209 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkUSNavigationCombinedModalityPersistence.h" #include "mitkUSCombinedModality.h" // Microservices #include <usServiceReference.h> #include <usModuleContext.h> #include <usGetModuleContext.h> #include <usModuleContext.h> // Qt #include <QSettings> #include <QVector> #include <QHash> #include <QStringList> #include "internal/org_mbi_gui_qt_usnavigation_Activator.h" mitk::USNavigationCombinedModalityPersistence::USNavigationCombinedModalityPersistence() { us::ModuleContext* context = us::GetModuleContext(); this->LoadStoredDevices(); // to be notified about every register and unregister of an USDevice std::string filterExcludeCombinedModalities = "(&(" + us::ServiceConstants::OBJECTCLASS() + "=" + "org.mitk.services.UltrasoundDevice)(!(" + mitk::USDevice::GetPropertyKeys().US_PROPKEY_CLASS + "=" + mitk::USCombinedModality::DeviceClassIdentifier + ")))"; context->AddServiceListener(this, &mitk::USNavigationCombinedModalityPersistence::OnServiceEvent, filterExcludeCombinedModalities); // to be notified about every register and unregister of an NavigationDataSource context->AddServiceListener(this, &mitk::USNavigationCombinedModalityPersistence::OnServiceEvent, "(" + us::ServiceConstants::OBJECTCLASS() + "=" + us_service_interface_iid<mitk::NavigationDataSource>() + ")"); } mitk::USNavigationCombinedModalityPersistence::~USNavigationCombinedModalityPersistence() { //this->StoreCurrentDevices(); //disabled because persistence is buggy } void mitk::USNavigationCombinedModalityPersistence::OnServiceEvent(const us::ServiceEvent event) { if ( event.GetType() == event.REGISTERED ) { //this->LoadStoredDevices(); //disabled because persistence is buggy } } void mitk::USNavigationCombinedModalityPersistence::StoreCurrentDevices() { QList<QVariant> devices; us::ModuleContext* context = us::GetModuleContext(); // get all combined modality from the service registry std::string filterOnlyCombinedModalities = "(&(" + us::ServiceConstants::OBJECTCLASS() + "=" + "org.mitk.services.UltrasoundDevice)(" + mitk::USDevice::GetPropertyKeys().US_PROPKEY_CLASS + "=" + mitk::USCombinedModality::DeviceClassIdentifier + "))"; std::vector<us::ServiceReference<USDevice> > services = context->GetServiceReferences<USDevice>(filterOnlyCombinedModalities); for ( std::vector<us::ServiceReference<USDevice> >::iterator it = services.begin(); it != services.end(); ++it ) { QStringList deviceStrings; mitk::USCombinedModality::Pointer currentDevice = dynamic_cast<mitk::USCombinedModality*>(context->GetService(*it)); if ( currentDevice.IsNotNull() ) { - // save manufacturer and model strig of the combined modality + // save manufacturer and model string of the combined modality deviceStrings.push_back(QString::fromStdString(currentDevice->GetUltrasoundDevice()->GetManufacturer())); deviceStrings.push_back(QString::fromStdString(currentDevice->GetUltrasoundDevice()->GetName())); // save name of the navigation data source mitk::NavigationDataSource::Pointer navigationDataSource = currentDevice->GetNavigationDataSource(); if ( currentDevice.IsNull() ) { continue; } deviceStrings.push_back(QString::fromStdString(navigationDataSource->GetName())); // save manufacturer, model and comment of the ultrasound device mitk::USDevice::Pointer ultrasoundDevice = currentDevice->GetUltrasoundDevice(); if ( ultrasoundDevice.IsNull() ) { continue; } deviceStrings.push_back(QString::fromStdString(ultrasoundDevice->GetManufacturer())); deviceStrings.push_back(QString::fromStdString(ultrasoundDevice->GetName())); deviceStrings.push_back(QString::fromStdString(ultrasoundDevice->GetComment())); // save calibration of the combined modality deviceStrings.push_back(QString::fromStdString(currentDevice->SerializeCalibration())); } devices.push_back(deviceStrings); } // store everything in QSettings QSettings settings; settings.setValue("combined-modalities", devices); } void mitk::USNavigationCombinedModalityPersistence::LoadStoredDevices() { // load everything from QSettings QSettings settings; QList<QVariant> devices = settings.value("combined-modalities").value< QList<QVariant> >(); for ( QList<QVariant>::iterator it = devices.begin(); it != devices.end(); ++it ) { // get the saved strings for the combined modality (there must be at least // the seven strings, which where saved before) QStringList stringList = it->toStringList(); // test if the combined modality wasn't restored before if (stringList.size() >= 7 && this->GetCombinedModality(stringList.at(0).toStdString(), stringList.at(1).toStdString()).IsNull()) { // try to get matching navigation data source and ultrasound device mitk::NavigationDataSource::Pointer navigationDataSource = this->GetNavigationDataSource(stringList.at(2).toStdString()); mitk::USDevice::Pointer usDevice = this->GetUSDevice(stringList.at(3).toStdString(), stringList.at(4).toStdString(), stringList.at(5).toStdString()); // create the combined modality if matching navigation data source and // ultrasound device werde found if ( navigationDataSource.IsNotNull() && usDevice.IsNotNull() ) { mitk::USCombinedModality::Pointer combinedModality = mitk::USCombinedModality::New(usDevice, navigationDataSource, false); combinedModality->DeserializeCalibration(stringList.at(6).toStdString()); combinedModality->GetUltrasoundDevice()->Initialize(); } } } } mitk::USCombinedModality::Pointer mitk::USNavigationCombinedModalityPersistence::GetCombinedModality(std::string manufacturer, std::string model) { us::ModuleContext* context = us::GetModuleContext(); std::string filterOnlyCombinedModalities = "(&(" + us::ServiceConstants::OBJECTCLASS() + "=" + "org.mitk.services.UltrasoundDevice)(" + mitk::USDevice::GetPropertyKeys().US_PROPKEY_CLASS + "=" + mitk::USCombinedModality::DeviceClassIdentifier + "))"; std::vector<us::ServiceReference<USDevice> > services = context->GetServiceReferences<USDevice>(filterOnlyCombinedModalities); for ( std::vector<us::ServiceReference<USDevice> >::iterator it = services.begin(); it != services.end(); ++it ) { mitk::USCombinedModality::Pointer currentDevice = dynamic_cast<mitk::USCombinedModality*>(context->GetService(*it)); if ( currentDevice.IsNotNull() ) { if ( currentDevice->GetUltrasoundDevice()->GetManufacturer() == manufacturer && currentDevice->GetUltrasoundDevice()->GetName() == model ) { return currentDevice; } } } return nullptr; } mitk::USDevice::Pointer mitk::USNavigationCombinedModalityPersistence::GetUSDevice(std::string manufacturer, std::string model, std::string comment) { us::ModuleContext* context = us::GetModuleContext(); std::string filterExcludeCombinedModalities = "(&(" + us::ServiceConstants::OBJECTCLASS() + "=" + "org.mitk.services.UltrasoundDevice)(!(" + mitk::USDevice::GetPropertyKeys().US_PROPKEY_CLASS + "=" + mitk::USCombinedModality::DeviceClassIdentifier + ")))"; std::vector<us::ServiceReference<USDevice> > services = context->GetServiceReferences<USDevice>(filterExcludeCombinedModalities); for ( std::vector<us::ServiceReference<USDevice> >::iterator it = services.begin(); it != services.end(); ++it ) { mitk::USDevice::Pointer currentDevice = dynamic_cast<mitk::USDevice*>(context->GetService(*it)); if ( currentDevice.IsNotNull() ) { if ( currentDevice->GetManufacturer() == manufacturer && currentDevice->GetName() == model && currentDevice->GetComment() == comment ) { return currentDevice; } } } return nullptr; } mitk::NavigationDataSource::Pointer mitk::USNavigationCombinedModalityPersistence::GetNavigationDataSource(std::string name) { us::ModuleContext* context = us::GetModuleContext(); std::vector<us::ServiceReference<mitk::NavigationDataSource> > services = context->GetServiceReferences<mitk::NavigationDataSource>(); for ( std::vector<us::ServiceReference<mitk::NavigationDataSource> >::iterator it = services.begin(); it != services.end(); ++it ) { mitk::NavigationDataSource::Pointer currentDevice = dynamic_cast<mitk::NavigationDataSource*>(context->GetService(*it)); if ( currentDevice.IsNotNull() ) { if ( currentDevice->GetName() == name ) { return currentDevice; } } } return nullptr; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationExperimentLogging.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationExperimentLogging.cpp index e58df0d54b..67714b7b70 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationExperimentLogging.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/IO/mitkUSNavigationExperimentLogging.cpp @@ -1,132 +1,132 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkUSNavigationExperimentLogging.h" #include "mitkDataNode.h" #include "itkRealTimeClock.h" #include "Poco/DOM/Document.h" #include "Poco/DOM/Element.h" #include "Poco/DOM/Text.h" #include "Poco/DOM/NodeList.h" #include "Poco/DOM/DOMWriter.h" #include "Poco/XML/XMLWriter.h" mitk::USNavigationExperimentLogging::USNavigationExperimentLogging() : m_CurrentResultNumber(0), m_RealTimeClock(itk::RealTimeClock::New()) { this->Reset(); } mitk::USNavigationExperimentLogging::~USNavigationExperimentLogging() { } void mitk::USNavigationExperimentLogging::Reset() { m_StartTime = m_RealTimeClock->GetTimeInSeconds(); m_OutputXML = new Poco::XML::Document(); m_OutputXMLRoot = m_OutputXML->createElement("ExperimentResults"); m_OutputXML->appendChild(m_OutputXMLRoot); } void mitk::USNavigationExperimentLogging::SetFileName(const std::string& fileName) { m_FileName = fileName; } void mitk::USNavigationExperimentLogging::SetResult(const itk::SmartPointer<mitk::DataNode> resultNode) { Poco::AutoPtr<Poco::XML::Element> currentResultElement = m_OutputXML->createElement(resultNode->GetName()); m_OutputXMLRoot->appendChild(currentResultElement); this->AddCurrentTimeAttributes(currentResultElement); const mitk::PropertyList::PropertyMap* propertyMap = resultNode->GetPropertyList()->GetMap(); for ( mitk::PropertyList::PropertyMap::const_iterator it = propertyMap->begin(); it != propertyMap->end(); ++it ) { size_t prefixSize = m_KeyPrefix.size(); - // only write properties with keys begining with the prefix (if a prefix was set) + // only write properties with keys beginning with the prefix (if a prefix was set) if ( ! m_KeyPrefix.empty() && it->first.substr(0, prefixSize) != m_KeyPrefix ) { continue; } if ( prefixSize >= it->first.size() ) { MITK_ERROR("USNavigationExperimentLogging") << "Property key must contain more characters then the key prefix."; mitkThrow() << "Property key must contain more characters then the key prefix."; } // create a xml element named like the key but without the prefix and // append it into the xml tree Poco::AutoPtr<Poco::XML::Element> mapElement = m_OutputXML->createElement(it->first.substr(prefixSize, it->first.size() - prefixSize)); currentResultElement->appendChild(mapElement); // get the class of the property and save it in the tree mapElement->setAttribute("class", it->second->GetNameOfClass()); // convert the value of the property to a string and save it in the tree Poco::AutoPtr<Poco::XML::Text> value = m_OutputXML->createTextNode(it->second->GetValueAsString()); mapElement->appendChild(value); } this->WriteXmlToFile(); } void mitk::USNavigationExperimentLogging::AddCurrentTimeAttributes(Poco::AutoPtr<Poco::XML::Element> element) { // get the current time and add it as attribute to the xml std::stringstream stringStreamTime; stringStreamTime.precision(2); stringStreamTime << std::fixed << m_RealTimeClock->GetTimeInSeconds(); element->setAttribute("time", stringStreamTime.str()); // get the duration since the start time and add it as attribute to the xml std::stringstream stringStreamExperimentTime; stringStreamExperimentTime.precision(2); stringStreamExperimentTime << std::fixed << m_RealTimeClock->GetTimeInSeconds() - m_StartTime; element->setAttribute("duration", stringStreamExperimentTime.str()); } void mitk::USNavigationExperimentLogging::WriteXmlToFile() { - // open file and write tree if successfull + // open file and write tree if successful std::ofstream filestream(m_FileName.c_str()); if ( filestream.is_open() ) { // print xml tree to the file Poco::XML::DOMWriter domWriter; domWriter.setNewLine("\n"); domWriter.setOptions(Poco::XML::XMLWriter::PRETTY_PRINT); try { domWriter.writeNode(filestream, m_OutputXML); } catch (const Poco::Exception &e) { MITK_ERROR("USNavigationExperimentLogging") << "Cannot write XML tree (" << e.displayText() << ")."; mitkThrow() << "Cannot write XML tree (" << e.displayText() << ")."; } filestream.close(); } else { MITK_ERROR("USNavigationExperimentLogging") << "Cannot open output file (" << m_FileName << "). Nothing will be stored at the file system."; mitkThrow() << "Cannot open output file (" << m_FileName << "). Nothing will be stored at the file system."; } } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Interactors/mitkUSZonesInteractor.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Interactors/mitkUSZonesInteractor.h index 52abbd4908..00cf07203c 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Interactors/mitkUSZonesInteractor.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Interactors/mitkUSZonesInteractor.h @@ -1,108 +1,108 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkUSZonesInteractor_h #define mitkUSZonesInteractor_h #include "mitkDataInteractor.h" namespace itk { template<class T> class SmartPointer; } namespace mitk { class Surface; class DataNode; /** * \brief DataInteractor for creating a sphere at a specific coordinate. * The origin is set by mitk::USZonesInteractor::AddCenter() and then the * radius can be updated by mitk::USZonesInteractor::ChangeRadius(). An * updated sphere is rendered every time the radius changes. * * DataNode attributes set by this class: * * zone.size (float) - the radius of the sphere * * zone.created (bool) - determines if the interactor reached its final state * * Two state machines for this interactor are available as resources of the * USNavigation module. * * USZoneInteractions.xml: Create a sphere by clicking left, moving the mouse * and clicking left againg. Aborting is possible by right mouse click. * * USZoneInteractionsHold.xml: Create a sphere by pressing the left mouse button, * moving the mouse while holding it pressed and finally release the button. * Aborting is possible by right mouse click. */ class USZonesInteractor : public DataInteractor { public: static const char* DATANODE_PROPERTY_SIZE; static const char* DATANODE_PROPERTY_CREATED; mitkClassMacro(USZonesInteractor, DataInteractor); itkNewMacro(Self); /** * \brief Creates Vtk Sphere according to current radius. * The radius is gotten from the float property "zone.size" of the * data node. */ static void UpdateSurface(itk::SmartPointer<mitk::DataNode>); protected: USZonesInteractor(); ~USZonesInteractor() override; /** * \brief Connects the functions from the state machine to methods of this class. */ void ConnectActionsAndFunctions() override; /** * \brief Sets empty surface as data for the new data node. * This is necessary as data nodes without data do not work * with data interactors. */ void DataNodeChanged() override; /** * \brief Sets origin of the data node to the coordinates of the position event. * \return false if interaction event isn't a position event, true otherwise */ void AddCenter(StateMachineAction*, InteractionEvent*); /** * \brief Updates radius attribute according to position event. * Calculates distance between the data node origin and the current position - * event and updates the data node attribue "zone.size" accordingly. The + * event and updates the data node attribute "zone.size" accordingly. The * mitk::USZonesInteractor::UpdateSurface() function is called then. * * \return false if interaction event isn't a position event, true otherwise */ void ChangeRadius(StateMachineAction*, InteractionEvent*); /** * \brief Sets the property "zone.created" of the data node to true. * \return always true */ void EndCreation(StateMachineAction*, InteractionEvent*); /** * \brief Removes Vtk Sphere from data node. * \return always true */ void AbortCreation(StateMachineAction*, InteractionEvent*); }; } // namespace mitk #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSAbstractNavigationStep.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSAbstractNavigationStep.h index 408c33bfc9..da23ff2e31 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSAbstractNavigationStep.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSAbstractNavigationStep.h @@ -1,307 +1,307 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSAbstractNavigationStep_h #define QmitkUSAbstractNavigationStep_h #include <QWidget> #include "mitkDataStorage.h" #include "mitkAbstractUltrasoundTrackerDevice.h" namespace itk { template<class T> class SmartPointer; } namespace mitk { class NavigationDataToNavigationDataFilter; } /** * \brief Abstract base class for navigation step widgets. * * This class defines a life cycle for navigation steps. Steps can be activated * and deactivated. The first time a step is activated, it is started before * the activation. Steps can be stopped, finished and restarted, too. * * On every state change, the corresponding virtual On... method is called * (OnStartStep(), OnActivateStep(), OnFinishStep(), ...). These methods are * to implement by concrete navigation step widgets. While a step is in the * "active" state, its OnUpdate() method is called periodically. */ class QmitkUSAbstractNavigationStep : public QWidget { Q_OBJECT signals: /** * \brief Signals that all necessary actions where done. * The user can proceed with the next stept after this was signaled. */ void SignalReadyForNextStep(); /** * \brief Signals that it is no longer possible to proceed with following steps. - * This signal is emmited when the result data of the step was removed or + * This signal is emitted when the result data of the step was removed or * changed, so that the old results are invalid for following steps. */ void SignalNoLongerReadyForNextStep(); /** * \brief Signals that the combined modality was changed by this step. * This signal is mainly for steps which creates the combined modality. The * new combined modality is given as a parameter. */ void SignalCombinedModalityChanged(itk::SmartPointer<mitk::AbstractUltrasoundTrackerDevice>); /** * \brief Signals that an intermediate result was produced. * The properties of the given data node must contain the results. This signal * can be used to log the intermediate results of an experiment, for example * by using the mitk::USNavigationExperimentLogging. */ void SignalIntermediateResult(const itk::SmartPointer<mitk::DataNode>); /** * \brief Signals that the settings node was changed. - * This signal must not be emited in an OnSettingsChanged() method. + * This signal must not be emitted in an OnSettingsChanged() method. */ void SignalSettingsNodeChanged(itk::SmartPointer<mitk::DataNode>); public: typedef std::vector< itk::SmartPointer<mitk::NavigationDataToNavigationDataFilter> > FilterVector; enum NavigationStepState { State_Stopped, State_Started, State_Active }; static const char* DATANAME_SETTINGS; static const char* DATANAME_IMAGESTREAM; static const char* DATANAME_BASENODE; explicit QmitkUSAbstractNavigationStep(QWidget *parent = nullptr); ~QmitkUSAbstractNavigationStep() override; /** * \brief Getter for the title of the navigation step. * This title should be human readable and can be used to display the * available steps and the currently active step to the user. * The method has to be implemented by a concrete subclass. */ virtual QString GetTitle() = 0; /** * \brief Indicates if it makes sense to be able to restart the step. * This method must be implemented by concrete subclasses if it should not be * possible to restart them. * * \return true for the default implementation */ virtual bool GetIsRestartable(); /** * \brief Called every time the settings for the navigation process where changed. * This method may be implemented by a concrete subclass. The default * implementation does nothing. */ virtual void OnSettingsChanged(const itk::SmartPointer<mitk::DataNode> /*settingsNode*/) { } /** * \brief Getter for navigation data filters of the navigation step. * This method may be implemented by a concrete subclass. The default * implementation returns an empty vector. * * \return all navigation data filters that should be updated during the navigation process */ virtual FilterVector GetFilter(); /** * \brief Sets the data storage for the exchange of results between navigation steps. */ void SetDataStorage(itk::SmartPointer<mitk::DataStorage> dataStorage); /** * \brief Sets the combined modality for the navigation step. * OnSetCombinedModality() is called internal. */ void SetCombinedModality(itk::SmartPointer<mitk::AbstractUltrasoundTrackerDevice> combinedModality); /** * \brief Should be called to start the navigation step. * \return true if the state was 'stopped' before and OnStartStep() returns true */ bool StartStep(); /** * \brief Should be called to stop the navigation step. * \return true if the state was 'started' (or 'active') and OnStopStep() (and OnDeactivateStep()) return true */ bool StopStep(); /** * \brief Should be called to restart the navigation step. * \return true if OnRestartStep() returns true */ bool RestartStep(); /** * \brief Should be called to finish the navigation step. * The state has to be 'active' before and is 'started' afterwards. * * \return true if the state was 'active' and DeactivateStep() and OnFinishStep() return true */ bool FinishStep(); /** * \brief Should be called to activate the navigation step. * The step gets started before if it was stopped. * * \return true if the state wasn't 'activated' and OnActivateStep() returns true */ bool ActivateStep(); /** * \brief Should be called to deactivate the navigation step. * \return true if the state was 'activated' and OnDeactivateStep() returns true */ bool DeactivateStep(); /** * \brief Should be called periodically while the navigation step is active. * Internal, the method OnUpdate() is called. */ void Update(); /** * \brief Get the current state of the navigation step. * \return State_Stopped, State_Started or State_Active */ NavigationStepState GetNavigationStepState(); protected: /** * \brief Called when the navigation step gets started. * This method has to be implemented by a concrete subclass to handle actions * necessary for starting the step (e.g. initializing that has only to be done * once). * * \return if the actions were done successfully */ virtual bool OnStartStep() = 0; /** * \brief Callen when the navigation step gets stopped. * This method may be implemented by a concrete subclass to handle actions * necessary for stopping the step (e.g. cleanup). The default implementation * does nothing. * * \return if the actions were done successfully; true on every call for the default implementation */ virtual bool OnStopStep() { return true; } /** * \brief Called when restarting a navigation step. * This method may be implemented by a concrete subclass to handle actions * necessary for restarting the navigation step. The default implementations * calls OnStopStep() followed by OnStartStep(). * * \return if the actions were done successfully */ virtual bool OnRestartStep(); /** * \brief Called when all necessary actions for the step where done. * This method has to be implemented by a concrete subclass to handle actions * necessary for finishing the navigation step. * * \return if the actions were done successfully */ virtual bool OnFinishStep() = 0; /** * \brief Called when the navigation step gets activated. * This method has to be implemented by a concrete subclass to handle actions * necessary on activating the navigation step. * * \return if the actions were done successfully */ virtual bool OnActivateStep() = 0; /** * \brief Called when the navigation step gets deactivated (-> state started). * This method may be implemented by a concrete subclass to handle actions * necessary on deactivating the navigation step, which means switching to * another step. * * \return if the actions were done successfully; true on every call for the default implementation */ virtual bool OnDeactivateStep() { return true; } /** * \brief Called periodically while a navigation step is active. * This method has to be implemented by a concrete subclass to handle all * periodic actions during the navigation step. */ virtual void OnUpdate() = 0; /** * \brief Called every time SetCombinedModality() was called. * This method may be implemented by a concrete subclass to handle this event. * The default implementation does nothing. */ virtual void OnSetCombinedModality() { } /** * \brief Returns the data storage set for the navigation step. * * \param throwNull if this method should throw an exception when the data storage is null (default: true) * \return the data storage set by SetDataStorage(); can only be null if the parameter throwNull is set to false * \throws mitk::Exception if the data storage is null and the parameter throwNull is set to true */ itk::SmartPointer<mitk::DataStorage> GetDataStorage(bool throwNull = true); /** * \brief Returns the combined modality set for the navigation step. * * \param throwNull if this method should throw an exception when the combined modality is null (default: true) * \return the combined modality set by SetCombinedModality(); can only be null if the parameter throwNull is set to false * \throws mitk::Exception if the combined modality is null and the parameter throwNull is set to true */ itk::SmartPointer<mitk::AbstractUltrasoundTrackerDevice> GetCombinedModality(bool throwNull = true); /** * \brief Returns node with the given name and the given source node (parent) from the data storage. * * \param name the name of the node which should be got from the data storage * \param sourceName name of the source node under which the node should be searched * \return node with the given name or null if no node with the given name and source node could be found * \throws mitk::Exception if the data storage (can be set by SetDataStorage()) is null */ itk::SmartPointer<mitk::DataNode> GetNamedDerivedNode(const char* name, const char* sourceName); /** * \brief Returns node with the given name and the given source node (parent) from the data storage. * The node is created if no matching node was found. * * \param name the name of the node which should be got from the data storage * \param sourceName name of the source node under which the node should be searched * \return node with the given name * \throws mitk::Exception if the data storage (can be set by SetDataStorage()) is null */ itk::SmartPointer<mitk::DataNode> GetNamedDerivedNodeAndCreate(const char* name, const char* sourceName); private: itk::SmartPointer<mitk::DataStorage> m_DataStorage; itk::SmartPointer<mitk::AbstractUltrasoundTrackerDevice> m_CombinedModality; NavigationStepState m_NavigationStepState; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp index 16b5a9a3b8..a2bac7f3d3 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp @@ -1,2014 +1,2014 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkUSNavigationStepCtUsRegistration.h" #include "ui_QmitkUSNavigationStepCtUsRegistration.h" #include <QMessageBox> #include "mitkNodeDisplacementFilter.h" #include "../Filter/mitkFloatingImageToUltrasoundRegistrationFilter.h" #include "../QmitkUSNavigationMarkerPlacement.h" #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkLabelSetImage.h> #include "mitkProperties.h" #include <mitkImage.h> #include <mitkImageCast.h> #include <mitkRenderingManager.h> #include <mitkStaticIGTHelperFunctions.h> #include <vtkLandmarkTransform.h> #include <vtkPoints.h> #include <itkImageRegionIterator.h> #include <itkGeometryUtilities.h> #include <mitkImagePixelReadAccessor.h> #include <itkZeroCrossingImageFilter.h> #include <itkSimpleContourExtractorImageFilter.h> #include <itkCannyEdgeDetectionImageFilter.h> static const int NUMBER_FIDUCIALS_NEEDED = 8; QmitkUSNavigationStepCtUsRegistration::QmitkUSNavigationStepCtUsRegistration(QWidget *parent) : QmitkUSAbstractNavigationStep(parent), ui(new Ui::QmitkUSNavigationStepCtUsRegistration), m_PerformingGroundTruthProtocolEvaluation(false), m_FloatingImageToUltrasoundRegistrationFilter(nullptr), m_FreezeCombinedModality(false) { this->UnsetFloatingImageGeometry(); this->DefineDataStorageImageFilter(); this->CreateQtPartControl(this); } QmitkUSNavigationStepCtUsRegistration::~QmitkUSNavigationStepCtUsRegistration() { delete ui; } bool QmitkUSNavigationStepCtUsRegistration::OnStartStep() { MITK_INFO << "OnStartStep()"; return true; } bool QmitkUSNavigationStepCtUsRegistration::OnStopStep() { MITK_INFO << "OnStopStep()"; return true; } bool QmitkUSNavigationStepCtUsRegistration::OnFinishStep() { MITK_INFO << "OnFinishStep()"; return true; } bool QmitkUSNavigationStepCtUsRegistration::OnActivateStep() { MITK_INFO << "OnActivateStep()"; ui->floatingImageComboBox->SetDataStorage(this->GetDataStorage()); ui->ctImagesToChooseComboBox->SetDataStorage(this->GetDataStorage()); ui->segmentationComboBox->SetDataStorage(this->GetDataStorage()); ui->selectedSurfaceComboBox->SetDataStorage(this->GetDataStorage()); ui->pointSetComboBox->SetDataStorage(this->GetDataStorage()); m_FloatingImageToUltrasoundRegistrationFilter = mitk::FloatingImageToUltrasoundRegistrationFilter::New(); return true; } bool QmitkUSNavigationStepCtUsRegistration::OnDeactivateStep() { MITK_INFO << "OnDeactivateStep()"; return true; } void QmitkUSNavigationStepCtUsRegistration::OnUpdate() { if (m_NavigationDataSource.IsNull()) { return; } m_NavigationDataSource->Update(); m_FloatingImageToUltrasoundRegistrationFilter->Update(); } void QmitkUSNavigationStepCtUsRegistration::OnSettingsChanged(const itk::SmartPointer<mitk::DataNode> settingsNode) { Q_UNUSED(settingsNode); } QString QmitkUSNavigationStepCtUsRegistration::GetTitle() { return "CT-to-US registration"; } QmitkUSAbstractNavigationStep::FilterVector QmitkUSNavigationStepCtUsRegistration::GetFilter() { return FilterVector(); } void QmitkUSNavigationStepCtUsRegistration::OnSetCombinedModality() { mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality = this->GetCombinedModality(false); if (combinedModality.IsNotNull()) { m_NavigationDataSource = combinedModality->GetNavigationDataSource(); } } void QmitkUSNavigationStepCtUsRegistration::UnsetFloatingImageGeometry() { m_ImageDimension[0] = 0; m_ImageDimension[1] = 0; m_ImageDimension[2] = 0; m_ImageSpacing[0] = 1; m_ImageSpacing[1] = 1; m_ImageSpacing[2] = 1; } void QmitkUSNavigationStepCtUsRegistration::SetFloatingImageGeometryInformation(mitk::Image * image) { m_ImageDimension[0] = image->GetDimension(0); m_ImageDimension[1] = image->GetDimension(1); m_ImageDimension[2] = image->GetDimension(2); m_ImageSpacing[0] = image->GetGeometry()->GetSpacing()[0]; m_ImageSpacing[1] = image->GetGeometry()->GetSpacing()[1]; m_ImageSpacing[2] = image->GetGeometry()->GetSpacing()[2]; } double QmitkUSNavigationStepCtUsRegistration::GetVoxelVolume() { if (m_FloatingImage.IsNull()) { return 0.0; } MITK_INFO << "ImageSpacing = " << m_ImageSpacing; return m_ImageSpacing[0] * m_ImageSpacing[1] * m_ImageSpacing[2]; } double QmitkUSNavigationStepCtUsRegistration::GetFiducialVolume(double radius) { return 1.333333333 * 3.141592 * (radius * radius * radius); } bool QmitkUSNavigationStepCtUsRegistration::FilterFloatingImage() { if (m_FloatingImage.IsNull()) { return false; } ImageType::Pointer itkImage1 = ImageType::New(); mitk::CastToItkImage(m_FloatingImage, itkImage1); this->InitializeImageFilters(); m_ThresholdFilter->SetInput(itkImage1); m_LaplacianFilter1->SetInput(m_ThresholdFilter->GetOutput()); m_LaplacianFilter2->SetInput(m_LaplacianFilter1->GetOutput()); m_BinaryThresholdFilter->SetInput(m_LaplacianFilter2->GetOutput()); m_HoleFillingFilter->SetInput(m_BinaryThresholdFilter->GetOutput()); m_BinaryImageToShapeLabelMapFilter->SetInput(m_HoleFillingFilter->GetOutput()); m_BinaryImageToShapeLabelMapFilter->Update(); ImageType::Pointer binaryImage = ImageType::New(); binaryImage = m_HoleFillingFilter->GetOutput(); this->EliminateTooSmallLabeledObjects(binaryImage); //mitk::CastToMitkImage(binaryImage, m_FloatingImage); return true; } void QmitkUSNavigationStepCtUsRegistration::InitializeImageFilters() { //Initialize threshold filters m_ThresholdFilter = itk::ThresholdImageFilter<ImageType>::New(); m_ThresholdFilter->SetOutsideValue(0); m_ThresholdFilter->SetLower(500); m_ThresholdFilter->SetUpper(3200); //Initialize binary threshold filter 1 m_BinaryThresholdFilter = BinaryThresholdImageFilterType::New(); m_BinaryThresholdFilter->SetOutsideValue(0); m_BinaryThresholdFilter->SetInsideValue(1); m_BinaryThresholdFilter->SetLowerThreshold(350); m_BinaryThresholdFilter->SetUpperThreshold(10000); //Initialize laplacian recursive gaussian image filter m_LaplacianFilter1 = LaplacianRecursiveGaussianImageFilterType::New(); m_LaplacianFilter2 = LaplacianRecursiveGaussianImageFilterType::New(); //Initialize binary hole filling filter m_HoleFillingFilter = VotingBinaryIterativeHoleFillingImageFilterType::New(); VotingBinaryIterativeHoleFillingImageFilterType::InputSizeType radius; radius.Fill(1); m_HoleFillingFilter->SetRadius(radius); m_HoleFillingFilter->SetBackgroundValue(0); m_HoleFillingFilter->SetForegroundValue(1); m_HoleFillingFilter->SetMaximumNumberOfIterations(5); //Initialize binary image to shape label map filter m_BinaryImageToShapeLabelMapFilter = BinaryImageToShapeLabelMapFilterType::New(); m_BinaryImageToShapeLabelMapFilter->SetInputForegroundValue(1); } double QmitkUSNavigationStepCtUsRegistration::GetCharacteristicDistanceAWithUpperMargin() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 12.07; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 18.105; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 24.14; } return 0.0; } double QmitkUSNavigationStepCtUsRegistration::GetCharacteristicDistanceBWithLowerMargin() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 12.07; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 18.105; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 24.14; } return 0.0; } double QmitkUSNavigationStepCtUsRegistration::GetCharacteristicDistanceBWithUpperMargin() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 15.73; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 23.595; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 31.46; } return 0.0; } double QmitkUSNavigationStepCtUsRegistration::GetMinimalFiducialConfigurationDistance() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 10.0; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 15.0; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 20.0; } return 0.0; } void QmitkUSNavigationStepCtUsRegistration::CreateMarkerModelCoordinateSystemPointSet() { if (m_MarkerModelCoordinateSystemPointSet.IsNull()) { m_MarkerModelCoordinateSystemPointSet = mitk::PointSet::New(); } else { m_MarkerModelCoordinateSystemPointSet->Clear(); } mitk::Point3D fiducial1; mitk::Point3D fiducial2; mitk::Point3D fiducial3; mitk::Point3D fiducial4; mitk::Point3D fiducial5; mitk::Point3D fiducial6; mitk::Point3D fiducial7; mitk::Point3D fiducial8; switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: fiducial1[0] = 0; fiducial1[1] = 0; fiducial1[2] = 0; fiducial2[0] = 0; fiducial2[1] = 10; fiducial2[2] = 0; fiducial3[0] = 10; fiducial3[1] = 0; fiducial3[2] = 0; fiducial4[0] = 20; fiducial4[1] = 20; fiducial4[2] = 0; fiducial5[0] = 0; fiducial5[1] = 20; fiducial5[2] = 10; fiducial6[0] = 10; fiducial6[1] = 20; fiducial6[2] = 10; fiducial7[0] = 20; fiducial7[1] = 10; fiducial7[2] = 10; fiducial8[0] = 20; fiducial8[1] = 0; fiducial8[2] = 10; break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: fiducial1[0] = 0; fiducial1[1] = 0; fiducial1[2] = 0; fiducial2[0] = 0; fiducial2[1] = 15; fiducial2[2] = 0; fiducial3[0] = 15; fiducial3[1] = 0; fiducial3[2] = 0; fiducial4[0] = 30; fiducial4[1] = 30; fiducial4[2] = 0; fiducial5[0] = 0; fiducial5[1] = 30; fiducial5[2] = 15; fiducial6[0] = 15; fiducial6[1] = 30; fiducial6[2] = 15; fiducial7[0] = 30; fiducial7[1] = 15; fiducial7[2] = 15; fiducial8[0] = 30; fiducial8[1] = 0; fiducial8[2] = 15; break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: fiducial1[0] = 0; fiducial1[1] = 0; fiducial1[2] = 0; fiducial2[0] = 0; fiducial2[1] = 20; fiducial2[2] = 0; fiducial3[0] = 20; fiducial3[1] = 0; fiducial3[2] = 0; fiducial4[0] = 40; fiducial4[1] = 40; fiducial4[2] = 0; fiducial5[0] = 0; fiducial5[1] = 40; fiducial5[2] = 20; fiducial6[0] = 20; fiducial6[1] = 40; fiducial6[2] = 20; fiducial7[0] = 40; fiducial7[1] = 20; fiducial7[2] = 20; fiducial8[0] = 40; fiducial8[1] = 0; fiducial8[2] = 20; break; } m_MarkerModelCoordinateSystemPointSet->InsertPoint(0, fiducial1); m_MarkerModelCoordinateSystemPointSet->InsertPoint(1, fiducial2); m_MarkerModelCoordinateSystemPointSet->InsertPoint(2, fiducial3); m_MarkerModelCoordinateSystemPointSet->InsertPoint(3, fiducial4); m_MarkerModelCoordinateSystemPointSet->InsertPoint(4, fiducial5); m_MarkerModelCoordinateSystemPointSet->InsertPoint(5, fiducial6); m_MarkerModelCoordinateSystemPointSet->InsertPoint(6, fiducial7); m_MarkerModelCoordinateSystemPointSet->InsertPoint(7, fiducial8); /*mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode("Marker Model Coordinate System Point Set"); if (node == nullptr) { node = mitk::DataNode::New(); node->SetName("Marker Model Coordinate System Point Set"); node->SetData(m_MarkerModelCoordinateSystemPointSet); this->GetDataStorage()->Add(node); } else { node->SetData(m_MarkerModelCoordinateSystemPointSet); this->GetDataStorage()->Modified(); }*/ } void QmitkUSNavigationStepCtUsRegistration::InitializePointsToTransformForGroundTruthProtocol() { m_PointsToTransformGroundTruthProtocol.clear(); mitk::Point3D point0mm; mitk::Point3D point20mm; mitk::Point3D point40mm; mitk::Point3D point60mm; mitk::Point3D point80mm; mitk::Point3D point100mm; point0mm[0] = 0.0; point0mm[1] = 0.0; point0mm[2] = 0.0; point20mm[0] = 0.0; point20mm[1] = 0.0; point20mm[2] = 0.0; point40mm[0] = 0.0; point40mm[1] = 0.0; point40mm[2] = 0.0; point60mm[0] = 0.0; point60mm[1] = 0.0; point60mm[2] = 0.0; point80mm[0] = 0.0; point80mm[1] = 0.0; point80mm[2] = 0.0; point100mm[0] = 0.0; point100mm[1] = 0.0; point100mm[2] = 0.0; m_PointsToTransformGroundTruthProtocol.insert(std::pair<int, mitk::Point3D>(0, point0mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair<int, mitk::Point3D>(20, point20mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair<int, mitk::Point3D>(40, point40mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair<int, mitk::Point3D>(60, point60mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair<int, mitk::Point3D>(80, point80mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair<int, mitk::Point3D>(100, point100mm)); } void QmitkUSNavigationStepCtUsRegistration::CreatePointsToTransformForGroundTruthProtocol() { this->InitializePointsToTransformForGroundTruthProtocol(); switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: MITK_WARN << "For this marker configuration (10mm) there does not exist a point to transform."; break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: m_PointsToTransformGroundTruthProtocol.at(0)[0] = 130; // = 30mm to end of clipping plate + 100 mm to middle axis of measurement plate m_PointsToTransformGroundTruthProtocol.at(0)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(0)[2] = -7; // = 5mm distance to clipping plate + 2mm to base m_PointsToTransformGroundTruthProtocol.at(20)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(20)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(20)[2] = -27; // = 5mm distance to clipping plate + 2mm to base + 20mm depth m_PointsToTransformGroundTruthProtocol.at(40)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(40)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(40)[2] = -47; // = 5mm distance to clipping plate + 2mm to base + 40mm depth m_PointsToTransformGroundTruthProtocol.at(60)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(60)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(60)[2] = -67; // = 5mm distance to clipping plate + 2mm to base + 60mm depth m_PointsToTransformGroundTruthProtocol.at(80)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(80)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(80)[2] = -87; // = 5mm distance to clipping plate + 2mm to base + 80mm depth m_PointsToTransformGroundTruthProtocol.at(100)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(100)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(100)[2] = -107; // = 5mm distance to clipping plate + 2mm to base + 100mm depth break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: m_PointsToTransformGroundTruthProtocol.at(0)[0] = 135; // = 20 + 15mm to end of clipping plate + 100 mm to middle axis of measurement plate m_PointsToTransformGroundTruthProtocol.at(0)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(0)[2] = -9; // = 7mm distance to clipping plate + 2mm to base m_PointsToTransformGroundTruthProtocol.at(20)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(20)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(20)[2] = -29; // = 7mm distance to clipping plate + 2mm to base + 20mm depth m_PointsToTransformGroundTruthProtocol.at(40)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(40)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(40)[2] = -49; // = 7mm distance to clipping plate + 2mm to base + 40mm depth m_PointsToTransformGroundTruthProtocol.at(60)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(60)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(60)[2] = -69; // = 7mm distance to clipping plate + 2mm to base + 60mm depth m_PointsToTransformGroundTruthProtocol.at(80)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(80)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(80)[2] = -89; // = 7mm distance to clipping plate + 2mm to base + 80mm depth m_PointsToTransformGroundTruthProtocol.at(100)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(100)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(100)[2] = -109; // = 7mm distance to clipping plate + 2mm to base + 100mm depth break; } } void QmitkUSNavigationStepCtUsRegistration::TransformPointsGroundTruthProtocol() { if (m_GroundTruthProtocolTransformedPoints.find(0) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(0))); m_GroundTruthProtocolTransformedPoints.insert(std::pair<int, mitk::PointSet::Pointer>(0, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(0)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(0))); } if (m_GroundTruthProtocolTransformedPoints.find(20) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(20))); m_GroundTruthProtocolTransformedPoints.insert(std::pair<int, mitk::PointSet::Pointer>(20, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(20)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(20))); } if (m_GroundTruthProtocolTransformedPoints.find(40) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(40))); m_GroundTruthProtocolTransformedPoints.insert(std::pair<int, mitk::PointSet::Pointer>(40, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(40)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(40))); } if (m_GroundTruthProtocolTransformedPoints.find(60) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(60))); m_GroundTruthProtocolTransformedPoints.insert(std::pair<int, mitk::PointSet::Pointer>(60, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(60)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(60))); } if (m_GroundTruthProtocolTransformedPoints.find(80) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(80))); m_GroundTruthProtocolTransformedPoints.insert(std::pair<int, mitk::PointSet::Pointer>(80, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(80)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(80))); } if (m_GroundTruthProtocolTransformedPoints.find(100) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(100))); m_GroundTruthProtocolTransformedPoints.insert(std::pair<int, mitk::PointSet::Pointer>(100, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(100)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(100))); } } void QmitkUSNavigationStepCtUsRegistration::AddTransformedPointsToDataStorage() { if (m_GroundTruthProtocolTransformedPoints.find(0) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(20) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(40) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(60) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(80) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(100) == m_GroundTruthProtocolTransformedPoints.end()) { QMessageBox msgBox; msgBox.setText("Cannot add transformed Points to DataStorage because they do not exist.\ Stopping evaluation the protocol."); msgBox.exec(); return; } std::string nameNode0mm = "GroundTruthProt-Depth0mm"; std::string nameNode20mm = "GroundTruthProt-Depth20mm"; std::string nameNode40mm = "GroundTruthProt-Depth40mm"; std::string nameNode60mm = "GroundTruthProt-Depth60mm"; std::string nameNode80mm = "GroundTruthProt-Depth80mm"; std::string nameNode100mm = "GroundTruthProt-Depth100mm"; //Add transformed points of depth 0mm to the data storage mitk::DataNode::Pointer node0mm = this->GetDataStorage()->GetNamedNode(nameNode0mm); if (node0mm.IsNull()) { node0mm = mitk::DataNode::New(); node0mm->SetName(nameNode0mm); node0mm->SetData(m_GroundTruthProtocolTransformedPoints.at(0)); this->GetDataStorage()->Add(node0mm); } else { node0mm->SetData(m_GroundTruthProtocolTransformedPoints.at(0)); this->GetDataStorage()->Modified(); } if(ui->protocolEvaluationTypeComboBox->currentText().compare("PLANE") == 0 ) { //Add transformed points of depth 20mm to the data storage mitk::DataNode::Pointer node20mm = this->GetDataStorage()->GetNamedNode(nameNode20mm); if (node20mm.IsNull()) { node20mm = mitk::DataNode::New(); node20mm->SetName(nameNode20mm); node20mm->SetData(m_GroundTruthProtocolTransformedPoints.at(20)); this->GetDataStorage()->Add(node20mm); } else { node20mm->SetData(m_GroundTruthProtocolTransformedPoints.at(20)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 40mm to the data storage mitk::DataNode::Pointer node40mm = this->GetDataStorage()->GetNamedNode(nameNode40mm); if (node40mm.IsNull()) { node40mm = mitk::DataNode::New(); node40mm->SetName(nameNode40mm); node40mm->SetData(m_GroundTruthProtocolTransformedPoints.at(40)); this->GetDataStorage()->Add(node40mm); } else { node40mm->SetData(m_GroundTruthProtocolTransformedPoints.at(40)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 60mm to the data storage mitk::DataNode::Pointer node60mm = this->GetDataStorage()->GetNamedNode(nameNode60mm); if (node60mm.IsNull()) { node60mm = mitk::DataNode::New(); node60mm->SetName(nameNode60mm); node60mm->SetData(m_GroundTruthProtocolTransformedPoints.at(60)); this->GetDataStorage()->Add(node60mm); } else { node60mm->SetData(m_GroundTruthProtocolTransformedPoints.at(60)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 80mm to the data storage mitk::DataNode::Pointer node80mm = this->GetDataStorage()->GetNamedNode(nameNode80mm); if (node80mm.IsNull()) { node80mm = mitk::DataNode::New(); node80mm->SetName(nameNode80mm); node80mm->SetData(m_GroundTruthProtocolTransformedPoints.at(80)); this->GetDataStorage()->Add(node80mm); } else { node80mm->SetData(m_GroundTruthProtocolTransformedPoints.at(80)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 100mm to the data storage mitk::DataNode::Pointer node100mm = this->GetDataStorage()->GetNamedNode(nameNode100mm); if (node100mm.IsNull()) { node100mm = mitk::DataNode::New(); node100mm->SetName(nameNode100mm); node100mm->SetData(m_GroundTruthProtocolTransformedPoints.at(100)); this->GetDataStorage()->Add(node100mm); } else { node100mm->SetData(m_GroundTruthProtocolTransformedPoints.at(100)); this->GetDataStorage()->Modified(); } } //Do a global reinit mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); } double QmitkUSNavigationStepCtUsRegistration::CalculateMeanFRE() { double meanFRE = 0.0; for (unsigned int counter = 0; counter < m_GroundTruthProtocolFRE.size(); ++counter) { meanFRE += m_GroundTruthProtocolFRE[counter]; } return meanFRE / m_GroundTruthProtocolFRE.size(); } double QmitkUSNavigationStepCtUsRegistration::CalculateStandardDeviationOfFRE(double meanFRE) { double variance = 0.0; for (unsigned int counter = 0; counter < m_GroundTruthProtocolFRE.size(); ++counter) { variance += ((meanFRE - m_GroundTruthProtocolFRE[counter]) * (meanFRE - m_GroundTruthProtocolFRE[counter])); } variance /= m_GroundTruthProtocolFRE.size(); // calculate the empirical variance (n) and not the sampling variance (n-1) return sqrt(variance); } void QmitkUSNavigationStepCtUsRegistration::CalculateGroundTruthProtocolTRE() { if (m_GroundTruthProtocolTransformedPoints.find(0) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(20) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(40) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(60) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(80) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(100) == m_GroundTruthProtocolTransformedPoints.end()) { QMessageBox msgBox; msgBox.setText("Cannot calculate TRE of Ground-Truth-Protocol because points were not transformed."); msgBox.exec(); return; } // clear the std::map containing possibly data of earlier TRE calculations m_GroundTruthProtocolTRE.clear(); // loop through all existing point sets containing the transformed points for (int counter = 0; m_GroundTruthProtocolTransformedPoints.find(counter) != m_GroundTruthProtocolTransformedPoints.end(); counter += 20) { //calculate the middle point of the point set mitk::PointSet::Pointer pointSet = m_GroundTruthProtocolTransformedPoints.at(counter); mitk::Point3D middlePoint; middlePoint[0] = 0.0; middlePoint[1] = 0.0; middlePoint[2] = 0.0; for (int position = 0; position < pointSet->GetSize(); ++position) { middlePoint[0] += pointSet->GetPoint(position)[0]; middlePoint[1] += pointSet->GetPoint(position)[1]; middlePoint[2] += pointSet->GetPoint(position)[2]; } middlePoint[0] /= pointSet->GetSize(); middlePoint[1] /= pointSet->GetSize(); middlePoint[2] /= pointSet->GetSize(); MITK_INFO << "Calculated MiddlePoint: " << middlePoint; //sum up the euclidean distances between the middle point and each transformed point double meanDistance = 0.0; for (int position = 0; position < pointSet->GetSize(); ++position) { meanDistance += middlePoint.SquaredEuclideanDistanceTo(pointSet->GetPoint(position)); MITK_INFO << "SquaredEuclideanDistance: " << middlePoint.SquaredEuclideanDistanceTo(pointSet->GetPoint(position)); } meanDistance /= pointSet->GetSize(); // this can be interpreted as empirical variance // the root of the empirical variance can be interpreted as the protocols registration TRE m_GroundTruthProtocolTRE.insert(std::pair<int, double>(counter, sqrt(meanDistance))); MITK_INFO << "Ground-Truth-Protocol TRE: " << sqrt(meanDistance); } } void QmitkUSNavigationStepCtUsRegistration::EliminateTooSmallLabeledObjects( ImageType::Pointer binaryImage) { BinaryImageToShapeLabelMapFilterType::OutputImageType::Pointer labelMap = m_BinaryImageToShapeLabelMapFilter->GetOutput(); double voxelVolume = this->GetVoxelVolume(); double fiducialVolume; unsigned int numberOfPixels; if (ui->fiducialDiameter3mmRadioButton->isChecked()) { fiducialVolume = this->GetFiducialVolume(1.5); numberOfPixels = ceil(fiducialVolume / voxelVolume); } else { fiducialVolume = this->GetFiducialVolume(2.5); numberOfPixels = ceil(fiducialVolume / voxelVolume); } MITK_INFO << "Voxel Volume = " << voxelVolume << "; Fiducial Volume = " << fiducialVolume; MITK_INFO << "Number of pixels = " << numberOfPixels; labelMap = m_BinaryImageToShapeLabelMapFilter->GetOutput(); // The output of this filter is an itk::LabelMap, which contains itk::LabelObject's MITK_INFO << "There are " << labelMap->GetNumberOfLabelObjects() << " objects."; // Loop over each region for (int i = labelMap->GetNumberOfLabelObjects() - 1; i >= 0; --i) { // Get the ith region BinaryImageToShapeLabelMapFilterType::OutputImageType::LabelObjectType* labelObject = labelMap->GetNthLabelObject(i); MITK_INFO << "Object " <Size() << " pixel"; //TODO: Threshold-Wert evtl. experimentell besser abstimmen, // um zu verhindern, dass durch Threshold wahre Fiducial-Kandidaten elimiert werden. if (labelObject->Size() < numberOfPixels * 0.8) { for (unsigned int pixelId = 0; pixelId < labelObject->Size(); pixelId++) { binaryImage->SetPixel(labelObject->GetIndex(pixelId), 0); } labelMap->RemoveLabelObject(labelObject); } } } bool QmitkUSNavigationStepCtUsRegistration::EliminateFiducialCandidatesByEuclideanDistances() { if (m_CentroidsOfFiducialCandidates.size() < NUMBER_FIDUCIALS_NEEDED) { return false; } for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { int amountOfAcceptedFiducials = 0; mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); //Loop through all fiducial candidates and calculate the distance between the chosen fiducial // candidate and the other candidates. For each candidate with a right distance between // Configuration A: 7.93mm and 31.0mm (10 mm distance between fiducial centers) or // Configuration B: 11.895mm and 45.0mm (15 mm distance between fiducial centers) or // Configuration C: 15.86mm and 59.0mm (20 mm distance between fiducial centers) // // increase the amountOfAcceptedFiducials. for (unsigned int position = 0; position < m_CentroidsOfFiducialCandidates.size(); ++position) { if (position == counter) { continue; } mitk::Point3D otherCentroid(m_CentroidsOfFiducialCandidates.at(position)); double distance = fiducialCentroid.EuclideanDistanceTo(otherCentroid); switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: if (distance > 7.93 && distance < 31.0) { ++amountOfAcceptedFiducials; } break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: if (distance > 11.895 && distance < 45.0) { ++amountOfAcceptedFiducials; } break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: if (distance > 15.86 && distance < 59.0) { ++amountOfAcceptedFiducials; } break; } } //The amountOfAcceptedFiducials must be at least 7. Otherwise delete the fiducial candidate // from the list of candidates. if (amountOfAcceptedFiducials < NUMBER_FIDUCIALS_NEEDED - 1) { MITK_INFO << "Deleting fiducial candidate at position: " << m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); if (m_CentroidsOfFiducialCandidates.size() < NUMBER_FIDUCIALS_NEEDED ) { return false; } counter = -1; } } //Classify the rested fiducial candidates by its characteristic Euclidean distances - // between the canidates and remove all candidates with a false distance configuration: + // between the candidates and remove all candidates with a false distance configuration: this->ClassifyFiducialCandidates(); return true; } void QmitkUSNavigationStepCtUsRegistration::ClassifyFiducialCandidates() { MITK_INFO << "ClassifyFiducialCandidates()"; std::vector<int> fiducialCandidatesToBeRemoved; std::vector<std::vector<double>> distanceVectorsFiducials; this->CalculateDistancesBetweenFiducials(distanceVectorsFiducials); for (unsigned int counter = 0; counter < distanceVectorsFiducials.size(); ++counter) { int distanceA = 0; // => 10,00mm distance int distanceB = 0; // => 14,14mm distance int distanceC = 0; // => 17,32mm distance int distanceD = 0; // => 22,36mm distance int distanceE = 0; // => 24,49mm distance int distanceF = 0; // => 28,28mm distance std::vector<double> &distances = distanceVectorsFiducials.at(counter); for (unsigned int number = 0; number < distances.size(); ++number) { double &distance = distances.at(number); switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: if (distance > 7.93 && distance <= 12.07) { ++distanceA; } else if (distance > 12.07 && distance <= 15.73) { ++distanceB; } else if (distance > 15.73 && distance <= 19.84) { ++distanceC; } else if (distance > 19.84 && distance <= 23.425) { ++distanceD; } else if (distance > 23.425 && distance <= 26.385) { ++distanceE; } else if (distance > 26.385 && distance <= 31.00) { ++distanceF; } break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: if (distance > 11.895 && distance <= 18.105) { ++distanceA; } else if (distance > 18.105 && distance <= 23.595) { ++distanceB; } else if (distance > 23.595 && distance <= 29.76) { ++distanceC; } else if (distance > 29.76 && distance <= 35.1375) { ++distanceD; if (distance > 33.54) { ++distanceE; } } else if (distance > 35.1375 && distance <= 39.5775) { ++distanceE; if (distance < 36.735) { ++distanceD; } } else if (distance > 39.5775 && distance <= 45.00) { ++distanceF; } break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: if (distance > 15.86 && distance <= 24.14) { ++distanceA; } else if (distance > 24.14 && distance <= 31.46) { ++distanceB; } else if (distance > 31.46 && distance <= 39.68) { ++distanceC; } else if (distance > 39.68 && distance <= 46.85) { ++distanceD; } else if (distance > 46.85 && distance <= 52.77) { ++distanceE; } else if (distance > 52.77 && distance <= 59.00) { ++distanceF; } break; } }// End for-loop distances-vector //Now, having looped through all distances of one fiducial candidate, check // if the combination of different distances is known. The >= is due to the // possible occurrence of other fiducial candidates that have an distance equal to // one of the distances A - E. However, false fiducial candidates outside // the fiducial marker does not have the right distance configuration: if (((distanceA >= 2 && distanceD >= 2 && distanceE >= 2 && distanceF >= 1) || (distanceA >= 1 && distanceB >= 2 && distanceC >= 1 && distanceD >= 2 && distanceE >= 1) || (distanceB >= 2 && distanceD >= 4 && distanceF >= 1) || (distanceA >= 1 && distanceB >= 1 && distanceD >= 3 && distanceE >= 1 && distanceF >= 1)) == false) { MITK_INFO << "Detected fiducial candidate with unknown distance configuration."; fiducialCandidatesToBeRemoved.push_back(counter); } } for (int count = fiducialCandidatesToBeRemoved.size() - 1; count >= 0; --count) { MITK_INFO << "Removing fiducial candidate " << fiducialCandidatesToBeRemoved.at(count); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + fiducialCandidatesToBeRemoved.at(count)); } } void QmitkUSNavigationStepCtUsRegistration::GetCentroidsOfLabeledObjects() { MITK_INFO << "GetCentroidsOfLabeledObjects()"; BinaryImageToShapeLabelMapFilterType::OutputImageType::Pointer labelMap = m_BinaryImageToShapeLabelMapFilter->GetOutput(); for (int i = labelMap->GetNumberOfLabelObjects() - 1; i >= 0; --i) { // Get the ith region BinaryImageToShapeLabelMapFilterType::OutputImageType::LabelObjectType* labelObject = labelMap->GetNthLabelObject(i); MITK_INFO << "Object " <Size() << " pixel"; mitk::Vector3D centroid; centroid[0] = labelObject->GetCentroid()[0]; centroid[1] = labelObject->GetCentroid()[1]; centroid[2] = labelObject->GetCentroid()[2]; m_CentroidsOfFiducialCandidates.push_back(centroid); } //evtl. for later: itk::LabelMapOverlayImageFilter } void QmitkUSNavigationStepCtUsRegistration::NumerateFiducialMarks() { MITK_INFO << "NumerateFiducialMarks()"; bool successFiducialNo1; bool successFiducialNo4; bool successFiducialNo2And3; bool successFiducialNo5; bool successFiducialNo8; bool successFiducialNo6; bool successFiducialNo7; std::vector<std::vector<double>> distanceVectorsFiducials; this->CalculateDistancesBetweenFiducials(distanceVectorsFiducials); successFiducialNo1 = this->FindFiducialNo1(distanceVectorsFiducials); successFiducialNo4 = this->FindFiducialNo4(distanceVectorsFiducials); successFiducialNo2And3 = this->FindFiducialNo2And3(); successFiducialNo5 = this->FindFiducialNo5(); successFiducialNo8 = this->FindFiducialNo8(); successFiducialNo6 = this->FindFiducialNo6(); successFiducialNo7 = this->FindFiducialNo7(); if (!successFiducialNo1 || !successFiducialNo4 || !successFiducialNo2And3 || !successFiducialNo5 || !successFiducialNo8 || !successFiducialNo6 || !successFiducialNo7) { QMessageBox msgBox; msgBox.setText("Cannot numerate/localize all fiducials successfully."); msgBox.exec(); return; } if (m_MarkerFloatingImageCoordinateSystemPointSet.IsNull()) { m_MarkerFloatingImageCoordinateSystemPointSet = mitk::PointSet::New(); } else if (m_MarkerFloatingImageCoordinateSystemPointSet->GetSize() != 0) { m_MarkerFloatingImageCoordinateSystemPointSet->Clear(); } for (unsigned int counter = 1; counter <= m_FiducialMarkerCentroids.size(); ++counter) { m_MarkerFloatingImageCoordinateSystemPointSet->InsertPoint(counter - 1, mitk::Point3D(m_FiducialMarkerCentroids.at(counter))); } if( !m_PerformingGroundTruthProtocolEvaluation ) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_MarkerFloatingImageCoordinateSystemPointSet); node->SetName("MarkerFloatingImageCSPointSet"); //node->SetFloatProperty("pointsize", 5.0); this->GetDataStorage()->Add(node); } } void QmitkUSNavigationStepCtUsRegistration::CalculateDistancesBetweenFiducials(std::vector<std::vector<double>>& distanceVectorsFiducials) { std::vector<double> distancesBetweenFiducials; for (unsigned int i = 0; i < m_CentroidsOfFiducialCandidates.size(); ++i) { distancesBetweenFiducials.clear(); mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(i)); for (unsigned int n = 0; n < m_CentroidsOfFiducialCandidates.size(); ++n) { mitk::Point3D otherCentroid(m_CentroidsOfFiducialCandidates.at(n)); distancesBetweenFiducials.push_back(fiducialCentroid.EuclideanDistanceTo(otherCentroid)); } //Sort the distances from low to big numbers std::sort(distancesBetweenFiducials.begin(), distancesBetweenFiducials.end()); //First entry of the distance vector must be 0, so erase it if (distancesBetweenFiducials.at(0) == 0.0) { distancesBetweenFiducials.erase(distancesBetweenFiducials.begin()); } //Add the distance vector to the collecting distances vector distanceVectorsFiducials.push_back(distancesBetweenFiducials); } for (unsigned int i = 0; i < distanceVectorsFiducials.size(); ++i) { MITK_INFO << "Vector " << i << ":"; for (unsigned int k = 0; k < distanceVectorsFiducials.at(i).size(); ++k) { MITK_INFO << distanceVectorsFiducials.at(i).at(k); } } } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo1(std::vector<std::vector<double>>& distanceVectorsFiducials) { for (unsigned int i = 0; i < distanceVectorsFiducials.size(); ++i) { std::vector<double> &distances = distanceVectorsFiducials.at(i); if (distances.size() < NUMBER_FIDUCIALS_NEEDED - 1 ) { MITK_WARN << "Cannot find fiducial 1, there aren't found enough fiducial candidates."; return false; } double characteristicDistanceAWithUpperMargin = this->GetCharacteristicDistanceAWithUpperMargin(); if (distances.at(0) <= characteristicDistanceAWithUpperMargin && distances.at(1) <= characteristicDistanceAWithUpperMargin) { MITK_INFO << "Found Fiducial 1 (PointSet number " <(1, m_CentroidsOfFiducialCandidates.at(i))); distanceVectorsFiducials.erase(distanceVectorsFiducials.begin() + i); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); return true; } } return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo2And3() { if (m_FiducialMarkerCentroids.find(1) == m_FiducialMarkerCentroids.end() ) { MITK_WARN << "Cannot find fiducial No 2 and 3. Before must be found fiducial No 1."; return false; } mitk::Point3D fiducialNo1(m_FiducialMarkerCentroids.at(1)); mitk::Vector3D fiducialVectorA; mitk::Vector3D fiducialVectorB; mitk::Point3D fiducialPointA; mitk::Point3D fiducialPointB; bool foundFiducialA = false; bool foundFiducialB = false; mitk::Vector3D vectorFiducial1ToFiducialA; mitk::Vector3D vectorFiducial1ToFiducialB; for (unsigned int i = 0; i < m_CentroidsOfFiducialCandidates.size(); ++i) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(i)); double distance = fiducialNo1.EuclideanDistanceTo(fiducialCentroid); if (distance <= this->GetCharacteristicDistanceAWithUpperMargin()) { fiducialVectorA = m_CentroidsOfFiducialCandidates.at(i); fiducialPointA = fiducialCentroid; m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); foundFiducialA = true; break; } } for (unsigned int i = 0; i < m_CentroidsOfFiducialCandidates.size(); ++i) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(i)); double distance = fiducialNo1.EuclideanDistanceTo(fiducialCentroid); if (distance <= this->GetCharacteristicDistanceAWithUpperMargin()) { fiducialVectorB = m_CentroidsOfFiducialCandidates.at(i); fiducialPointB = fiducialCentroid; m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); foundFiducialB = true; break; } } if (!foundFiducialA || !foundFiducialB) { MITK_WARN << "Cannot identify fiducial candidates 2 and 3"; return false; } else if (m_CentroidsOfFiducialCandidates.size() == 0) { MITK_WARN << "Too less fiducials detected. Cannot identify fiducial candidates 2 and 3"; return false; } vectorFiducial1ToFiducialA = fiducialVectorA - m_FiducialMarkerCentroids.at(1); vectorFiducial1ToFiducialB = fiducialVectorB - m_FiducialMarkerCentroids.at(1); vnl_vector<double> crossProductVnl = vnl_cross_3d(vectorFiducial1ToFiducialA.GetVnlVector(), vectorFiducial1ToFiducialB.GetVnlVector()); mitk::Vector3D crossProduct; crossProduct.SetVnlVector(crossProductVnl); mitk::Vector3D vectorFiducial1ToRandomLeftFiducial = m_CentroidsOfFiducialCandidates.at(0) - m_FiducialMarkerCentroids.at(1); double scalarProduct = (crossProduct * vectorFiducial1ToRandomLeftFiducial) / (crossProduct.GetNorm() * vectorFiducial1ToRandomLeftFiducial.GetNorm()); double alpha = acos(scalarProduct) * 57.29578; //Transform into degree MITK_INFO << "Scalar Product = " << alpha; if (alpha <= 90) { m_FiducialMarkerCentroids[3] = fiducialVectorA; m_FiducialMarkerCentroids[2] = fiducialVectorB; } else { m_FiducialMarkerCentroids[2] = fiducialVectorA; m_FiducialMarkerCentroids[3] = fiducialVectorB; } MITK_INFO << "Found Fiducial 2, PointSet: " << m_FiducialMarkerCentroids.at(2); MITK_INFO << "Found Fiducial 3, PointSet: " << m_FiducialMarkerCentroids.at(3); return true; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo4(std::vector<std::vector<double>>& distanceVectorsFiducials) { double characteristicDistanceBWithLowerMargin = this->GetCharacteristicDistanceBWithLowerMargin(); double characteristicDistanceBWithUpperMargin = this->GetCharacteristicDistanceBWithUpperMargin(); for (unsigned int i = 0; i < distanceVectorsFiducials.size(); ++i) { std::vector<double> &distances = distanceVectorsFiducials.at(i); if (distances.size() < NUMBER_FIDUCIALS_NEEDED - 1) { MITK_WARN << "Cannot find fiducial 4, there aren't found enough fiducial candidates."; return false; } if (distances.at(0) > characteristicDistanceBWithLowerMargin && distances.at(0) <= characteristicDistanceBWithUpperMargin && distances.at(1) > characteristicDistanceBWithLowerMargin && distances.at(1) <= characteristicDistanceBWithUpperMargin) { MITK_INFO << "Found Fiducial 4 (PointSet number " <(4, m_CentroidsOfFiducialCandidates.at(i))); distanceVectorsFiducials.erase(distanceVectorsFiducials.begin() + i); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); return true; } } return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo5() { if (m_FiducialMarkerCentroids.find(2) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 5, fiducial No 2 has to be found before."; return false; } double characteristicDistanceBWithUpperMargin = this->GetCharacteristicDistanceBWithUpperMargin(); mitk::Point3D fiducialNo2(m_FiducialMarkerCentroids.at(2)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo2.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceBWithUpperMargin) { m_FiducialMarkerCentroids[5] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 5, PointSet: " << m_FiducialMarkerCentroids[5]; return true; } } MITK_WARN << "Cannot find fiducial No 5."; return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo6() { if (m_FiducialMarkerCentroids.find(5) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 6, fiducial No 5 has to be found before."; return false; } double characteristicDistanceAWithUpperMargin = this->GetCharacteristicDistanceAWithUpperMargin(); mitk::Point3D fiducialNo5(m_FiducialMarkerCentroids.at(5)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo5.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceAWithUpperMargin) { m_FiducialMarkerCentroids[6] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 6, PointSet: " << m_FiducialMarkerCentroids[6]; return true; } } MITK_WARN << "Cannot find fiducial No 6."; return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo7() { if (m_FiducialMarkerCentroids.find(8) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 7, fiducial No 8 has to be found before."; return false; } double characteristicDistanceAWithUpperMargin = this->GetCharacteristicDistanceAWithUpperMargin(); mitk::Point3D fiducialNo8(m_FiducialMarkerCentroids.at(8)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo8.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceAWithUpperMargin) { m_FiducialMarkerCentroids[7] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 7, PointSet: " << m_FiducialMarkerCentroids[7]; return true; } } MITK_WARN << "Cannot find fiducial No 7."; return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo8() { if (m_FiducialMarkerCentroids.find(3) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 8, fiducial No 3 has to be found before."; return false; } double characteristicDistanceBWithUpperMargin = this->GetCharacteristicDistanceBWithUpperMargin(); mitk::Point3D fiducialNo3(m_FiducialMarkerCentroids.at(3)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo3.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceBWithUpperMargin) { m_FiducialMarkerCentroids[8] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 8, PointSet: " << m_FiducialMarkerCentroids[8]; return true; } } MITK_WARN << "Cannot find fiducial No 8."; return false; } void QmitkUSNavigationStepCtUsRegistration::DefineDataStorageImageFilter() { m_IsAPointSetPredicate = mitk::TNodePredicateDataType<mitk::PointSet>::New(); mitk::TNodePredicateDataType<mitk::Image>::Pointer isImage = mitk::TNodePredicateDataType<mitk::Image>::New(); auto isSegmentation = mitk::NodePredicateDataType::New("Segment"); m_IsASurfacePredicate = mitk::NodePredicateDataType::New("Surface"); mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegmentation))); mitk::NodePredicateNot::Pointer isNotAHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); m_IsOfTypeImagePredicate = mitk::NodePredicateAnd::New(validImages, isNotAHelperObject); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New(isBinaryPredicate); mitk::NodePredicateAnd::Pointer isABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isBinaryPredicate); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isNotBinaryPredicate); m_IsASegmentationImagePredicate = mitk::NodePredicateOr::New(isABinaryImagePredicate, mitk::TNodePredicateDataType<mitk::LabelSetImage>::New()); m_IsAPatientImagePredicate = mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, mitk::NodePredicateNot::New(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New())); } void QmitkUSNavigationStepCtUsRegistration::CreateQtPartControl(QWidget *parent) { ui->setupUi(parent); ui->floatingImageComboBox->SetPredicate(m_IsAPatientImagePredicate); ui->ctImagesToChooseComboBox->SetPredicate(m_IsAPatientImagePredicate); ui->segmentationComboBox->SetPredicate(m_IsASegmentationImagePredicate); ui->selectedSurfaceComboBox->SetPredicate(m_IsASurfacePredicate); ui->pointSetComboBox->SetPredicate(m_IsAPointSetPredicate); // create signal/slot connections connect(ui->floatingImageComboBox, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnFloatingImageComboBoxSelectionChanged(const mitk::DataNode*))); connect(ui->doRegistrationMarkerToImagePushButton, SIGNAL(clicked()), this, SLOT(OnRegisterMarkerToFloatingImageCS())); connect(ui->localizeFiducialMarkerPushButton, SIGNAL(clicked()), this, SLOT(OnLocalizeFiducials())); connect(ui->visualizeCTtoUSregistrationPushButton, SIGNAL(clicked()), this, SLOT(OnVisualizeCTtoUSregistration())); connect(ui->freezeUnfreezePushButton, SIGNAL(clicked()), this, SLOT(OnFreeze())); connect(ui->addCtImagePushButton, SIGNAL(clicked()), this, SLOT(OnAddCtImageClicked())); connect(ui->removeCtImagePushButton, SIGNAL(clicked()), this, SLOT(OnRemoveCtImageClicked())); connect(ui->evaluateProtocolPushButton, SIGNAL(clicked()), this, SLOT(OnEvaluateGroundTruthFiducialLocalizationProtocol())); connect(ui->actualizeSegmentationSurfacePSetDataPushButton, SIGNAL(clicked()), this, SLOT(OnActualizeSegmentationSurfacePointSetData())); connect(ui->calculateTREPushButton, SIGNAL(clicked()), this, SLOT(OnGetCursorPosition())); connect(ui->calculateCenterPushButton, SIGNAL(clicked()), this, SLOT(OnCalculateCenter())); } void QmitkUSNavigationStepCtUsRegistration::OnFloatingImageComboBoxSelectionChanged(const mitk::DataNode* node) { MITK_INFO << "OnFloatingImageComboBoxSelectionChanged()"; if (m_FloatingImage.IsNotNull()) { //TODO: Define, what will happen if the imageCT is not null... } if (node == nullptr) { this->UnsetFloatingImageGeometry(); m_FloatingImage = nullptr; return; } mitk::DataNode* selectedFloatingImage = ui->floatingImageComboBox->GetSelectedNode(); if (selectedFloatingImage == nullptr) { this->UnsetFloatingImageGeometry(); m_FloatingImage = nullptr; return; } mitk::Image::Pointer floatingImage = dynamic_cast<mitk::Image*>(selectedFloatingImage->GetData()); if (floatingImage.IsNull()) { MITK_WARN << "Failed to cast selected segmentation node to mitk::Image*"; this->UnsetFloatingImageGeometry(); m_FloatingImage = nullptr; return; } m_FloatingImage = floatingImage; this->SetFloatingImageGeometryInformation(floatingImage.GetPointer()); } void QmitkUSNavigationStepCtUsRegistration::OnRegisterMarkerToFloatingImageCS() { this->CreateMarkerModelCoordinateSystemPointSet(); //Check for initialization if( m_MarkerModelCoordinateSystemPointSet.IsNull() || m_MarkerFloatingImageCoordinateSystemPointSet.IsNull() ) { MITK_WARN << "Fiducial Landmarks are not initialized yet, cannot register"; return; } //Retrieve fiducials if (m_MarkerFloatingImageCoordinateSystemPointSet->GetSize() != m_MarkerModelCoordinateSystemPointSet->GetSize()) { MITK_WARN << "Not the same number of fiducials, cannot register"; return; } else if (m_MarkerFloatingImageCoordinateSystemPointSet->GetSize() < 3) { MITK_WARN << "Need at least 3 fiducials, cannot register"; return; } //############### conversion to vtk data types (we will use the vtk landmark based transform) ########################## //convert point sets to vtk poly data vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New(); vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New(); for (int i = 0; i<m_MarkerModelCoordinateSystemPointSet->GetSize(); i++) { double point[3] = { m_MarkerModelCoordinateSystemPointSet->GetPoint(i)[0], m_MarkerModelCoordinateSystemPointSet->GetPoint(i)[1], m_MarkerModelCoordinateSystemPointSet->GetPoint(i)[2] }; sourcePoints->InsertNextPoint(point); double point_targets[3] = { m_MarkerFloatingImageCoordinateSystemPointSet->GetPoint(i)[0], m_MarkerFloatingImageCoordinateSystemPointSet->GetPoint(i)[1], m_MarkerFloatingImageCoordinateSystemPointSet->GetPoint(i)[2] }; targetPoints->InsertNextPoint(point_targets); } //########################### here, the actual transform is computed ########################## //compute transform vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); //compute FRE of transform double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(m_MarkerModelCoordinateSystemPointSet, m_MarkerFloatingImageCoordinateSystemPointSet, transform); MITK_INFO << "FRE: " << FRE << " mm"; if (m_PerformingGroundTruthProtocolEvaluation) { m_GroundTruthProtocolFRE.push_back(FRE); } //############################################################################################# //############### conversion back to itk/mitk data types ########################## //convert from vtk to itk data types itk::Matrix<float, 3, 3> rotationFloat = itk::Matrix<float, 3, 3>(); itk::Vector<float, 3> translationFloat = itk::Vector<float, 3>(); itk::Matrix<double, 3, 3> rotationDouble = itk::Matrix<double, 3, 3>(); itk::Vector<double, 3> translationDouble = itk::Vector<double, 3>(); vtkSmartPointer<vtkMatrix4x4> m = transform->GetMatrix(); for (int k = 0; k<3; k++) for (int l = 0; l<3; l++) { rotationFloat[k][l] = m->GetElement(k, l); rotationDouble[k][l] = m->GetElement(k, l); } for (int k = 0; k<3; k++) { translationFloat[k] = m->GetElement(k, 3); translationDouble[k] = m->GetElement(k, 3); } //create mitk affine transform 3D and save it to the class member m_TransformMarkerCSToFloatingImageCS = mitk::AffineTransform3D::New(); m_TransformMarkerCSToFloatingImageCS->SetMatrix(rotationDouble); m_TransformMarkerCSToFloatingImageCS->SetOffset(translationDouble); MITK_INFO << m_TransformMarkerCSToFloatingImageCS; //################################################################ //############### object is transformed ########################## //transform surface/image //only move image if we have one. Sometimes, this widget is used just to register point sets without images. /*if (m_ImageNode.IsNotNull()) { //first we have to store the original ct image transform to compose it with the new transform later mitk::AffineTransform3D::Pointer imageTransform = m_ImageNode->GetData()->GetGeometry()->GetIndexToWorldTransform(); imageTransform->Compose(mitkTransform); mitk::AffineTransform3D::Pointer newImageTransform = mitk::AffineTransform3D::New(); //create new image transform... setting the composed directly leads to an error itk::Matrix<mitk::ScalarType, 3, 3> rotationFloatNew = imageTransform->GetMatrix(); itk::Vector<mitk::ScalarType, 3> translationFloatNew = imageTransform->GetOffset(); newImageTransform->SetMatrix(rotationFloatNew); newImageTransform->SetOffset(translationFloatNew); m_ImageNode->GetData()->GetGeometry()->SetIndexToWorldTransform(newImageTransform); }*/ - //If this option is set, each point will be transformed and the acutal coordinates of the points change. + //If this option is set, each point will be transformed and the actual coordinates of the points change. if( !m_PerformingGroundTruthProtocolEvaluation ) { mitk::PointSet* pointSet_orig = m_MarkerModelCoordinateSystemPointSet; mitk::PointSet::Pointer pointSet_moved = mitk::PointSet::New(); for (int i = 0; i < pointSet_orig->GetSize(); i++) { pointSet_moved->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(pointSet_orig->GetPoint(i))); } pointSet_orig->Clear(); for (int i = 0; i < pointSet_moved->GetSize(); i++) pointSet_orig->InsertPoint(pointSet_moved->GetPoint(i)); //Do a global reinit mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); } } void QmitkUSNavigationStepCtUsRegistration::OnLocalizeFiducials() { m_FiducialMarkerCentroids.clear(); m_CentroidsOfFiducialCandidates.clear(); if (m_MarkerFloatingImageCoordinateSystemPointSet.IsNotNull()) { m_MarkerFloatingImageCoordinateSystemPointSet->Clear(); } if (!this->FilterFloatingImage()) { QMessageBox msgBox; msgBox.setText("Cannot perform filtering of the image. The floating image = nullptr."); msgBox.exec(); return; } mitk::AffineTransform3D::Pointer transform = m_FloatingImage->GetGeometry()->GetIndexToWorldTransform(); MITK_WARN << "IndexToWorldTransform_CTimage = " << transform; this->GetCentroidsOfLabeledObjects(); if (!this->EliminateFiducialCandidatesByEuclideanDistances() || m_CentroidsOfFiducialCandidates.size() != NUMBER_FIDUCIALS_NEEDED) { QMessageBox msgBox; QString text = QString("Have found %1 instead of 8 fiducial candidates.\ Cannot perform fiducial localization procedure.").arg(m_CentroidsOfFiducialCandidates.size()); msgBox.setText(text); msgBox.exec(); return; } //Before calling NumerateFiducialMarks it must be sure, // that there rested only 8 fiducial candidates. this->NumerateFiducialMarks(); } void QmitkUSNavigationStepCtUsRegistration::OnVisualizeCTtoUSregistration() { emit this->ActualizeCtToUsRegistrationWidget(); mitk::DataNode* segmentationNode = ui->segmentationComboBox->GetSelectedNode(); if (segmentationNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration. There is no segmentation selected."); msgBox.exec(); return; } mitk::AffineTransform3D::Pointer transform = segmentationNode->GetData()->GetGeometry()->GetIndexToWorldTransform(); MITK_WARN << "IndexToWorldTransform_segmentation = " << transform; mitk::DataNode* surfaceNode = ui->selectedSurfaceComboBox->GetSelectedNode(); if (surfaceNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration. There is no surface selected."); msgBox.exec(); return; } mitk::DataNode* pointSetNode = ui->pointSetComboBox->GetSelectedNode(); if (pointSetNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration. There is no pointSet selected."); msgBox.exec(); return; } if (this->GetCombinedModality(false).IsNull()) { QMessageBox msgBox; msgBox.setText("CombinedModality not yet set.\nPlease try again and click on the button."); msgBox.exec(); return; } if (m_FloatingImageToUltrasoundRegistrationFilter.IsNull()) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration.\ The FloatingImageToUltrasoundRegistrationFilter is not initialized."); msgBox.exec(); return; } //Set the transformation from marker-CS to the sensor-CS accordingly to the chosen user-option m_FloatingImageToUltrasoundRegistrationFilter ->InitializeTransformationMarkerCSToSensorCS(ui->useNdiTrackerCheckBox->isChecked()); m_FloatingImageToUltrasoundRegistrationFilter->SetPointSet(pointSetNode); m_FloatingImageToUltrasoundRegistrationFilter->SetSegmentation(segmentationNode, m_FloatingImage); m_FloatingImageToUltrasoundRegistrationFilter->SetSurface(surfaceNode); m_FloatingImageToUltrasoundRegistrationFilter ->SetTransformMarkerCSToFloatingImageCS(m_TransformMarkerCSToFloatingImageCS); m_FloatingImageToUltrasoundRegistrationFilter ->SetTransformUSimageCSToTrackingCS(this->GetCombinedModality()->GetCalibration()); m_FloatingImageToUltrasoundRegistrationFilter ->ConnectTo(this->GetCombinedModality()->GetNavigationDataSource()); } void QmitkUSNavigationStepCtUsRegistration::OnFreeze() { if (this->GetCombinedModality(false).IsNull()) { return; } if (!m_FreezeCombinedModality) { m_FreezeCombinedModality = true; ui->freezeUnfreezePushButton->setText("Unfreeze"); this->GetCombinedModality()->SetIsFreezed(true); } else { m_FreezeCombinedModality = false; ui->freezeUnfreezePushButton->setText("Freeze"); this->GetCombinedModality()->SetIsFreezed(false); } } void QmitkUSNavigationStepCtUsRegistration::OnActualizeSegmentationSurfacePointSetData() { mitk::DataNode* segmentationNode = ui->segmentationComboBox->GetSelectedNode(); if (segmentationNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot actualize segmentation + surface + pointset data. There is no segmentation selected."); msgBox.exec(); return; } mitk::DataNode* surfaceNode = ui->selectedSurfaceComboBox->GetSelectedNode(); if (surfaceNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot actualize segmentation + surface + pointset data. There is no surface selected."); msgBox.exec(); return; } mitk::DataNode* pointSetNode = ui->pointSetComboBox->GetSelectedNode(); if (pointSetNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot actualize segmentation + surface + pointset data. There is no pointSet selected."); msgBox.exec(); return; } m_FloatingImageToUltrasoundRegistrationFilter->SetPointSet(pointSetNode); m_FloatingImageToUltrasoundRegistrationFilter->SetSegmentation(segmentationNode, m_FloatingImage); m_FloatingImageToUltrasoundRegistrationFilter->SetSurface(surfaceNode); } void QmitkUSNavigationStepCtUsRegistration::OnGetCursorPosition() { emit GetCursorPosition(); } void QmitkUSNavigationStepCtUsRegistration::OnCalculateTRE(mitk::Point3D centroidOfTargetInUSImage) { mitk::DataNode::Pointer pointSetNode = ui->pointSetComboBox->GetSelectedNode(); if (pointSetNode.IsNull()) { QMessageBox msgBox; msgBox.setText("Cannot calculate TRE. The pointSetComboBox node returned a nullptr."); msgBox.exec(); return; } mitk::PointSet::Pointer pointSet = dynamic_cast<mitk::PointSet*>(pointSetNode->GetData()); if (pointSet.IsNull()) { ui->distanceTREValue->setText(QString("Unknown")); return; } double distance = pointSet->GetPoint(0).EuclideanDistanceTo(centroidOfTargetInUSImage); ui->distanceTREValue->setText(QString("%1").arg(distance)); } void QmitkUSNavigationStepCtUsRegistration::OnCalculateCenter() { mitk::DataNode::Pointer node = ui->segmentationComboBox->GetSelectedNode(); if (node.IsNull()) { QMessageBox msgBox; msgBox.setText("Cannot calculate the centroid of the segmentation."\ "The segmentationComboBox node returned a nullptr."); msgBox.exec(); return; } mitk::LabelSetImage::Pointer image = dynamic_cast<mitk::LabelSetImage*>(node->GetData()); if (image.IsNull()) { MITK_WARN << "Cannot CalculateCenter - the segmentation cannot be converted to mitk::Image"; return; } ImageType::Pointer itkImage = ImageType::New(); mitk::CastToItkImage(image, itkImage); //Initialize binary image to shape label map filter BinaryImageToShapeLabelMapFilterType::Pointer shapeLabelMapFilter = BinaryImageToShapeLabelMapFilterType::New(); shapeLabelMapFilter->SetInputForegroundValue(1); shapeLabelMapFilter->SetInput(itkImage); shapeLabelMapFilter->Update(); BinaryImageToShapeLabelMapFilterType::OutputImageType::Pointer labelMap = shapeLabelMapFilter->GetOutput(); for (int i = labelMap->GetNumberOfLabelObjects() - 1; i >= 0; --i) { // Get the ith region BinaryImageToShapeLabelMapFilterType::OutputImageType::LabelObjectType* labelObject = labelMap->GetNthLabelObject(i); mitk::Vector3D centroid; centroid[0] = labelObject->GetCentroid()[0]; centroid[1] = labelObject->GetCentroid()[1]; centroid[2] = labelObject->GetCentroid()[2]; MITK_INFO << "Centroid of segmentation = " << centroid; } } void QmitkUSNavigationStepCtUsRegistration::OnAddCtImageClicked() { mitk::DataNode* selectedCtImage = ui->ctImagesToChooseComboBox->GetSelectedNode(); if (selectedCtImage == nullptr) { return; } mitk::Image::Pointer ctImage = dynamic_cast<mitk::Image*>(selectedCtImage->GetData()); if (ctImage.IsNull()) { MITK_WARN << "Failed to cast selected segmentation node to mitk::Image*"; return; } QString name = QString::fromStdString(selectedCtImage->GetName()); for( int counter = 0; counter < ui->chosenCtImagesListWidget->count(); ++counter) { MITK_INFO << ui->chosenCtImagesListWidget->item(counter)->text() << " - " << counter; MITK_INFO << m_ImagesGroundTruthProtocol.at(counter).GetPointer(); if (ui->chosenCtImagesListWidget->item(counter)->text().compare(name) == 0) { MITK_INFO << "CT image already exist in list of chosen CT images. Do not add the image."; return; } } ui->chosenCtImagesListWidget->addItem(name); m_ImagesGroundTruthProtocol.push_back(ctImage); } void QmitkUSNavigationStepCtUsRegistration::OnRemoveCtImageClicked() { int position = ui->chosenCtImagesListWidget->currentRow(); if (ui->chosenCtImagesListWidget->count() == 0 || position < 0) { return; } m_ImagesGroundTruthProtocol.erase(m_ImagesGroundTruthProtocol.begin() + position); QListWidgetItem *item = ui->chosenCtImagesListWidget->currentItem(); ui->chosenCtImagesListWidget->removeItemWidget(item); delete item; } void QmitkUSNavigationStepCtUsRegistration::OnEvaluateGroundTruthFiducialLocalizationProtocol() { m_GroundTruthProtocolFRE.clear(); if (m_ImagesGroundTruthProtocol.size() != 6) { QMessageBox msgBox; msgBox.setText("For evaluating the Ground-Truth-Fiducial-Localization-Protocol there must be loaded 6 different CT images."); msgBox.exec(); return; } m_PerformingGroundTruthProtocolEvaluation = true; this->CreatePointsToTransformForGroundTruthProtocol(); m_GroundTruthProtocolTransformedPoints.clear(); for (unsigned int cycleNo = 0; cycleNo < m_ImagesGroundTruthProtocol.size(); ++cycleNo) { m_FloatingImage = m_ImagesGroundTruthProtocol.at(cycleNo); this->SetFloatingImageGeometryInformation(m_FloatingImage.GetPointer()); this->OnLocalizeFiducials(); this->OnRegisterMarkerToFloatingImageCS(); this->TransformPointsGroundTruthProtocol(); } this->AddTransformedPointsToDataStorage(); double meanFRE = this->CalculateMeanFRE(); double sdOfFRE = this->CalculateStandardDeviationOfFRE(meanFRE); this->CalculateGroundTruthProtocolTRE(); ui->meanFREValue->setText(QString("%1").arg(meanFRE)); ui->sdFREValue->setText(QString("%1").arg(sdOfFRE)); if (ui->protocolEvaluationTypeComboBox->currentText().compare("ANGLE") == 0) { if (m_GroundTruthProtocolTRE.find(0) != m_GroundTruthProtocolTRE.end()) { ui->TREValue->setText(QString("%1").arg(m_GroundTruthProtocolTRE.at(0))); } } else if (ui->protocolEvaluationTypeComboBox->currentText().compare("PLANE") == 0) { if (m_GroundTruthProtocolTRE.find(0) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(20) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(40) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(60) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(80) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(100) != m_GroundTruthProtocolTRE.end()) { ui->TREValue->setText(QString("Depth 0mm: %1\nDepth 20mm: %2\nDepth 40mm: %3\ \nDepth 60mm: %4\nDepth 80mm: %5\nDepth 100mm: %6") .arg(m_GroundTruthProtocolTRE.at(0)) .arg(m_GroundTruthProtocolTRE.at(20)) .arg(m_GroundTruthProtocolTRE.at(40)) .arg(m_GroundTruthProtocolTRE.at(60)) .arg(m_GroundTruthProtocolTRE.at(80)) .arg(m_GroundTruthProtocolTRE.at(100))); } } m_PerformingGroundTruthProtocolEvaluation = false; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPlacementPlanning.ui b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPlacementPlanning.ui index 48e011bcf9..1df2b219c0 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPlacementPlanning.ui +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPlacementPlanning.ui @@ -1,352 +1,352 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkUSNavigationStepPlacementPlanning</class> <widget class="QWidget" name="QmitkUSNavigationStepPlacementPlanning"> <property name="enabled"> <bool>true</bool> </property> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>396</width> <height>448</height> </rect> </property> <property name="windowTitle"> <string>Form</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QLabel" name="bodyMarkerTrackingStatusLabel"> <property name="styleSheet"> <string notr="true"> background-color: #ff7878; margin-right: 1em; margin-left: 1em; border: 1px solid grey </string> </property> <property name="text"> <string>Body marker is not inside the tracking volume.</string> </property> <property name="alignment"> <set>Qt::AlignCenter</set> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QLabel" name="currentTargetLabel"> <property name="font"> <pointsize>10</pointsize> <weight>75</weight> <bold>true</bold> </property> <property name="text"> <string>Planning Target %1 of %2</string> </property> <property name="alignment"> <set>Qt::AlignCenter</set> </property> </widget> </item> <item> <widget class="QLabel" name="label_4"> <property name="text"> <string>Placement planning can be done either by using the tracked needle or by clicking with the mouse. Correcting the position is always possible by selecting the target with the "Previous" and "Next" buttons and placing it just again the.</string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> <string>Placement by Needle Path</string> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QLabel" name="label_3"> <property name="text"> <string>A target can be placed (or replaced) by pointing the needle to the desired position on the target surface and hitting the button below.</string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QPushButton" name="placeTargetButton"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Place Target on Current Needle Path</string> </property> <property name="icon"> <iconset resource="../../../resources/USNavigation.qrc"> <normaloff>:/USNavigation/accept.png</normaloff>:/USNavigation/accept.png</iconset> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_2"> <property name="title"> <string>Placment by Mouse Click</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QLabel" name="label_2"> <property name="text"> - <string>A target can be placed (or replaced) by freezing the imaging and then left clicking into the render window at the desired positon.</string> + <string>A target can be placed (or replaced) by freezing the imaging and then left clicking into the render window at the desired position.</string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QmitkUSNavigationFreezeButton" name="freezeImageButton"> <property name="enabled"> <bool>false</bool> </property> </widget> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="allTargetsPlannedLabel"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>All Targets are planned. You can proceed with the next step if the planning result is satisfactory. Otherwise you can replace a target by switching to it witch the "Previous" and "Next" buttons and replace it as it was placed before.</string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <layout class="QFormLayout" name="formLayout"> <item row="0" column="0"> <widget class="QLabel" name="centersOfMassLabel"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Centers of Mass Distances:</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="angleDifferenceLabel"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Mean Angle Difference:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="centersOfMassValue"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string/> </property> </widget> </item> <item row="1" column="1"> <widget class="QLabel" name="angleDifferenceValue"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string/> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QPushButton" name="removeButton"> <property name="text"> <string>Remove Current</string> </property> <property name="icon"> <iconset resource="../../../resources/USNavigation.qrc"> <normaloff>:/USNavigation/minus.png</normaloff>:/USNavigation/minus.png</iconset> </property> </widget> </item> <item> <widget class="QPushButton" name="previousButton"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Previous</string> </property> <property name="icon"> <iconset resource="../../../resources/USNavigation.qrc"> <normaloff>:/USNavigation/go-previous.png</normaloff>:/USNavigation/go-previous.png</iconset> </property> </widget> </item> <item> <widget class="QPushButton" name="nextButton"> <property name="text"> <string>Next</string> </property> <property name="icon"> <iconset resource="../../../resources/USNavigation.qrc"> <normaloff>:/USNavigation/go-next.png</normaloff>:/USNavigation/go-next.png</iconset> </property> </widget> </item> </layout> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkUSNavigationFreezeButton</class> <extends>QPushButton</extends> <header>src/internal/Widgets/QmitkUSNavigationFreezeButton.h</header> </customwidget> </customwidgets> <resources> <include location="../../../resources/USNavigation.qrc"/> </resources> <connections> <connection> <sender>previousButton</sender> <signal>clicked()</signal> <receiver>QmitkUSNavigationStepPlacementPlanning</receiver> <slot>OnGoToPreviousTarget()</slot> <hints> <hint type="sourcelabel"> <x>71</x> <y>40</y> </hint> <hint type="destinationlabel"> <x>199</x> <y>65</y> </hint> </hints> </connection> <connection> <sender>nextButton</sender> <signal>clicked()</signal> <receiver>QmitkUSNavigationStepPlacementPlanning</receiver> <slot>OnGoToNextTarget()</slot> <hints> <hint type="sourcelabel"> <x>328</x> <y>40</y> </hint> <hint type="destinationlabel"> <x>199</x> <y>65</y> </hint> </hints> </connection> <connection> <sender>placeTargetButton</sender> <signal>clicked()</signal> <receiver>QmitkUSNavigationStepPlacementPlanning</receiver> <slot>OnPlaceTargetButtonClicked()</slot> <hints> <hint type="sourcelabel"> <x>199</x> <y>119</y> </hint> <hint type="destinationlabel"> <x>199</x> <y>72</y> </hint> </hints> </connection> <connection> <sender>removeButton</sender> <signal>clicked()</signal> <receiver>QmitkUSNavigationStepPlacementPlanning</receiver> <slot>OnRemoveCurrentTargetClicked()</slot> <hints> <hint type="sourcelabel"> <x>71</x> <y>59</y> </hint> <hint type="destinationlabel"> <x>199</x> <y>83</y> </hint> </hints> </connection> </connections> <slots> <slot>OnGoToPreviousTarget()</slot> <slot>OnGoToNextTarget()</slot> <slot>OnPlaceTargetButtonClicked()</slot> <slot>OnRemoveCurrentTargetClicked()</slot> <slot>OnFreeze(bool)</slot> </slots> </ui> diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h index 24c340a4fb..e322ed1590 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h @@ -1,119 +1,119 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSNavigationStepPunctuationIntervention_h #define QmitkUSNavigationStepPunctuationIntervention_h #include "QmitkUSAbstractNavigationStep.h" #include <mitkPointSet.h> #include <mitkNavigationTool.h> #include <vtkSmartPointer.h> #include <vtkSphereSource.h> #include <vtkLine.h> #include <vtkOBBTree.h> namespace mitk { class DataNode; class NeedleProjectionFilter; class NodeDisplacementFilter; class USNavigationGrabCutSegmentationUpdateFilter; class USNavigationTargetUpdateFilter; class USNavigationTargetOcclusionFilter; class USPointMarkInteractor; class LookupTableProperty; class Surface; } namespace Ui { class QmitkUSNavigationStepPunctuationIntervention; } class QmitkZoneProgressBar; /** * \brief Navigations step for the actual punctuation intervention. * The needle path is projected onto the image plane and the distances to all * risk structures are displayed in the widget. * * The risk structures are expected to be in the data storage under * DATANAME_BASENODE -> DATANAME_ZONES. They should contain a property named * "zone.size" and it is assumed that they are spherical. */ class QmitkUSNavigationStepPunctuationIntervention : public QmitkUSAbstractNavigationStep { Q_OBJECT public: /** Sets the navigation tool of the needle for the meta data (tool axis etc.)*/ void SetNeedleMetaData(mitk::NavigationTool::Pointer needleNavigationTool); explicit QmitkUSNavigationStepPunctuationIntervention(QWidget *parent = nullptr); ~QmitkUSNavigationStepPunctuationIntervention() override; bool OnStartStep() override; bool OnRestartStep() override; bool OnFinishStep() override; bool OnActivateStep() override; void OnUpdate() override; void OnSettingsChanged(const itk::SmartPointer<mitk::DataNode>) override; QString GetTitle() override; bool GetIsRestartable() override; FilterVector GetFilter() override; signals: void AddAblationZoneClicked(int); void AblationZoneChanged(int,int); protected slots: void OnAddAblationZoneClicked(); void OnEnableAblationZoneMarkingClicked(); void OnAblationZoneSizeSliderChanged(int size); void OnShowToolAxisEnabled(int enabled); protected: void OnSetCombinedModality() override; void ClearZones(); void UpdateBodyMarkerStatus(mitk::NavigationData::Pointer bodyMarker); /** Updates the critical structures which means that the distance to the needle tip is updated and also the color changes to red if the path projection intersects the critical structure. */ void UpdateCriticalStructures(mitk::NavigationData::Pointer needle, mitk::PointSet::Pointer path); /** Checks if the given line intersects the given sphere. */ bool CheckSphereLineIntersection(mitk::Point3D& sphereOrigin, float& sphereRadius, mitk::Point3D& lineStart, mitk::Point3D& lineEnd); private: Ui::QmitkUSNavigationStepPunctuationIntervention *m_Ui; mitk::DataStorage::SetOfObjects::ConstPointer m_ZoneNodes; /** \brief Creates a Pointset that projects the needle's path */ itk::SmartPointer<mitk::NeedleProjectionFilter> m_NeedleProjectionFilter; /** holds the navigation tool of the needle for the meta data (tool axis etc.)*/ mitk::NavigationTool::Pointer m_NeedleNavigationTool; - std::map<mitk::DataNode::Pointer,mitk::Color> m_OldColors; //stores the original color of the critical structrue nodes + std::map<mitk::DataNode::Pointer,mitk::Color> m_OldColors; //stores the original color of the critical structure nodes //some help variables for the CheckSphereLineIntersection()-Method vtkSmartPointer<vtkSphereSource> m_SphereSource; vtkSmartPointer<vtkOBBTree> m_OBBTree; vtkSmartPointer<vtkPoints> m_IntersectPoints; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepTumourSelection.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepTumourSelection.h index e443cb43b5..66ac77a026 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepTumourSelection.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepTumourSelection.h @@ -1,164 +1,164 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSNavigationStepTumourSelection_h #define QmitkUSNavigationStepTumourSelection_h #include "QmitkUSAbstractNavigationStep.h" namespace itk { template<class T> class SmartPointer; } namespace mitk { class NavigationDataSource; class DataStorage; class DataNode; class USZonesInteractor; class NodeDisplacementFilter; class Surface; } namespace Ui { class QmitkUSNavigationStepTumourSelection; } class USNavigationMarkerPlacement; class QmitkUSNavigationStepCombinedModality; /** * \brief Navigation step for marking the tumor position and extent. * The user can mark the position by interacting with the render windows. The * tumor size can be changed afterwards and the tumor can be removed. */ class QmitkUSNavigationStepTumourSelection : public QmitkUSAbstractNavigationStep { Q_OBJECT protected slots: /** * \brief Activates or deactivates the ineractor for tumour creation. */ void OnFreeze(bool freezed); /** * \brief Updates the surface of the tumor node according to the new size. */ void OnTumourSizeChanged(int); /** * \brief Just restarts the navigation step for deleting the tumour. */ void OnDeleteButtonClicked(); public: explicit QmitkUSNavigationStepTumourSelection(QWidget* parent = nullptr); ~QmitkUSNavigationStepTumourSelection() override; void SetTargetSelectionOptional (bool t); /** * \brief Initializes tumour and target surface. * \return always true */ bool OnStartStep() override; /** * \brief Removes target surface and tumour node from the data storage. * Additionally an unfreeze is done and the node displacement filter is - * resetted. + * reset. * \return always true */ bool OnStopStep() override; /** * \brief Reinitializes buttons and sliders in addition of calling the default implementation. * \return result of the superclass implementation */ bool OnRestartStep() override; /** * \brief (Re)creates the target surface. * \return always true */ bool OnFinishStep() override; /** * \brief Initializes (but not activates) the interactor for tumour selection. * \return always true */ bool OnActivateStep() override; /** * \brief Deactivates the interactor for tumour selection * and removes data of the tumour node if selection wasn't finished yet. * * \return always true */ bool OnDeactivateStep() override; /** * \brief Updates tracking validity status and checks tumour node for the end of tumour creation. */ void OnUpdate() override; /** * The properties "settings.security-distance" and * "settings.interaction-concept" are used. */ void OnSettingsChanged(const itk::SmartPointer<mitk::DataNode> settingsNode) override; QString GetTitle() override; /** * @return a node displacement filter for tumour and target surfaces */ FilterVector GetFilter() override; void SetTumorColor(mitk::Color c); - /** @return Returns the current NodeDisplacementFilter which ist used for updating the targets pose. */ + /** @return Returns the current NodeDisplacementFilter which is used for updating the targets pose. */ itk::SmartPointer<mitk::NodeDisplacementFilter> GetTumourNodeDisplacementFilter(); protected: void OnSetCombinedModality() override; void TumourNodeChanged(const mitk::DataNode*); itk::SmartPointer<mitk::Surface> CreateTargetSurface(); void UpdateReferenceSensorName(); itk::SmartPointer<mitk::NavigationDataSource> m_NavigationDataSource; bool m_targetSelectionOptional; float m_SecurityDistance; itk::SmartPointer<mitk::USZonesInteractor> m_Interactor; itk::SmartPointer<mitk::DataNode> m_TumourNode; itk::SmartPointer<mitk::DataNode> m_TargetSurfaceNode; itk::SmartPointer<mitk::NodeDisplacementFilter> m_NodeDisplacementFilter; std::string m_StateMachineFilename; std::string m_ReferenceSensorName; unsigned int m_ReferenceSensorIndex; mitk::Color m_SphereColor; private: mitk::MessageDelegate1<QmitkUSNavigationStepTumourSelection, const mitk::DataNode*> m_ListenerChangeNode; Ui::QmitkUSNavigationStepTumourSelection *ui; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.cpp index 2842412f7e..90ffb1f02e 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.cpp @@ -1,800 +1,800 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkUSNavigationMarkerPlacement.h" #include "ui_QmitkUSNavigationMarkerPlacement.h" #include "NavigationStepWidgets/QmitkUSNavigationStepCombinedModality.h" #include "NavigationStepWidgets/QmitkUSNavigationStepMarkerIntervention.h" #include "NavigationStepWidgets/QmitkUSNavigationStepPlacementPlanning.h" #include "NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.h" #include "NavigationStepWidgets/QmitkUSNavigationStepTumourSelection.h" #include "NavigationStepWidgets/QmitkUSNavigationStepZoneMarking.h" #include "SettingsWidgets/QmitkUSNavigationCombinedSettingsWidget.h" #include "mitkAbstractUltrasoundTrackerDevice.h" #include "mitkIRenderingManager.h" #include "mitkNodeDisplacementFilter.h" #include "mitkTrackedUltrasound.h" #include <mitkIOUtil.h> #include "IO/mitkUSNavigationStepTimer.h" #include <QDateTime> #include <QDir> #include <QInputDialog> #include <QMessageBox> #include <QSignalMapper> #include <QTimer> #include "QmitkRenderWindow.h" #include "QmitkStdMultiWidget.h" #include "QmitkStdMultiWidgetEditor.h" #include "mitkCameraController.h" #include "mitkLayoutAnnotationRenderer.h" #include <vtkSmartPointer.h> // scene serialization #include <mitkConvert2Dto3DImageFilter.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkSceneIO.h> #include <mitkSurface.h> const std::string QmitkUSNavigationMarkerPlacement::VIEW_ID = "org.mitk.views.usmarkerplacement"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TUMOUR = "Tumour"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TARGETSURFACE = "Target Surface"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_ZONES = "Zones"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TARGETS = "Targets"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_TARGETS_PATHS = "Target Paths"; const char *QmitkUSNavigationMarkerPlacement::DATANAME_REACHED_TARGETS = "Reached Targets"; QmitkUSNavigationMarkerPlacement::QmitkUSNavigationMarkerPlacement() : m_Parent(nullptr), m_UpdateTimer(new QTimer(this)), m_ImageAndNavigationDataLoggingTimer(new QTimer(this)), m_StdMultiWidget(nullptr), m_CombinedModality(nullptr), m_ReinitAlreadyDone(false), m_IsExperimentRunning(false), m_CurrentApplicationName(), m_NavigationStepTimer(mitk::USNavigationStepTimer::New()), m_IconRunning(QPixmap(":/USNavigation/record.png")), m_IconNotRunning(QPixmap(":/USNavigation/record-gray.png")), m_ResultsDirectory(), m_ExperimentName(), m_ExperimentResultsSubDirectory(), m_NavigationStepNames(), m_LoggingBackend(), m_USImageLoggingFilter(mitk::USImageLoggingFilter::New()), m_NavigationDataRecorder(mitk::NavigationDataRecorder::New()), m_TargetNodeDisplacementFilter(nullptr), m_AblationZonesDisplacementFilter(mitk::NodeDisplacementFilter::New()), m_ToolVisualizationFilter(nullptr), m_AblationZonesVector(), m_NeedleIndex(0), m_MarkerIndex(1), m_SceneNumber(1), m_WarnOverlay(mitk::TextAnnotation2D::New()), m_NavigationDataSource(nullptr), m_CurrentStorage(nullptr), m_ImageStreamNode(nullptr), ui(new Ui::QmitkUSNavigationMarkerPlacement) { connect(m_UpdateTimer, SIGNAL(timeout()), this, SLOT(OnTimeout())); connect( m_ImageAndNavigationDataLoggingTimer, SIGNAL(timeout()), this, SLOT(OnImageAndNavigationDataLoggingTimeout())); // scale running (and not running) icon the specific height m_IconRunning = m_IconRunning.scaledToHeight(20, Qt::SmoothTransformation); m_IconNotRunning = m_IconNotRunning.scaledToHeight(20, Qt::SmoothTransformation); } QmitkUSNavigationMarkerPlacement::~QmitkUSNavigationMarkerPlacement() { this->GetDataStorage()->Remove(m_InstrumentNode); delete ui; } void QmitkUSNavigationMarkerPlacement::OnChangeAblationZone(int id, int newSize) { if ((static_cast<int>(m_AblationZonesVector.size()) < id) || (id < 0)) { return; } MITK_INFO << "Ablation Zone " << id << " changed, new size: " << newSize; // create a vtk sphere with given radius vtkSmartPointer<vtkSphereSource> vtkSphere = vtkSmartPointer<vtkSphereSource>::New(); vtkSphere->SetRadius(newSize / 2); vtkSphere->SetCenter(0, 0, 0); vtkSphere->SetPhiResolution(20); vtkSphere->SetThetaResolution(20); vtkSphere->Update(); mitk::Surface::Pointer zoneSurface = dynamic_cast<mitk::Surface *>(m_AblationZonesVector.at(id)->GetData()); zoneSurface->SetVtkPolyData(vtkSphere->GetOutput()); } void QmitkUSNavigationMarkerPlacement::OnAddAblationZone(int size) { m_AblationZonesDisplacementFilter->SetInitialReferencePose( m_CombinedModality->GetNavigationDataSource()->GetOutput(m_MarkerIndex)); mitk::DataNode::Pointer NewAblationZone = mitk::DataNode::New(); mitk::Point3D origin = m_CombinedModality->GetNavigationDataSource()->GetOutput(m_NeedleIndex)->GetPosition(); MITK_INFO("USNavigationLogging") << "Ablation Zone Added, initial size: " << size << ", origin: " << origin; mitk::Surface::Pointer zone = mitk::Surface::New(); // create a vtk sphere with given radius vtkSmartPointer<vtkSphereSource> vtkSphere = vtkSmartPointer<vtkSphereSource>::New(); vtkSphere->SetRadius(size / 2); vtkSphere->SetCenter(0, 0, 0); vtkSphere->SetPhiResolution(20); vtkSphere->SetThetaResolution(20); vtkSphere->Update(); zone->SetVtkPolyData(vtkSphere->GetOutput()); // set vtk sphere and origin to data node (origin must be set // again, because of the new sphere set as data) NewAblationZone->SetData(zone); NewAblationZone->GetData()->GetGeometry()->SetOrigin(origin); mitk::Color SphereColor = mitk::Color(); // default color SphereColor[0] = 102; SphereColor[1] = 0; SphereColor[2] = 204; NewAblationZone->SetColor(SphereColor); NewAblationZone->SetOpacity(0.3); // set name of zone std::stringstream name; name << "Ablation Zone" << m_AblationZonesVector.size(); NewAblationZone->SetName(name.str()); // add zone to filter m_AblationZonesDisplacementFilter->AddNode(NewAblationZone); m_AblationZonesVector.push_back(NewAblationZone); this->GetDataStorage()->Add(NewAblationZone); } void QmitkUSNavigationMarkerPlacement::CreateQtPartControl(QWidget *parent) { m_Parent = parent; ui->setupUi(parent); connect(ui->startExperimentButton, SIGNAL(clicked()), this, SLOT(OnStartExperiment())); connect(ui->finishExperimentButton, SIGNAL(clicked()), this, SLOT(OnFinishExperiment())); connect(ui->m_enableNavigationLayout, SIGNAL(clicked()), this, SLOT(OnChangeLayoutClicked())); connect(ui->m_RenderWindowSelection, SIGNAL(valueChanged(int)), this, SLOT(OnRenderWindowSelection())); connect(ui->m_RefreshView, SIGNAL(clicked()), this, SLOT(OnRefreshView())); m_BaseNode = this->GetDataStorage()->GetNamedNode(QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if (m_BaseNode.IsNull()) { m_BaseNode = mitk::DataNode::New(); m_BaseNode->SetName(QmitkUSAbstractNavigationStep::DATANAME_BASENODE); this->GetDataStorage()->Add(m_BaseNode); } connect(ui->m_CtToUsRegistrationWidget, SIGNAL(GetCursorPosition()), this, SLOT(OnGetCursorPosition())); connect(ui->m_CtToUsRegistrationWidget, SIGNAL(ActualizeCtToUsRegistrationWidget()), this, SLOT(OnActualizeCtToUsRegistrationWidget())); connect(ui->m_initializeCtToUsRegistration, SIGNAL(clicked()), this, SLOT(OnInitializeCtToUsRegistration())); connect(ui->m_initializeTargetMarking, SIGNAL(clicked()), this, SLOT(OnInitializeTargetMarking())); connect(ui->m_initializeCritStructureMarking, SIGNAL(clicked()), this, SLOT(OnInitializeCriticalStructureMarking())); connect(ui->m_initializeNavigation, SIGNAL(clicked()), this, SLOT(OnInitializeNavigation())); // indicate that no experiment is running at start ui->runningLabel->setPixmap(m_IconNotRunning); connect(ui->m_settingsWidget, SIGNAL(SettingsChanged(itk::SmartPointer<mitk::DataNode>)), this, SLOT(OnSettingsChanged(itk::SmartPointer<mitk::DataNode>))); } void QmitkUSNavigationMarkerPlacement::ReInitializeSettingsNodesAndImageStream() { //If update timer is not stopped (signals stopped), setting the m_CombinedModality // will cause a crash of the workbench in some times. m_UpdateTimer->blockSignals(true); m_UpdateTimer->stop(); m_SettingsNode = mitk::DataNode::New(); ui->m_settingsWidget->OnSetSettingsNode(m_SettingsNode, true); InitImageStream(); m_CombinedModality = ui->m_CombinedModalityCreationWidget->GetSelectedCombinedModality(); // Having set the m_CombinedModality reactivate the update timer again m_UpdateTimer->start(50); // every 50 Milliseconds = 20 Frames/Second m_UpdateTimer->blockSignals(false); } void QmitkUSNavigationMarkerPlacement::OnGetCursorPosition() { auto centroid = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetSelectedPosition(); ui->m_CtToUsRegistrationWidget->OnCalculateTRE(centroid); } void QmitkUSNavigationMarkerPlacement::OnActualizeCtToUsRegistrationWidget() { m_SettingsNode = mitk::DataNode::New(); ui->m_settingsWidget->OnSetSettingsNode(m_SettingsNode, true); this->InitImageStream(); if (ui->m_CombinedModalityCreationWidget->GetSelectedCombinedModality().IsNull()) { return; } ui->m_CtToUsRegistrationWidget->SetCombinedModality( ui->m_CombinedModalityCreationWidget->GetSelectedCombinedModality()); m_CombinedModality = ui->m_CombinedModalityCreationWidget->GetSelectedCombinedModality(); if (!m_StdMultiWidget) { // try to get the standard multi widget if it couldn't be got before mitk::IRenderWindowPart *renderWindowPart = this->GetRenderWindowPart(); QmitkStdMultiWidgetEditor *multiWidgetEditor = dynamic_cast<QmitkStdMultiWidgetEditor *>(renderWindowPart); // if there is a standard multi widget now, disable the level window and // change the layout to 2D up and 3d down if (multiWidgetEditor) { m_StdMultiWidget = dynamic_cast<QmitkStdMultiWidget *>(multiWidgetEditor->GetMultiWidget()); multiWidgetEditor->ShowLevelWindowWidget(false); SetTwoWindowView(); } } else { this->OnRefreshView(); } m_UpdateTimer->start(50); // every 50 Milliseconds = 20 Frames/Second } void QmitkUSNavigationMarkerPlacement::OnInitializeCtToUsRegistration() { ui->m_CtToUsRegistrationWidget->SetDataStorage(this->GetDataStorage()); ui->m_CtToUsRegistrationWidget->OnSettingsChanged(m_SettingsNode); ui->m_CtToUsRegistrationWidget->OnActivateStep(); ui->m_CtToUsRegistrationWidget->OnStartStep(); ui->m_CtToUsRegistrationWidget->Update(); } void QmitkUSNavigationMarkerPlacement::OnInitializeTargetMarking() { ReInitializeSettingsNodesAndImageStream(); ui->m_TargetMarkingWidget->SetCombinedModality(m_CombinedModality); ui->m_TargetMarkingWidget->SetDataStorage(this->GetDataStorage()); ui->m_TargetMarkingWidget->OnSettingsChanged(m_SettingsNode); ui->m_TargetMarkingWidget->OnActivateStep(); ui->m_TargetMarkingWidget->OnStartStep(); ui->m_TargetMarkingWidget->Update(); } void QmitkUSNavigationMarkerPlacement::OnInitializeCriticalStructureMarking() { ReInitializeSettingsNodesAndImageStream(); ui->m_CriticalStructuresWidget->SetCombinedModality(m_CombinedModality); ui->m_CriticalStructuresWidget->SetDataStorage(this->GetDataStorage()); ui->m_CriticalStructuresWidget->OnSettingsChanged(m_SettingsNode); ui->m_CriticalStructuresWidget->OnActivateStep(); ui->m_CriticalStructuresWidget->OnStartStep(); ui->m_CriticalStructuresWidget->Update(); } void QmitkUSNavigationMarkerPlacement::OnInitializeNavigation() { ReInitializeSettingsNodesAndImageStream(); ui->m_NavigationWidget->SetCombinedModality(m_CombinedModality); ui->m_NavigationWidget->SetDataStorage(this->GetDataStorage()); ui->m_NavigationWidget->OnSettingsChanged(m_SettingsNode); ui->m_NavigationWidget->OnActivateStep(); ui->m_NavigationWidget->OnStartStep(); ui->m_NavigationWidget->Update(); // test if it is tracked US, if yes add visualization filter if (m_CombinedModality->GetIsTrackedUltrasoundActive()) { m_InstrumentNode = mitk::DataNode::New(); m_InstrumentNode->SetName("Tracked US Instrument"); m_InstrumentNode->SetData( m_CombinedModality->GetNavigationDataSource()->GetToolMetaData(0)->GetToolSurface()->Clone()); this->GetDataStorage()->Add(m_InstrumentNode); m_ToolVisualizationFilter = mitk::NavigationDataObjectVisualizationFilter::New(); m_ToolVisualizationFilter->ConnectTo(m_CombinedModality->GetNavigationDataSource()); m_ToolVisualizationFilter->SetRepresentationObject(0, m_InstrumentNode->GetData()); //caution: currently hard coded that instrument has id 0 //set dummy objects to avoid spamming of console mitk::Surface::Pointer dummyObject = mitk::Surface::New(); m_ToolVisualizationFilter->SetRepresentationObject(1, dummyObject.GetPointer()); m_ToolVisualizationFilter->SetRepresentationObject(2, dummyObject.GetPointer()); } } void QmitkUSNavigationMarkerPlacement::InitImageStream() { if (m_ImageStreamNode.IsNull()) { m_ImageStreamNode = mitk::DataNode::New(); m_ImageStreamNode->SetName("US Navigation Viewing Stream"); this->GetDataStorage()->Add(m_ImageStreamNode); } } void QmitkUSNavigationMarkerPlacement::OnCombinedModalityPropertyChanged(const std::string &key, const std::string &) { if (key == mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH) { m_ReinitAlreadyDone = false; this->ReinitOnImage(); if (m_CombinedModality.IsNotNull() && !m_CombinedModality->GetIsCalibratedForCurrentStatus()) { mitk::LayoutAnnotationRenderer::AddAnnotation( m_WarnOverlay.GetPointer(), "stdmulti.widget0", mitk::LayoutAnnotationRenderer::TopLeft); MITK_WARN << "No calibration available for the selected ultrasound image depth."; } } } void QmitkUSNavigationMarkerPlacement::SetFocus() { this->ReinitOnImage(); } void QmitkUSNavigationMarkerPlacement::OnTimeout() { if (m_CombinedModality.IsNull()) return; - m_CombinedModality->Modified(); // shouldn't be nessecary ... fix in abstract ultrasound tracker device! + m_CombinedModality->Modified(); // shouldn't be necessary ... fix in abstract ultrasound tracker device! m_CombinedModality->Update(); if (m_ToolVisualizationFilter.IsNotNull()) { m_ToolVisualizationFilter->Update(); } ui->m_CtToUsRegistrationWidget->Update(); ui->m_TargetMarkingWidget->Update(); ui->m_CriticalStructuresWidget->Update(); ui->m_NavigationWidget->Update(); mitk::Image::Pointer image = m_CombinedModality->GetOutput(); // make sure that always the current image is set to the data node if (image.IsNotNull() && m_ImageStreamNode->GetData() != image.GetPointer() && image->IsInitialized()) { m_ImageStreamNode->SetData(image); } if (!m_StdMultiWidget) { // try to get the standard multi widget if it couldn't be got before mitk::IRenderWindowPart *renderWindowPart = this->GetRenderWindowPart(); QmitkStdMultiWidgetEditor *multiWidgetEditor = dynamic_cast<QmitkStdMultiWidgetEditor*>(renderWindowPart); // if there is a standard multi widget now, disable the level window and // change the layout to 2D up and 3d down if (multiWidgetEditor) { m_StdMultiWidget = dynamic_cast<QmitkStdMultiWidget*>(multiWidgetEditor->GetMultiWidget()); multiWidgetEditor->ShowLevelWindowWidget(false); SetTwoWindowView(); } this->CreateOverlays(); } if (m_CombinedModality.IsNotNull() && !this->m_CombinedModality->GetIsFreezed()) // if the combined modality is freezed: do nothing { m_AblationZonesDisplacementFilter->Update(); // update the 3D window only every fourth time to speed up the rendering (at least in 2D) this->RequestRenderWindowUpdate(mitk::RenderingManager::REQUEST_UPDATE_2DWINDOWS); // make sure that a reinit was performed on the image this->ReinitOnImage(); } } void QmitkUSNavigationMarkerPlacement::OnEnableNavigationLayout() { MITK_INFO << "Navigation Layout"; // try to get the standard multi widget if it couldn't be got before mitk::IRenderWindowPart *renderWindowPart = this->GetRenderWindowPart(); QmitkStdMultiWidgetEditor *multiWidgetEditor = dynamic_cast<QmitkStdMultiWidgetEditor*>(renderWindowPart); // if there is a standard multi widget now, disable the level window and // change the layout to 2D up and 3d down if (multiWidgetEditor) { m_StdMultiWidget = dynamic_cast<QmitkStdMultiWidget*>(multiWidgetEditor->GetMultiWidget()); multiWidgetEditor->ShowLevelWindowWidget(false); SetTwoWindowView(); } } void QmitkUSNavigationMarkerPlacement::OnRenderWindowSelection() { SetTwoWindowView(); } void QmitkUSNavigationMarkerPlacement::OnRefreshView() { if (!ui->m_enableNavigationLayout->isChecked()) OnResetStandardLayout(); else { // Reinit the US Image Stream (this might be broken if there was a global reinit somewhere...) try { mitk::RenderingManager::GetInstance()->InitializeViews( // Reinit this ->GetDataStorage() // GetDataStorage ->GetNamedNode("US Viewing Stream - Image 0") ->GetData() ->GetTimeGeometry()); // GetNode } catch (...) { MITK_DEBUG << "No reinit possible"; } SetTwoWindowView(); } } void QmitkUSNavigationMarkerPlacement::SetTwoWindowView() { if (m_StdMultiWidget) { int i, j, k; switch (this->ui->m_RenderWindowSelection->value()) { case 1: mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))->GetCameraController()->SetViewToCaudal(); i = 1; j = 2; // other windows k = 0; break; case 2: mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))->GetCameraController()->SetViewToSinister(); i = 0; j = 2; k = 1; break; case 3: mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))->GetCameraController()->SetViewToAnterior(); i = 1; j = 0; k = 2; break; default: return; } // get the render window which is defined by index "k" and set it as "current render window widget" // chose the layout that will set the current 2D window as top render window and the 3D windows as bottom render window auto renderWindowWidget = m_StdMultiWidget->GetRenderWindowWidget(m_StdMultiWidget->GetNameFromIndex(k)); m_StdMultiWidget->GetMultiWidgetLayoutManager()->SetCurrentRenderWindowWidget(renderWindowWidget.get()); m_StdMultiWidget->GetMultiWidgetLayoutManager()->SetOneTop3DBottomLayout(); ////Crosshair invisible in 3D view this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(i) + ".plane") ->SetBoolProperty("visible", false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(j) + ".plane") ->SetBoolProperty("visible", false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(k) + ".plane") ->SetBoolProperty("visible", true, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget4"))); this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(i) + ".plane") ->SetIntProperty("Crosshair.Gap Size", 0); this->GetDataStorage()->GetNamedNode("stdmulti.widget" + std::to_string(j) + ".plane") ->SetIntProperty("Crosshair.Gap Size", 0); } } void QmitkUSNavigationMarkerPlacement::OnResetStandardLayout() { if (m_StdMultiWidget) { //reset render windows m_StdMultiWidget->SetCrosshairVisibility(true); m_StdMultiWidget->GetMultiWidgetLayoutManager()->SetDefaultLayout(); } } void QmitkUSNavigationMarkerPlacement::OnChangeLayoutClicked() { if (ui->m_enableNavigationLayout->isChecked()) OnEnableNavigationLayout(); else OnResetStandardLayout(); } void QmitkUSNavigationMarkerPlacement::OnImageAndNavigationDataLoggingTimeout() { // update filter for logging navigation data and ultrasound images if (m_CombinedModality.IsNotNull()) { m_NavigationDataRecorder->Update(); // get last messages for logging filer and store them std::vector<std::string> messages = m_LoggingBackend.GetNavigationMessages(); std::string composedMessage = ""; for (std::size_t i = 0; i < messages.size(); i++) { composedMessage += messages.at(i); } m_USImageLoggingFilter->AddMessageToCurrentImage(composedMessage); m_LoggingBackend.ClearNavigationMessages(); // update logging filter m_USImageLoggingFilter->Update(); } } void QmitkUSNavigationMarkerPlacement::OnStartExperiment() { // get name for the experiment by a QInputDialog bool ok; if (m_ExperimentName.isEmpty()) { // default: current date m_ExperimentName = QString::number(QDateTime::currentDateTime().date().year()) + "_" + QString::number(QDateTime::currentDateTime().date().month()) + "_" + QString::number(QDateTime::currentDateTime().date().day()) + "_experiment_" + QString::number(QDateTime::currentDateTime().time().hour()) + "." + QString::number(QDateTime::currentDateTime().time().minute()); } m_ExperimentName = QInputDialog::getText( m_Parent, QString("Experiment Name"), QString("Name of the Experiment"), QLineEdit::Normal, m_ExperimentName, &ok); MITK_INFO("USNavigationLogging") << "Experiment started: " << m_ExperimentName.toStdString(); if (ok && !m_ExperimentName.isEmpty()) { // display error message and call the function recursively if a directory // with the given name already exists QDir experimentResultsDir(m_ResultsDirectory + QDir::separator() + m_ExperimentName); if (experimentResultsDir.exists()) { QMessageBox::critical( m_Parent, "Results Directory Exists", "The result directory already exists.\nPlease choose an other name."); this->OnStartExperiment(); } else { QDir(m_ResultsDirectory).mkdir(m_ExperimentName); m_ExperimentResultsSubDirectory = m_ResultsDirectory + QDir::separator() + m_ExperimentName; // experiment is running now ui->runningLabel->setPixmap(m_IconRunning); // (re)start timer for navigation step durations m_NavigationStepTimer->Reset(); m_NavigationStepTimer->SetOutputFileName( QString(m_ExperimentResultsSubDirectory + QDir::separator() + QString("durations.cvs")).toStdString()); m_NavigationStepTimer->SetActiveIndex(0, "Initialization"); ui->finishExperimentButton->setEnabled(true); ui->startExperimentButton->setDisabled(true); // initialize and register logging backend QString loggingFilename = m_ExperimentResultsSubDirectory + QDir::separator() + "logging.txt"; m_LoggingBackend.SetOutputFileName(loggingFilename.toStdString()); mitk::RegisterBackend(&m_LoggingBackend); // initialize and start navigation data recorder form xml recording m_NavigationDataRecorder->StartRecording(); m_IsExperimentRunning = true; m_ImageAndNavigationDataLoggingTimer->start(1000); } } } void QmitkUSNavigationMarkerPlacement::OnFinishExperiment() { this->WaitCursorOn(); MITK_INFO("USNavigationLogging") << "Experiment finished!"; MITK_INFO("USNavigationLogging") << "Position/Orientation of needle tip: " << (dynamic_cast<mitk::NavigationData *>( m_CombinedModality->GetTrackingDeviceDataSource()->GetOutput(0))) ->GetPosition(); MITK_INFO("USNavigationLogging") << "Position of target: " << m_TargetNodeDisplacementFilter->GetRawDisplacementNavigationData(0)->GetPosition(); MITK_INFO("USNavigationLogging") << "Total duration: " << m_NavigationStepTimer->GetTotalDuration(); m_ImageAndNavigationDataLoggingTimer->stop(); ui->runningLabel->setPixmap(m_IconNotRunning); m_NavigationStepTimer->Stop(); ui->finishExperimentButton->setDisabled(true); ui->startExperimentButton->setEnabled(true); MITK_INFO("USNavigationLogging") << "Writing logging data to " << m_ExperimentResultsSubDirectory.toStdString(); // save ultrasound images to the file system QDir(m_ExperimentResultsSubDirectory).mkdir("ImageStream"); m_USImageLoggingFilter->Update(); m_USImageLoggingFilter->SetImageFilesExtension(".jpg"); m_USImageLoggingFilter->SaveImages( QString(m_ExperimentResultsSubDirectory + QDir::separator() + "ImageStream" + QDir::separator()).toStdString()); m_USImageLoggingFilter = mitk::USImageLoggingFilter::New(); m_NavigationDataRecorder->StopRecording(); // Write data to csv and xml file mitk::IOUtil::Save( m_NavigationDataRecorder->GetNavigationDataSet(), (QString(m_ExperimentResultsSubDirectory + QDir::separator() + "navigation-data.xml").toStdString().c_str())); mitk::IOUtil::Save( m_NavigationDataRecorder->GetNavigationDataSet(), (QString(m_ExperimentResultsSubDirectory + QDir::separator() + "navigation-data.csv").toStdString().c_str())); // write logged navigation data messages to separate file std::stringstream csvNavigationMessagesFilename; csvNavigationMessagesFilename << m_ExperimentResultsSubDirectory.toStdString() << QDir::separator().toLatin1() << "CSVNavigationMessagesLogFile.csv"; MITK_INFO("USNavigationLogging") << "Writing logged navigation messages to separate csv file: " << csvNavigationMessagesFilename.str(); m_LoggingBackend.WriteCSVFileWithNavigationMessages(csvNavigationMessagesFilename.str()); mitk::UnregisterBackend(&m_LoggingBackend); m_IsExperimentRunning = false; m_ImageAndNavigationDataLoggingTimer->stop(); m_CombinedModality = nullptr; // reset scene number for next experiment m_SceneNumber = 1; this->WaitCursorOff(); MITK_INFO("USNavigationLogging") << "Finished!"; } void QmitkUSNavigationMarkerPlacement::OnSettingsChanged(itk::SmartPointer<mitk::DataNode> settings) { // initialize gui according to the experiment mode setting bool experimentMode = false; settings->GetBoolProperty("settings.experiment-mode", experimentMode); ui->startExperimentButton->setVisible(experimentMode); ui->finishExperimentButton->setVisible(experimentMode); ui->runningLabel->setVisible(experimentMode); if (experimentMode && !m_IsExperimentRunning) { ui->runningLabel->setPixmap(m_IconNotRunning); } else if (!experimentMode) { if (m_IsExperimentRunning) { this->OnFinishExperiment(); } } // get the results directory from the settings and use home directory if // there is no results directory configured std::string resultsDirectory; if (settings->GetStringProperty("settings.experiment-results-directory", resultsDirectory)) { m_ResultsDirectory = QString::fromStdString(resultsDirectory); } else { m_ResultsDirectory = QDir::homePath(); } // make sure that the results directory exists QDir resultsDirectoryQDir = QDir(m_ResultsDirectory); if (!resultsDirectoryQDir.exists()) { resultsDirectoryQDir.mkpath(m_ResultsDirectory); } MITK_INFO("USNavigation") << "Results Directory: " << m_ResultsDirectory.toStdString(); } void QmitkUSNavigationMarkerPlacement::ReinitOnImage() { if (!m_ReinitAlreadyDone && m_CombinedModality.IsNotNull()) { // make sure that the output is already calibrated correctly // (if the zoom level was changed recently) m_CombinedModality->Modified(); m_CombinedModality->Update(); mitk::Image::Pointer image = m_CombinedModality->GetOutput(); if (image.IsNotNull() && image->IsInitialized()) { // make a reinit on the ultrasound image mitk::IRenderWindowPart *renderWindowPart = this->GetRenderWindowPart(); if (renderWindowPart != nullptr && image->GetTimeGeometry()->IsValid()) { renderWindowPart->GetRenderingManager()->InitializeViews(image->GetTimeGeometry()); } this->RequestRenderWindowUpdate(); m_ReinitAlreadyDone = true; } } } void QmitkUSNavigationMarkerPlacement::Convert2DImagesTo3D(mitk::DataStorage::SetOfObjects::ConstPointer nodes) { for (mitk::DataStorage::SetOfObjects::ConstIterator it = nodes->Begin(); it != nodes->End(); ++it) { if (it->Value()->GetData() && strcmp(it->Value()->GetData()->GetNameOfClass(), "Image") == 0) { // convert image to 3d image if it is 2d at the moment mitk::Image::Pointer image = dynamic_cast<mitk::Image *>(it->Value()->GetData()); if (image.IsNotNull() && image->GetDimension() == 2 && !image->GetGeometry()->Is2DConvertable()) { mitk::Convert2Dto3DImageFilter::Pointer convert2DTo3DImageFilter = mitk::Convert2Dto3DImageFilter::New(); convert2DTo3DImageFilter->SetInput(image); convert2DTo3DImageFilter->Update(); it->Value()->SetData(convert2DTo3DImageFilter->GetOutput()); } } } } void QmitkUSNavigationMarkerPlacement::CreateOverlays() { // initialize warning overlay (and do not display it, yet) m_WarnOverlay->SetText("Warning: No calibration available for current depth."); // set position and font size for the text overlay - // (nonesense postition as a layouter is used, but it ignored + // (nonsense position as a layouter is used, but it ignored // the overlay without setting a position here) mitk::Point2D overlayPosition; overlayPosition.SetElement(0, -50.0f); overlayPosition.SetElement(1, -50.0f); m_WarnOverlay->SetPosition2D(overlayPosition); m_WarnOverlay->SetFontSize(22); m_WarnOverlay->SetColor(1, 0, 0); // overlay should be red } void QmitkUSNavigationMarkerPlacement::UpdateToolStorage() { if (m_NavigationDataSource.IsNull()) { m_NavigationDataSource = m_CombinedModality->GetNavigationDataSource(); } if (m_NavigationDataSource.IsNull()) { MITK_WARN << "Found an invalid navigation data source object!"; } us::ModuleContext *context = us::GetModuleContext(); std::string id = m_NavigationDataSource->US_PROPKEY_ID; std::string filter = "(" + mitk::NavigationToolStorage::US_PROPKEY_SOURCE_ID + "=" + id + ")"; // Get Storage std::vector<us::ServiceReference<mitk::NavigationToolStorage>> refs = context->GetServiceReferences<mitk::NavigationToolStorage>(); m_CurrentStorage = context->GetService(refs.front()); if (m_CurrentStorage.IsNull()) { MITK_WARN << "Found an invalid storage object!"; } else if (m_CurrentStorage->GetToolCount() != m_NavigationDataSource->GetNumberOfOutputs()) // there is something wrong with the storage { MITK_WARN << "Found a tool storage, but it has not the same number of tools like the NavigationDataSource. This " "storage won't be used because it isn't the right one."; m_CurrentStorage = nullptr; } } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.h index 357fafcf48..33d2d43b81 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUSNavigationMarkerPlacement.h @@ -1,209 +1,209 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSNavigationMarkerPlacement_h #define QmitkUSNavigationMarkerPlacement_h #include <QmitkAbstractView.h> #include "IO/mitkUSNavigationLoggingBackend.h" #include "mitkNavigationDataRecorder.h" #include "mitkNodeDisplacementFilter.h" #include "mitkUSImageLoggingFilter.h" #include <mitkMessage.h> #include <mitkTextAnnotation2D.h> #include <mitkAbstractUltrasoundTrackerDevice.h> #include <mitkNavigationToolStorage.h> #include <mitkNavigationDataObjectVisualizationFilter.h> namespace itk { template <class T> class SmartPointer; } namespace mitk { class USNavigationStepTimer; } namespace Ui { class QmitkUSNavigationMarkerPlacement; } class QmitkUSAbstractNavigationStep; class QmitkUSNavigationStepPunctuationIntervention; class QmitkStdMultiWidget; class QTimer; class QSignalMapper; /** * \brief View for navigated marker placement using the combined modality. * This view utilizes the QmitkUSNavigationProcessWidget to do the navigation * process. It can be switched between widgets for marker placement and widgets * for punctuation. * * An experiment mode allows for logging results, durations and the ultrasound * images. */ class QmitkUSNavigationMarkerPlacement : public QmitkAbstractView { Q_OBJECT protected slots: void OnGetCursorPosition(); void OnActualizeCtToUsRegistrationWidget(); void OnInitializeCtToUsRegistration(); void OnInitializeTargetMarking(); void OnInitializeCriticalStructureMarking(); void OnInitializeNavigation(); /** * \brief Called periodically to update the rendering. * The standard multi widget is changed to fit the navigation process once it * is available and a reinit on the ultrasound image is done for a new image * node. */ void OnTimeout(); /** * \brief Called periodically during an experiment for logging the ultrasound images. */ void OnImageAndNavigationDataLoggingTimeout(); /** - * \brief Initializes anything neccessary for an experiment. + * \brief Initializes anything necessary for an experiment. * The user is asked for a directory for storing the results and the logging * is started. */ void OnStartExperiment(); /** * \brief Stops logging and saves everything to the file system. */ void OnFinishExperiment(); /** * \brief Switches the navigation step widgets if the navigation application was changed. */ void OnSettingsChanged(itk::SmartPointer<mitk::DataNode>); void OnAddAblationZone(int size); void OnEnableNavigationLayout(); void OnResetStandardLayout(); void OnChangeLayoutClicked(); void OnChangeAblationZone(int id, int newSize); void OnRenderWindowSelection(); void OnRefreshView(); public: static const char *DATANAME_TUMOUR; static const char *DATANAME_TARGETSURFACE; static const char *DATANAME_ZONES; static const char *DATANAME_TARGETS; static const char *DATANAME_TARGETS_PATHS; static const char *DATANAME_REACHED_TARGETS; explicit QmitkUSNavigationMarkerPlacement(); ~QmitkUSNavigationMarkerPlacement() override; void CreateQtPartControl(QWidget *parent) override; static const std::string VIEW_ID; void OnCombinedModalityPropertyChanged(const std::string &, const std::string &); protected: /** * \brief A reinit on the ultrasound image is performed every time the view gets the focus. */ void SetFocus() override; /** * \brief Helper function which performs a reinit on the ultrasound image. */ void ReinitOnImage(); /** * \brief Sets the multiwidget to two windows, axial on top and 3D render window on the bottom. */ virtual void SetTwoWindowView(); /** * \brief Helper function for being able to serialize the 2d ultrasound image. */ void Convert2DImagesTo3D(mitk::DataStorage::SetOfObjects::ConstPointer nodes); void ReInitializeSettingsNodesAndImageStream(); void UpdateToolStorage(); void CreateOverlays(); void InitImageStream(); QWidget *m_Parent; QTimer *m_UpdateTimer; QTimer *m_ImageAndNavigationDataLoggingTimer; QmitkStdMultiWidget *m_StdMultiWidget; itk::SmartPointer<mitk::AbstractUltrasoundTrackerDevice> m_CombinedModality; itk::SmartPointer<mitk::DataNode> m_SettingsNode; bool m_ReinitAlreadyDone; bool m_IsExperimentRunning; std::string m_CurrentApplicationName; itk::SmartPointer<mitk::USNavigationStepTimer> m_NavigationStepTimer; QPixmap m_IconRunning; QPixmap m_IconNotRunning; QString m_ResultsDirectory; QString m_ExperimentName; QString m_ExperimentResultsSubDirectory; std::vector<QString> m_NavigationStepNames; // stores the names of the navigation steps which are currently used (for logging purposes) mitk::USNavigationLoggingBackend m_LoggingBackend; mitk::USImageLoggingFilter::Pointer m_USImageLoggingFilter; mitk::NavigationDataRecorder::Pointer m_NavigationDataRecorder; // records navigation data files mitk::NodeDisplacementFilter::Pointer m_TargetNodeDisplacementFilter; mitk::NodeDisplacementFilter::Pointer m_AblationZonesDisplacementFilter; mitk::NavigationDataObjectVisualizationFilter::Pointer m_ToolVisualizationFilter; mitk::DataNode::Pointer m_InstrumentNode; std::vector<mitk::DataNode::Pointer> m_AblationZonesVector; int m_NeedleIndex; int m_MarkerIndex; int m_SceneNumber; itk::SmartPointer<mitk::TextAnnotation2D> m_WarnOverlay; //To get tool storage mitk::NavigationDataSource::Pointer m_NavigationDataSource; mitk::NavigationToolStorage::Pointer m_CurrentStorage; itk::SmartPointer<mitk::DataNode> m_BaseNode; itk::SmartPointer<mitk::DataNode> m_ImageStreamNode; private: Ui::QmitkUSNavigationMarkerPlacement *ui; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.cpp index be23087d0c..3cc5c90e06 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.cpp @@ -1,1398 +1,1398 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkUltrasoundCalibration.h" #include <QTimer> // Qt #include <QFileDialog> #include <QMessageBox> #include <QTextStream> #include <QmitkServiceListWidget.h> // MITK #include <mitkVector.h> #include "mitkIOUtil.h" #include <mitkBaseData.h> #include <mitkImageGenerator.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkPointSet.h> #include <mitkPointSetDataInteractor.h> #include <mitkPointSetShapeProperty.h> #include <mitkSceneIO.h> // us #include <usServiceReference.h> // VTK #include <vtkLandmarkTransform.h> #include <vtkMatrix4x4.h> #include <vtkPlane.h> #include <vtkPoints.h> #include <vtkSphereSource.h> #include <vtkTransform.h> #include <vtkVertexGlyphFilter.h> #include "internal/org_mbi_gui_qt_usnavigation_Activator.h" // sleep headers #include <chrono> #include <thread> const std::string QmitkUltrasoundCalibration::VIEW_ID = "org.mitk.views.ultrasoundcalibration"; QmitkUltrasoundCalibration::QmitkUltrasoundCalibration() : m_PhantomConfigurationPointSet(nullptr), m_USDeviceChanged(this, &QmitkUltrasoundCalibration::OnUSDepthChanged) { ctkPluginContext *pluginContext = mitk::PluginActivator::GetContext(); if (pluginContext) { // to be notified about service event of an USDevice pluginContext->connectServiceListener(this, "OnDeviceServiceEvent", QString::fromStdString("(" + us::ServiceConstants::OBJECTCLASS() + "=" + us_service_interface_iid<mitk::USDevice>() + ")")); } } QmitkUltrasoundCalibration::~QmitkUltrasoundCalibration() { m_Controls.m_CombinedModalityManagerWidget->blockSignals(true); mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality; combinedModality = m_Controls.m_CombinedModalityManagerWidget->GetSelectedCombinedModality(); if (combinedModality.IsNotNull()) { combinedModality->GetUltrasoundDevice()->RemovePropertyChangedListener(m_USDeviceChanged); } m_Timer->stop(); this->OnStopCalibrationProcess(); this->OnStopPlusCalibration(); mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode("Needle Path"); if (node.IsNotNull()) this->GetDataStorage()->Remove(node); this->GetDataStorage()->Remove(m_VerificationReferencePointsDataNode); this->GetDataStorage()->Remove(m_SpacingNode); delete m_Timer; // remove observer for phantom-based point adding m_CalibPointsImage->RemoveAllObservers(); } void QmitkUltrasoundCalibration::SetFocus() { m_Controls.m_ToolBox->setFocus(); } void QmitkUltrasoundCalibration::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.m_CombinedModalityManagerWidget->SetCalibrationLoadedNecessary(false); m_Timer = new QTimer(this); m_StreamingTimer = new QTimer(this); m_Controls.m_SpacingBtnFreeze->setEnabled(true); m_Controls.m_SpacingAddPoint->setEnabled(false); m_Controls.m_CalculateSpacing->setEnabled(false); m_SpacingPointsCount = 0; m_SpacingPoints = mitk::PointSet::New(); m_SpacingNode = mitk::DataNode::New(); m_SpacingNode->SetName("Spacing Points"); m_SpacingNode->SetData(this->m_SpacingPoints); this->GetDataStorage()->Add(m_SpacingNode); // Pointset for Calibration Points m_CalibPointsTool = mitk::PointSet::New(); // Pointset for Worldpoints m_CalibPointsImage = mitk::PointSet::New(); m_CalibPointsCount = 0; // Evaluation Pointsets (Non-Visualized) m_EvalPointsImage = mitk::PointSet::New(); m_EvalPointsTool = mitk::PointSet::New(); m_EvalPointsProjected = mitk::PointSet::New(); // Neelde Projection Filter m_NeedleProjectionFilter = mitk::NeedleProjectionFilter::New(); // Tracking Status Widgets m_Controls.m_CalibTrackingStatus->ShowStatusLabels(); m_Controls.m_EvalTrackingStatus->ShowStatusLabels(); // General & Device Selection connect(m_Timer, SIGNAL(timeout()), this, SLOT(Update())); // Calibration connect(m_Controls.m_CalibBtnFreeze, SIGNAL(clicked()), this, SLOT(SwitchFreeze())); // Freeze connect(m_Controls.m_CalibBtnAddPoint, SIGNAL(clicked()), this, SLOT(OnAddCalibPoint())); // Tracking & Image Points (Calibration) connect(m_Controls.m_CalibBtnCalibrate, SIGNAL(clicked()), this, SLOT(OnCalibration())); // Perform Calibration // Phantom-based calibration connect(m_Controls.m_CalibBtnLoadPhantomConfiguration, SIGNAL(clicked()), this, SLOT(OnLoadPhantomConfiguration())); // Phantom configuration connect(m_Controls.m_CalibBtnMatchAnnotationToPhantomConfiguration, SIGNAL(clicked()), this, SLOT(OnMatchAnnotationToPhantomConfiguration())); connect(m_Controls.m_CalibBtnMoveUp, SIGNAL(clicked()), this, SLOT(OnMovePhantomAnnotationsUp())); connect(m_Controls.m_CalibBtnMoveDown, SIGNAL(clicked()), this, SLOT(OnMovePhantomAnnotationsDown())); connect(m_Controls.m_CalibBtnMoveLeft, SIGNAL(clicked()), this, SLOT(OnMovePhantomAnnotationsLeft())); connect(m_Controls.m_CalibBtnMoveRight, SIGNAL(clicked()), this, SLOT(OnMovePhantomAnnotationsRight())); connect(m_Controls.m_CalibBtnRotateRight, SIGNAL(clicked()), this, SLOT(OnRotatePhantomAnnotationsRight())); connect(m_Controls.m_CalibBtnRotateLeft, SIGNAL(clicked()), this, SLOT(OnRotatePhantomAnnotationsLeft())); connect(m_Controls.m_CalibBtnPerformPhantomCalibration, SIGNAL(clicked()), this, SLOT(OnPhantomBasedCalibration())); // Perform phantom-based calibration connect(m_Controls.m_CalibBtnSavePhantomCalibration, SIGNAL(clicked()), this, SLOT(OnSaveCalibration())); // Save phantom-based calibration // Evaluation connect(m_Controls.m_EvalBtnStep1, SIGNAL(clicked()), this, SLOT(OnAddEvalProjectedPoint())); // Needle Projection connect(m_Controls.m_EvalBtnStep2, SIGNAL(clicked()), this, SLOT(SwitchFreeze())); // Freeze connect(m_Controls.m_EvalBtnStep3, SIGNAL(clicked()), this, SLOT(OnAddEvalTargetPoint())); // Tracking & Image Points (Evaluation) connect(m_Controls.m_EvalBtnSave, SIGNAL(clicked()), this, SLOT(OnSaveEvaluation())); // Save Evaluation Results connect(m_Controls.m_CalibBtnSaveCalibration, SIGNAL(clicked()), this, SLOT(OnSaveCalibration())); // Save Evaluation Results connect(m_Controls.m_BtnReset, SIGNAL(clicked()), this, SLOT(OnReset())); // Reset Pointsets // PLUS Calibration connect(m_Controls.m_GetCalibrationFromPLUS, SIGNAL(clicked()), this, SLOT(OnGetPlusCalibration())); connect(m_Controls.m_StartStreaming, SIGNAL(clicked()), this, SLOT(OnStartStreaming())); connect(m_StreamingTimer, SIGNAL(timeout()), this, SLOT(OnStreamingTimerTimeout())); connect(m_Controls.m_StopPlusCalibration, SIGNAL(clicked()), this, SLOT(OnStopPlusCalibration())); connect(m_Controls.m_SavePlusCalibration, SIGNAL(clicked()), this, SLOT(OnSaveCalibration())); connect(this, SIGNAL(NewConnectionSignal()), this, SLOT(OnNewConnection())); // Determine Spacing for Calibration of USVideoDevice connect(m_Controls.m_SpacingBtnFreeze, SIGNAL(clicked()), this, SLOT(OnFreezeClicked())); connect(m_Controls.m_SpacingAddPoint, SIGNAL(clicked()), this, SLOT(OnAddSpacingPoint())); connect(m_Controls.m_CalculateSpacing, SIGNAL(clicked()), this, SLOT(OnCalculateSpacing())); connect(m_Controls.m_CombinedModalityManagerWidget, SIGNAL(SignalReadyForNextStep()), this, SLOT(OnDeviceSelected())); connect(m_Controls.m_CombinedModalityManagerWidget, SIGNAL(SignalNoLongerReadyForNextStep()), this, SLOT(OnDeviceDeselected())); connect(m_Controls.m_StartCalibrationButton, SIGNAL(clicked()), this, SLOT(OnStartCalibrationProcess())); connect(m_Controls.m_StartPlusCalibrationButton, SIGNAL(clicked()), this, SLOT(OnStartPlusCalibration())); connect(m_Controls.m_CalibBtnRestartCalibration, SIGNAL(clicked()), this, SLOT(OnReset())); connect(m_Controls.m_CalibBtnStopCalibration, SIGNAL(clicked()), this, SLOT(OnStopCalibrationProcess())); connect(m_Controls.m_AddReferencePoints, SIGNAL(clicked()), this, SLOT(OnAddCurrentTipPositionToReferencePoints())); connect(m_Controls.m_AddCurrentPointerTipForVerification, SIGNAL(clicked()), this, SLOT(OnAddCurrentTipPositionForVerification())); connect(m_Controls.m_StartVerification, SIGNAL(clicked()), this, SLOT(OnStartVerification())); // initialize data storage combo box m_Controls.m_ReferencePointsComboBox->SetDataStorage(this->GetDataStorage()); m_Controls.m_ReferencePointsComboBox->SetAutoSelectNewItems(true); m_Controls.m_ReferencePointsComboBox->SetPredicate(mitk::NodePredicateDataType::New("PointSet")); // initialize point list widget if (m_VerificationReferencePoints.IsNull()) { m_VerificationReferencePoints = mitk::PointSet::New(); } if (m_VerificationReferencePointsDataNode.IsNull()) { m_VerificationReferencePointsDataNode = mitk::DataNode::New(); m_VerificationReferencePointsDataNode->SetName("US Verification Reference Points"); m_VerificationReferencePointsDataNode->SetData(m_VerificationReferencePoints); this->GetDataStorage()->Add(m_VerificationReferencePointsDataNode); } m_Controls.m_ReferencePointsPointListWidget->SetPointSetNode(m_VerificationReferencePointsDataNode); m_Controls.m_ToolBox->setCurrentIndex(0); } void QmitkUltrasoundCalibration::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList<mitk::DataNode::Pointer> & /*nodes*/) { } void QmitkUltrasoundCalibration::OnTabSwitch(int index) { switch (index) { case 0: if (m_Controls.m_ToolBox->isItemEnabled(1) || m_Controls.m_ToolBox->isItemEnabled(2)) { this->OnStopCalibrationProcess(); } break; default:; } } void QmitkUltrasoundCalibration::OnDeviceSelected() { mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality; combinedModality = m_Controls.m_CombinedModalityManagerWidget->GetSelectedCombinedModality(); if (combinedModality.IsNotNull()) { combinedModality->GetUltrasoundDevice()->AddPropertyChangedListener(m_USDeviceChanged); m_Controls.m_StartCalibrationButton->setEnabled(true); m_Controls.m_StartPlusCalibrationButton->setEnabled(true); m_Controls.m_ToolBox->setItemEnabled(1, true); m_Controls.m_ToolBox->setItemEnabled(2, true); } } void QmitkUltrasoundCalibration::OnDeviceDeselected() { mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality; combinedModality = m_Controls.m_CombinedModalityManagerWidget->GetSelectedCombinedModality(); if (combinedModality.IsNotNull()) { combinedModality->GetUltrasoundDevice()->RemovePropertyChangedListener(m_USDeviceChanged); } m_Controls.m_StartCalibrationButton->setEnabled(false); m_Controls.m_StartPlusCalibrationButton->setEnabled(false); m_Controls.m_ToolBox->setCurrentIndex(0); m_Controls.m_ToolBox->setItemEnabled(1, false); m_Controls.m_ToolBox->setItemEnabled(2, false); } void QmitkUltrasoundCalibration::OnAddCurrentTipPositionToReferencePoints() { if (m_Controls.m_VerificationPointerChoser->GetSelectedNavigationDataSource().IsNull() || (m_Controls.m_VerificationPointerChoser->GetSelectedToolID() == -1)) { MITK_WARN << "No tool selected, aborting"; return; } mitk::NavigationData::Pointer currentPointerData = m_Controls.m_VerificationPointerChoser->GetSelectedNavigationDataSource()->GetOutput( m_Controls.m_VerificationPointerChoser->GetSelectedToolID()); mitk::Point3D currentTipPosition = currentPointerData->GetPosition(); m_VerificationReferencePoints->InsertPoint(m_VerificationReferencePoints->GetSize(), currentTipPosition); } void QmitkUltrasoundCalibration::OnStartVerification() { m_currentPoint = 0; mitk::PointSet::Pointer selectedPointSet = dynamic_cast<mitk::PointSet *>(m_Controls.m_ReferencePointsComboBox->GetSelectedNode()->GetData()); m_Controls.m_CurrentPointLabel->setText("Point " + QString::number(m_currentPoint) + " of " + QString::number(selectedPointSet->GetSize())); m_allErrors = std::vector<double>(); m_allReferencePoints = std::vector<mitk::Point3D>(); for (int i = 0; i < selectedPointSet->GetSize(); i++) { m_allReferencePoints.push_back(selectedPointSet->GetPoint(i)); } } void QmitkUltrasoundCalibration::OnAddCurrentTipPositionForVerification() { if (m_currentPoint == -1) { MITK_WARN << "Cannot add point"; return; } if (m_Controls.m_VerificationPointerChoser->GetSelectedNavigationDataSource().IsNull() || (m_Controls.m_VerificationPointerChoser->GetSelectedToolID() == -1)) { MITK_WARN << "No tool selected, aborting"; return; } mitk::NavigationData::Pointer currentPointerData = m_Controls.m_VerificationPointerChoser->GetSelectedNavigationDataSource()->GetOutput( m_Controls.m_VerificationPointerChoser->GetSelectedToolID()); mitk::Point3D currentTipPosition = currentPointerData->GetPosition(); double currentError = m_allReferencePoints.at(m_currentPoint).EuclideanDistanceTo(currentTipPosition); MITK_INFO << "Current Error: " << currentError << " mm"; m_allErrors.push_back(currentError); if (++m_currentPoint < static_cast<int>(m_allReferencePoints.size())) { m_Controls.m_CurrentPointLabel->setText("Point " + QString::number(m_currentPoint) + " of " + QString::number(m_allReferencePoints.size())); } else { m_currentPoint = -1; double meanError = 0; for (std::size_t i = 0; i < m_allErrors.size(); ++i) { meanError += m_allErrors[i]; } meanError /= m_allErrors.size(); QString result = "Finished verification! \n Verification of " + QString::number(m_allErrors.size()) + " points, mean error: " + QString::number(meanError) + " mm"; m_Controls.m_ResultsTextEdit->setText(result); MITK_INFO << result.toStdString(); } } void QmitkUltrasoundCalibration::OnStartCalibrationProcess() { // US Image Stream m_Node = dynamic_cast<mitk::DataNode*>(this->GetDataStorage()->GetNamedNode("US Viewing Stream - Image 0")->CreateAnother().GetPointer()); m_Node->SetName("US Calibration Viewing Stream"); this->GetDataStorage()->Add(m_Node); // data node for calibration point set m_CalibNode = mitk::DataNode::New(); m_CalibNode->SetName("Tool Calibration Points"); m_CalibNode->SetData(this->m_CalibPointsTool); this->GetDataStorage()->Add(m_CalibNode); // data node for world point set m_WorldNode = mitk::DataNode::New(); m_WorldNode->SetName("Image Calibration Points"); m_WorldNode->SetData(this->m_CalibPointsImage); this->GetDataStorage()->Add(m_WorldNode); m_CombinedModality = m_Controls.m_CombinedModalityManagerWidget->GetSelectedCombinedModality(); m_CombinedModality->SetCalibration(mitk::AffineTransform3D::New()); // dummy calibration because without a calibration // the comined modality was laggy (maybe a bug?) if (m_CombinedModality.IsNull()) { return; } m_Tracker = m_CombinedModality->GetNavigationDataSource(); // Construct Pipeline this->m_NeedleProjectionFilter->SetInput(0, m_Tracker->GetOutput(0)); QApplication::setOverrideCursor(Qt::WaitCursor); // make sure that the combined modality is in connected state before using it if (m_CombinedModality->GetUltrasoundDevice()->GetDeviceState() < mitk::USDevice::State_Connected) { m_CombinedModality->GetUltrasoundDevice()->Connect(); } if (m_CombinedModality->GetUltrasoundDevice()->GetDeviceState() < mitk::USDevice::State_Activated) { m_CombinedModality->GetUltrasoundDevice()->Activate(); } QApplication::restoreOverrideCursor(); this->SwitchFreeze(); // Trigger the ProbeChanged method for initializing/updating the spacing of the ultrasound image correctly std::string probeName = m_CombinedModality->GetUltrasoundDevice()->GetCurrentProbe()->GetName(); m_CombinedModality->GetUltrasoundDevice()->ProbeChanged(probeName); mitk::DataNode::Pointer usNode = this->GetDataStorage()->GetNamedNode("US Viewing Stream - Image 0"); if (usNode.IsNotNull()) { this->GetDataStorage()->Remove(usNode); } // Todo: Maybe display this elsewhere this->ShowNeedlePath(); // Switch active tab to Calibration page m_Controls.m_ToolBox->setItemEnabled(1, true); m_Controls.m_ToolBox->setCurrentIndex(1); } void QmitkUltrasoundCalibration::OnStartPlusCalibration() { if (m_CombinedModality.IsNull()) { m_CombinedModality = m_Controls.m_CombinedModalityManagerWidget->GetSelectedCombinedModality(); if (m_CombinedModality.IsNull()) { return; } // something went wrong, there is no combined modality } // setup server to send UltrasoundImages to PLUS mitk::IGTLServer::Pointer m_USServer = mitk::IGTLServer::New(true); m_USServer->SetName("EchoTrack Image Source"); m_USServer->SetHostname("127.0.0.1"); m_USServer->SetPortNumber(18944); m_USMessageProvider = mitk::IGTLMessageProvider::New(); m_USMessageProvider->SetIGTLDevice(m_USServer); m_USMessageProvider->SetFPS(5); m_USImageToIGTLMessageFilter = mitk::ImageToIGTLMessageFilter::New(); m_USImageToIGTLMessageFilter->ConnectTo(m_CombinedModality->GetUltrasoundDevice()); m_USImageToIGTLMessageFilter->SetName("USImage Filter"); // setup server to send TrackingData to PLUS m_TrackingServer = mitk::IGTLServer::New(true); m_TrackingServer->SetName("EchoTrack Tracking Source"); m_TrackingServer->SetHostname("127.0.0.1"); m_TrackingServer->SetPortNumber(18945); m_TrackingMessageProvider = mitk::IGTLMessageProvider::New(); m_TrackingMessageProvider->SetIGTLDevice(m_TrackingServer); m_TrackingMessageProvider->SetFPS(5); m_TrackingToIGTLMessageFilter = mitk::NavigationDataToIGTLMessageFilter::New(); m_TrackingToIGTLMessageFilter->ConnectTo(m_CombinedModality->GetTrackingDeviceDataSource()); m_TrackingToIGTLMessageFilter->SetName("Tracker Filter"); typedef itk::SimpleMemberCommand<QmitkUltrasoundCalibration> CurCommandType; CurCommandType::Pointer newConnectionCommand = CurCommandType::New(); newConnectionCommand->SetCallbackFunction(this, &QmitkUltrasoundCalibration::OnPlusConnected); this->m_NewConnectionObserverTag = this->m_TrackingServer->AddObserver(mitk::NewClientConnectionEvent(), newConnectionCommand); // Open connections of both servers if (m_USServer->OpenConnection()) { MITK_INFO << "US Server opened its connection successfully"; m_USServer->StartCommunication(); } else { MITK_INFO << "US Server could not open its connection"; } if (m_TrackingServer->OpenConnection()) { MITK_INFO << "Tracking Server opened its connection successfully"; m_TrackingServer->StartCommunication(); } else { MITK_INFO << "Tracking Server could not open its connection"; } if (m_USMessageProvider->IsCommunicating() && m_TrackingMessageProvider->IsCommunicating()) { m_Controls.m_StartPlusCalibrationButton->setEnabled(false); m_Controls.m_GetCalibrationFromPLUS->setEnabled(true); m_Controls.m_StartStreaming->setEnabled(false); m_Controls.m_SavePlusCalibration->setEnabled(false); m_Controls.m_SetupStatus->setStyleSheet("QLabel { color : green; }"); - m_Controls.m_SetupStatus->setText("Setup successfull you can now connect PLUS"); + m_Controls.m_SetupStatus->setText("Setup successful you can now connect PLUS"); } else { m_Controls.m_SetupStatus->setStyleSheet("QLabel { color : red; }"); m_Controls.m_SetupStatus->setText("Something went wrong. Please try again"); } } void QmitkUltrasoundCalibration::OnStopPlusCalibration() { // closing all server and clients when PlusCalibration is finished if (m_USMessageProvider.IsNotNull()) { if (m_USMessageProvider->IsStreaming()) { m_USMessageProvider->StopStreamingOfSource(m_USImageToIGTLMessageFilter); } } if (m_TrackingMessageProvider.IsNotNull()) { if (m_TrackingMessageProvider->IsStreaming()) { m_TrackingMessageProvider->StopStreamingOfSource(m_TrackingToIGTLMessageFilter); } } if (m_USServer.IsNotNull()) { m_USServer->CloseConnection(); } if (m_TrackingServer.IsNotNull()) { m_TrackingServer->CloseConnection(); } if (m_TransformClient.IsNotNull()) { m_TransformClient->CloseConnection(); } m_Controls.m_GotCalibrationLabel->setText(""); m_Controls.m_ConnectionStatus->setText(""); m_Controls.m_SetupStatus->setText(""); m_Controls.m_StartPlusCalibrationButton->setEnabled(true); m_StreamingTimer->stop(); delete m_StreamingTimer; } void QmitkUltrasoundCalibration::OnPlusConnected() { emit NewConnectionSignal(); } void QmitkUltrasoundCalibration::OnNewConnection() { m_Controls.m_StartStreaming->setEnabled(true); m_Controls.m_ConnectionStatus->setStyleSheet("QLabel { color : green; }"); - m_Controls.m_ConnectionStatus->setText("Connection successfull you can now start streaming"); + m_Controls.m_ConnectionStatus->setText("Connection successful you can now start streaming"); } void QmitkUltrasoundCalibration::OnStreamingTimerTimeout() { m_USMessageProvider->Update(); m_TrackingMessageProvider->Update(); } void QmitkUltrasoundCalibration::OnStartStreaming() { m_USMessageProvider->StartStreamingOfSource(m_USImageToIGTLMessageFilter, 5); m_TrackingMessageProvider->StartStreamingOfSource(m_TrackingToIGTLMessageFilter, 5); m_Controls.m_StartStreaming->setEnabled(false); m_Controls.m_ConnectionStatus->setText(""); m_StreamingTimer->start((1.0 / 5.0 * 1000.0)); } void QmitkUltrasoundCalibration::OnGetPlusCalibration() { m_TransformClient = mitk::IGTLClient::New(true); m_TransformClient->SetHostname("127.0.0.1"); m_TransformClient->SetPortNumber(18946); m_TransformDeviceSource = mitk::IGTLDeviceSource::New(); m_TransformDeviceSource->SetIGTLDevice(m_TransformClient); m_TransformDeviceSource->Connect(); if (m_TransformDeviceSource->IsConnected()) { MITK_INFO << "successfully connected"; m_TransformDeviceSource->StartCommunication(); if (m_TransformDeviceSource->IsCommunicating()) { MITK_INFO << "communication started"; mitk::IGTLMessage::Pointer receivedMessage; bool condition = false; igtl::Matrix4x4 transformPLUS; while (!(receivedMessage.IsNotNull() && receivedMessage->IsDataValid())) { std::this_thread::sleep_for(std::chrono::milliseconds(50)); m_TransformDeviceSource->Update(); receivedMessage = m_TransformDeviceSource->GetOutput(); igtl::TransformMessage::Pointer msg = dynamic_cast<igtl::TransformMessage *>(m_TransformDeviceSource->GetOutput()->GetMessage().GetPointer()); if (msg == nullptr || msg.IsNull()) { MITK_INFO << "Received message could not be casted to TransformMessage. Skipping..."; continue; } else { if (std::strcmp(msg->GetDeviceName(), "ImageToTracker") != 0) { MITK_INFO << "Was not Image to Tracker Transform. Skipping..."; continue; } else { msg->GetMatrix(transformPLUS); condition = true; break; } } } if (condition) { this->ProcessPlusCalibration(transformPLUS); } else { m_Controls.m_GotCalibrationLabel->setStyleSheet("QLabel { color : red; }"); m_Controls.m_GotCalibrationLabel->setText("Something went wrong. Please try again"); } } else { MITK_INFO << " no connection"; m_Controls.m_GotCalibrationLabel->setStyleSheet("QLabel { color : red; }"); m_Controls.m_GotCalibrationLabel->setText("Something went wrong. Please try again"); } } else { m_Controls.m_GotCalibrationLabel->setStyleSheet("QLabel { color : red; }"); m_Controls.m_GotCalibrationLabel->setText("Something went wrong. Please try again"); } } void QmitkUltrasoundCalibration::ProcessPlusCalibration(igtl::Matrix4x4 &imageToTracker) { mitk::AffineTransform3D::Pointer imageToTrackerTransform = mitk::AffineTransform3D::New(); itk::Matrix<mitk::ScalarType, 3, 3> rotationFloat = itk::Matrix<mitk::ScalarType, 3, 3>(); itk::Vector<mitk::ScalarType, 3> translationFloat = itk::Vector<mitk::ScalarType, 3>(); rotationFloat[0][0] = imageToTracker[0][0]; rotationFloat[0][1] = imageToTracker[0][1]; rotationFloat[0][2] = imageToTracker[0][2]; rotationFloat[1][0] = imageToTracker[1][0]; rotationFloat[1][1] = imageToTracker[1][1]; rotationFloat[1][2] = imageToTracker[1][2]; rotationFloat[2][0] = imageToTracker[2][0]; rotationFloat[2][1] = imageToTracker[2][1]; rotationFloat[2][2] = imageToTracker[2][2]; translationFloat[0] = imageToTracker[0][3]; translationFloat[1] = imageToTracker[1][3]; translationFloat[2] = imageToTracker[2][3]; imageToTrackerTransform->SetTranslation(translationFloat); imageToTrackerTransform->SetMatrix(rotationFloat); m_CombinedModality->SetCalibration(imageToTrackerTransform); m_Controls.m_ToolBox->setItemEnabled(2, true); m_Controls.m_SavePlusCalibration->setEnabled(true); m_Controls.m_GotCalibrationLabel->setStyleSheet("QLabel { color : green; }"); - m_Controls.m_GotCalibrationLabel->setText("Recieved Calibration from PLUS you can now save it"); + m_Controls.m_GotCalibrationLabel->setText("Received Calibration from PLUS you can now save it"); } void QmitkUltrasoundCalibration::OnStopCalibrationProcess() { this->ClearTemporaryMembers(); m_Timer->stop(); this->GetDataStorage()->Remove(m_Node); m_Node = nullptr; this->GetDataStorage()->Remove(m_CalibNode); m_CalibNode = nullptr; this->GetDataStorage()->Remove(m_WorldNode); m_WorldNode = nullptr; m_Controls.m_ToolBox->setCurrentIndex(0); } void QmitkUltrasoundCalibration::OnDeviceServiceEvent(const ctkServiceEvent event) { if (m_CombinedModality.IsNull() || event.getType() != ctkServiceEvent::MODIFIED) { return; } ctkServiceReference service = event.getServiceReference(); QString curDepth = service.getProperty(QString::fromStdString(mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH)).toString(); if (m_CurrentDepth != curDepth) { m_CurrentDepth = curDepth; this->OnReset(); } } void QmitkUltrasoundCalibration::OnAddCalibPoint() { auto world = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetSelectedPosition(); this->m_CalibPointsImage->InsertPoint(m_CalibPointsCount, world); this->m_CalibPointsTool->InsertPoint(m_CalibPointsCount, this->m_FreezePoint); QString text = text.number(m_CalibPointsCount + 1); text = "Point " + text; this->m_Controls.m_CalibPointList->addItem(text); m_CalibPointsCount++; SwitchFreeze(); } void QmitkUltrasoundCalibration::OnCalibration() { if (m_CombinedModality.IsNull()) { return; } // Compute transformation vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); transform->SetSourceLandmarks(this->ConvertPointSetToVtkPolyData(m_CalibPointsImage)->GetPoints()); transform->SetTargetLandmarks(this->ConvertPointSetToVtkPolyData(m_CalibPointsTool)->GetPoints()); if (!m_CombinedModality->GetIsTrackedUltrasoundActive()) { if (m_Controls.m_ScaleTransform->isChecked()) { transform->SetModeToSimilarity(); } // use affine transform else { transform->SetModeToRigidBody(); } // use similarity transform: scaling is not touched MITK_INFO << "TEST"; } else { transform->SetModeToRigidBody(); // use similarity transform: scaling is not touched } transform->Modified(); transform->Update(); // Convert from vtk to itk data types itk::Matrix<mitk::ScalarType, 3, 3> rotationFloat = itk::Matrix<mitk::ScalarType, 3, 3>(); itk::Vector<mitk::ScalarType, 3> translationFloat = itk::Vector<mitk::ScalarType, 3>(); vtkSmartPointer<vtkMatrix4x4> m = transform->GetMatrix(); rotationFloat[0][0] = m->GetElement(0, 0); rotationFloat[0][1] = m->GetElement(0, 1); rotationFloat[0][2] = m->GetElement(0, 2); rotationFloat[1][0] = m->GetElement(1, 0); rotationFloat[1][1] = m->GetElement(1, 1); rotationFloat[1][2] = m->GetElement(1, 2); rotationFloat[2][0] = m->GetElement(2, 0); rotationFloat[2][1] = m->GetElement(2, 1); rotationFloat[2][2] = m->GetElement(2, 2); translationFloat[0] = m->GetElement(0, 3); translationFloat[1] = m->GetElement(1, 3); translationFloat[2] = m->GetElement(2, 3); mitk::PointSet::Pointer ImagePointsTransformed = m_CalibPointsImage->Clone(); this->ApplyTransformToPointSet(ImagePointsTransformed, transform); mitk::DataNode::Pointer CalibPointsImageTransformed = this->GetDataStorage()->GetNamedNode("Calibration Points Image (Transformed)"); if (CalibPointsImageTransformed.IsNull()) { CalibPointsImageTransformed = mitk::DataNode::New(); CalibPointsImageTransformed->SetName("Calibration Points Image (Transformed)"); this->GetDataStorage()->Add(CalibPointsImageTransformed); } CalibPointsImageTransformed->SetData(ImagePointsTransformed); // Set new calibration transform m_Transformation = mitk::AffineTransform3D::New(); m_Transformation->SetTranslation(translationFloat); m_Transformation->SetMatrix(rotationFloat); MITK_INFO << "New Calibration transform: " << m_Transformation; mitk::SlicedGeometry3D::Pointer sliced3d = dynamic_cast<mitk::SlicedGeometry3D *>(m_Node->GetData()->GetGeometry()); mitk::PlaneGeometry::Pointer plane = const_cast<mitk::PlaneGeometry *>(sliced3d->GetPlaneGeometry(0)); plane->SetIndexToWorldTransform(m_Transformation); // Save to US-Device m_CombinedModality->SetCalibration(m_Transformation); m_Controls.m_ToolBox->setItemEnabled(2, true); // Save to NeedleProjectionFilter m_NeedleProjectionFilter->SetTargetPlane(m_Transformation); // Update Calibration FRE m_CalibrationStatistics = mitk::PointSetDifferenceStatisticsCalculator::New(); mitk::PointSet::Pointer p1 = this->m_CalibPointsTool->Clone(); // We use clones to calculate statistics to avoid concurrency Problems // Create point set with transformed image calibration points for // calculating the difference of image calibration and tool // calibration points in one geometry space mitk::PointSet::Pointer p2 = mitk::PointSet::New(); int n = 0; for (mitk::PointSet::PointsConstIterator it = m_CalibPointsImage->Begin(); it != m_CalibPointsImage->End(); ++it, ++n) { p2->InsertPoint(n, m_Transformation->TransformPoint(it->Value())); } m_CalibrationStatistics->SetPointSets(p1, p2); // QString text = text.number(m_CalibrationStatistics->GetRMS()); QString text = QString::number(ComputeFRE(m_CalibPointsImage, m_CalibPointsTool, transform)); MITK_INFO << "Calibration FRE: " << text.toStdString().c_str(); m_Controls.m_EvalLblCalibrationFRE->setText(text); m_Node->SetStringProperty("Calibration FRE", text.toStdString().c_str()); // Enable Button to save Calibration m_Controls.m_CalibBtnSaveCalibration->setEnabled(true); } void QmitkUltrasoundCalibration::OnLoadPhantomConfiguration() { // clear all data ClearTemporaryMembers(); // reset UI m_Controls.m_CalibBtnMatchAnnotationToPhantomConfiguration->setEnabled(false); m_Controls.m_RefinePhantomAnnotationsGroupBox->setEnabled(false); m_Controls.m_CalibBtnPerformPhantomCalibration->setEnabled(false); m_Controls.m_CalibBtnSavePhantomCalibration->setEnabled(false); // open phantom configuration QString fileName = QFileDialog::getOpenFileName(nullptr, "Load phantom configuration", "", "*.mps"); // dialog closed or selection canceled if (fileName.isNull()) { return; } m_PhantomConfigurationPointSet = dynamic_cast<mitk::PointSet *>(mitk::IOUtil::Load(fileName.toStdString()).at(0).GetPointer()); // transform phantom fiducials to tracking space mitk::NavigationData::Pointer currentSensorData = this->m_Tracker->GetOutput(0)->Clone(); for (int i = 0; i < m_PhantomConfigurationPointSet->GetSize(); i++) { mitk::Point3D phantomPoint = m_PhantomConfigurationPointSet->GetPoint(i); mitk::Point3D transformedPoint = currentSensorData->TransformPoint(phantomPoint); this->m_CalibPointsTool->InsertPoint(i, transformedPoint); } // add point set interactor for image calibration points mitk::PointSetDataInteractor::Pointer imageCalibrationPointSetInteractor = mitk::PointSetDataInteractor::New(); imageCalibrationPointSetInteractor->LoadStateMachine("PointSet.xml"); imageCalibrationPointSetInteractor->SetEventConfig("PointSetConfig.xml"); imageCalibrationPointSetInteractor->SetDataNode(m_WorldNode); imageCalibrationPointSetInteractor->SetMaxPoints(m_PhantomConfigurationPointSet->GetSize()); // Call On AddCalibPointPhantomBased() when point was added itk::SimpleMemberCommand<QmitkUltrasoundCalibration>::Pointer pointAddedCommand = itk::SimpleMemberCommand<QmitkUltrasoundCalibration>::New(); pointAddedCommand->SetCallbackFunction(this, &QmitkUltrasoundCalibration::OnPhantomCalibPointsChanged); m_CalibPointsImage->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand); m_CalibPointsImage->AddObserver(mitk::PointSetMoveEvent(), pointAddedCommand); // Set size of image points points m_WorldNode->ReplaceProperty("point 2D size", mitk::FloatProperty::New(10.0)); } void QmitkUltrasoundCalibration::OnPhantomCalibPointsChanged() { int currentIndex = m_CalibPointsImage->SearchSelectedPoint(); mitk::Point3D currentImagePoint = m_CalibPointsImage->GetPoint(currentIndex); UpdatePhantomAnnotationPointVisualization(currentIndex); // create sphere to show radius in which next point has to be placed this->GetDataStorage()->Remove(this->GetDataStorage()->GetNamedNode("NextPointIndicator")); if (currentIndex < m_CalibPointsTool->GetSize() - 1) { float distanceToNextPoint = m_CalibPointsTool->GetPoint(currentIndex).EuclideanDistanceTo(m_CalibPointsTool->GetPoint(currentIndex + 1)); vtkSmartPointer<vtkSphereSource> vtkHelperSphere = vtkSmartPointer<vtkSphereSource>::New(); vtkHelperSphere->SetCenter(currentImagePoint[0], currentImagePoint[1], currentImagePoint[2]); vtkHelperSphere->SetRadius(distanceToNextPoint); vtkHelperSphere->SetPhiResolution(40); vtkHelperSphere->SetThetaResolution(40); vtkHelperSphere->Update(); mitk::Surface::Pointer helperSphere = mitk::Surface::New(); helperSphere->SetVtkPolyData(vtkHelperSphere->GetOutput()); mitk::DataNode::Pointer helperSphereNode = mitk::DataNode::New(); helperSphereNode->SetName("NextPointIndicator"); helperSphereNode->SetData(helperSphere); helperSphereNode->SetColor(0.0, 1.0, 0.0); this->GetDataStorage()->Add(helperSphereNode); } if (m_CalibPointsTool->GetSize() == m_CalibPointsImage->GetSize()) { m_Controls.m_CalibBtnMatchAnnotationToPhantomConfiguration->setEnabled(true); } } void QmitkUltrasoundCalibration::UpdatePhantomAnnotationPointVisualization(int index) { mitk::Point3D currentImagePoint = m_CalibPointsImage->GetPoint(index); // create sphere to show current fiducial std::stringstream pointName; pointName << "Point"; pointName << index; this->GetDataStorage()->Remove(this->GetDataStorage()->GetNamedNode(pointName.str())); vtkSmartPointer<vtkSphereSource> vtkPointSphere = vtkSmartPointer<vtkSphereSource>::New(); vtkPointSphere->SetCenter(currentImagePoint[0], currentImagePoint[1], currentImagePoint[2]); vtkPointSphere->SetRadius(5.0); vtkPointSphere->SetPhiResolution(40); vtkPointSphere->SetThetaResolution(40); vtkPointSphere->Update(); mitk::Surface::Pointer pointSphere = mitk::Surface::New(); pointSphere->SetVtkPolyData(vtkPointSphere->GetOutput()); mitk::DataNode::Pointer sphereNode = mitk::DataNode::New(); sphereNode->SetName(pointName.str()); sphereNode->SetData(pointSphere); sphereNode->SetColor(1.0, 1.0, 0.0); this->GetDataStorage()->Add(sphereNode); } void QmitkUltrasoundCalibration::OnMatchAnnotationToPhantomConfiguration() { // Transform pointset of phantom configuration to currently annotated image points vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); transform->SetModeToRigidBody(); vtkSmartPointer<vtkPoints> toolLandmarks = this->ConvertPointSetToVtkPolyData(m_CalibPointsTool)->GetPoints(); transform->SetSourceLandmarks(toolLandmarks); transform->SetTargetLandmarks(this->ConvertPointSetToVtkPolyData(m_CalibPointsImage)->GetPoints()); transform->Update(); // update image annotation with matched phantom configuration vtkSmartPointer<vtkPoints> transformedToolLandmarks = vtkSmartPointer<vtkPoints>::New(); transform->TransformPoints(toolLandmarks, transformedToolLandmarks); for (int i = 0; i < transformedToolLandmarks->GetNumberOfPoints(); i++) { m_CalibPointsImage->InsertPoint(i, transformedToolLandmarks->GetPoint(i)); UpdatePhantomAnnotationPointVisualization(i); } m_Controls.m_RefinePhantomAnnotationsGroupBox->setEnabled(true); m_Controls.m_CalibBtnPerformPhantomCalibration->setEnabled(true); } void QmitkUltrasoundCalibration::TranslatePhantomAnnotations(double tx, double ty, double tz) { vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New(); transform->Translate(tx, ty, tz); vtkSmartPointer<vtkPoints> currentPoints = this->ConvertPointSetToVtkPolyData(m_CalibPointsImage)->GetPoints(); vtkSmartPointer<vtkPoints> transformedPoints = vtkSmartPointer<vtkPoints>::New(); transform->TransformPoints(currentPoints, transformedPoints); for (int i = 0; i < transformedPoints->GetNumberOfPoints(); i++) { m_CalibPointsImage->InsertPoint(i, transformedPoints->GetPoint(i)); UpdatePhantomAnnotationPointVisualization(i); } } void QmitkUltrasoundCalibration::RotatePhantomAnnotations(double angle) { vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New(); transform->RotateZ(angle); vtkSmartPointer<vtkPoints> currentPoints = this->ConvertPointSetToVtkPolyData(m_CalibPointsImage)->GetPoints(); vtkSmartPointer<vtkPoints> transformedPoints = vtkSmartPointer<vtkPoints>::New(); transform->TransformPoints(currentPoints, transformedPoints); for (int i = 0; i < transformedPoints->GetNumberOfPoints(); i++) { m_CalibPointsImage->InsertPoint(i, transformedPoints->GetPoint(i)); UpdatePhantomAnnotationPointVisualization(i); } } void QmitkUltrasoundCalibration::OnMovePhantomAnnotationsUp() { this->TranslatePhantomAnnotations(0, -m_Image->GetGeometry()->GetSpacing()[1], 0); } void QmitkUltrasoundCalibration::OnMovePhantomAnnotationsDown() { this->TranslatePhantomAnnotations(0, m_Image->GetGeometry()->GetSpacing()[1], 0); } void QmitkUltrasoundCalibration::OnMovePhantomAnnotationsLeft() { this->TranslatePhantomAnnotations(-m_Image->GetGeometry()->GetSpacing()[0], 0, 0); } void QmitkUltrasoundCalibration::OnMovePhantomAnnotationsRight() { this->TranslatePhantomAnnotations(m_Image->GetGeometry()->GetSpacing()[0], 0, 0); } void QmitkUltrasoundCalibration::OnRotatePhantomAnnotationsRight() { mitk::BoundingBox::PointType centerOfPointSet = m_CalibPointsImage->GetGeometry()->GetBoundingBox()->GetCenter(); this->TranslatePhantomAnnotations(-centerOfPointSet[0], -centerOfPointSet[1], -centerOfPointSet[2]); this->RotatePhantomAnnotations(0.5); this->TranslatePhantomAnnotations(centerOfPointSet[0], centerOfPointSet[1], centerOfPointSet[2]); } void QmitkUltrasoundCalibration::OnRotatePhantomAnnotationsLeft() { mitk::BoundingBox::PointType centerOfPointSet = m_CalibPointsImage->GetGeometry()->GetBoundingBox()->GetCenter(); this->TranslatePhantomAnnotations(-centerOfPointSet[0], -centerOfPointSet[1], -centerOfPointSet[2]); this->RotatePhantomAnnotations(-0.5); this->TranslatePhantomAnnotations(centerOfPointSet[0], centerOfPointSet[1], centerOfPointSet[2]); } void QmitkUltrasoundCalibration::OnPhantomBasedCalibration() { // perform calibration OnCalibration(); m_Controls.m_CalibBtnSavePhantomCalibration->setEnabled(true); } void QmitkUltrasoundCalibration::OnAddEvalTargetPoint() { auto world = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetSelectedPosition(); this->m_EvalPointsImage->InsertPoint(m_EvalPointsImage->GetSize(), world); this->m_EvalPointsTool->InsertPoint(m_EvalPointsTool->GetSize(), this->m_FreezePoint); QString text = text.number(this->m_EvalPointsTool->GetSize()); this->m_Controls.m_EvalLblNumTargetPoints->setText(text); // Update FREs // Update Evaluation FRE, but only if it contains more than one point (will crash otherwise) if ((m_EvalPointsProjected->GetSize() > 1) && (m_EvalPointsTool->GetSize() > 1)) { m_EvaluationStatistics = mitk::PointSetDifferenceStatisticsCalculator::New(); m_ProjectionStatistics = mitk::PointSetDifferenceStatisticsCalculator::New(); mitk::PointSet::Pointer p1 = this->m_EvalPointsTool->Clone(); // We use clones to calculate statistics to avoid concurrency Problems mitk::PointSet::Pointer p2 = this->m_EvalPointsImage->Clone(); mitk::PointSet::Pointer p3 = this->m_EvalPointsProjected->Clone(); m_EvaluationStatistics->SetPointSets(p1, p2); m_ProjectionStatistics->SetPointSets(p1, p3); QString evalText = evalText.number(m_EvaluationStatistics->GetRMS()); QString projText = projText.number(m_ProjectionStatistics->GetRMS()); m_Controls.m_EvalLblEvaluationFRE->setText(evalText); m_Controls.m_EvalLblProjectionFRE->setText(projText); } SwitchFreeze(); } void QmitkUltrasoundCalibration::OnAddEvalProjectedPoint() { MITK_WARN << "Projection Evaluation may currently be inaccurate."; // TODO: Verify correct Evaluation. Is the Point that is added really current? mitk::Point3D projection = this->m_NeedleProjectionFilter->GetProjection()->GetPoint(1); m_EvalPointsProjected->InsertPoint(m_EvalPointsProjected->GetSize(), projection); QString text = text.number(this->m_EvalPointsProjected->GetSize()); this->m_Controls.m_EvalLblNumProjectionPoints->setText(text); } void QmitkUltrasoundCalibration::OnSaveEvaluation() { // Filename without suffix QString filename = m_Controls.m_EvalFilePath->text() + "//" + m_Controls.m_EvalFilePrefix->text(); MITK_WARN << "CANNOT SAVE, ABORTING!"; /* not working any more TODO! mitk::PointSetWriter::Pointer psWriter = mitk::PointSetWriter::New(); psWriter->SetInput(0, m_CalibPointsImage); psWriter->SetInput(1, m_CalibPointsTool); psWriter->SetInput(2, m_EvalPointsImage); psWriter->SetInput(3, m_EvalPointsTool); psWriter->SetInput(4, m_EvalPointsProjected); psWriter->SetFileName(filename.toStdString() + ".xml"); psWriter->Write(); */ // TODO: New writer for transformations must be implemented. /* mitk::TransformationFileWriter::Pointer tWriter = mitk::TransformationFileWriter::New(); tWriter->SetInput(0, m_CalibPointsImage); tWriter->SetInput(1, m_CalibPointsTool); tWriter->SetInput(2, m_EvalPointsImage); tWriter->SetInput(3, m_EvalPointsTool); tWriter->SetInput(4, m_EvalPointsProjected); tWriter->SetOutputFilename(filename.toStdString() + ".txt"); tWriter->DoWrite(this->m_Transformation); */ } void QmitkUltrasoundCalibration::OnSaveCalibration() { m_Controls.m_GotCalibrationLabel->setText(""); QString filename = QFileDialog::getSaveFileName(QApplication::activeWindow(), "Save Calibration", "", "Calibration files *.cal"); QFile file(filename); if (!file.open(QIODevice::WriteOnly | QIODevice::Text | QIODevice::Truncate)) { MITK_WARN << "Cannot open file '" << filename.toStdString() << "' for writing."; return; } std::string calibrationSerialization = m_CombinedModality->SerializeCalibration(); QTextStream outStream(&file); outStream << QString::fromStdString(calibrationSerialization); // save additional information if (m_Controls.m_saveAdditionalCalibrationLog->isChecked()) { mitk::SceneIO::Pointer mySceneIO = mitk::SceneIO::New(); QString filenameScene = filename + "_mitkScene.mitk"; mitk::NodePredicateNot::Pointer isNotHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); mitk::DataStorage::SetOfObjects::ConstPointer nodesToBeSaved = this->GetDataStorage()->GetSubset(isNotHelperObject); mySceneIO->SaveScene(nodesToBeSaved, this->GetDataStorage(), filenameScene.toStdString().c_str()); } } void QmitkUltrasoundCalibration::OnReset() { this->ClearTemporaryMembers(); if (m_Transformation.IsNull()) { m_Transformation = mitk::AffineTransform3D::New(); } m_Transformation->SetIdentity(); if (m_Node.IsNotNull() && (m_Node->GetData() != nullptr) && (m_Node->GetData()->GetGeometry() != nullptr)) { mitk::SlicedGeometry3D::Pointer sliced3d = dynamic_cast<mitk::SlicedGeometry3D *>(m_Node->GetData()->GetGeometry()); mitk::PlaneGeometry::Pointer plane = const_cast<mitk::PlaneGeometry *>(sliced3d->GetPlaneGeometry(0)); plane->SetIndexToWorldTransform(m_Transformation); } QString text1 = text1.number(this->m_EvalPointsTool->GetSize()); this->m_Controls.m_EvalLblNumTargetPoints->setText(text1); QString text2 = text2.number(this->m_EvalPointsProjected->GetSize()); this->m_Controls.m_EvalLblNumProjectionPoints->setText(text2); } void QmitkUltrasoundCalibration::Update() { // Update Tracking Data std::vector<mitk::NavigationData::Pointer> *datas = new std::vector<mitk::NavigationData::Pointer>(); datas->push_back(m_Tracker->GetOutput()); m_Controls.m_CalibTrackingStatus->SetNavigationDatas(datas); m_Controls.m_CalibTrackingStatus->Refresh(); m_Controls.m_EvalTrackingStatus->SetNavigationDatas(datas); m_Controls.m_EvalTrackingStatus->Refresh(); m_CombinedModality->Modified(); m_CombinedModality->Update(); // Update US Image mitk::Image::Pointer image = m_CombinedModality->GetOutput(); // make sure that always the current image is set to the data node if (image.IsNotNull() && m_Node->GetData() != image.GetPointer() && image->IsInitialized()) { m_Node->SetData(image); } // Update Needle Projection m_NeedleProjectionFilter->Update(); // only update 2d window because it is faster this->RequestRenderWindowUpdate(mitk::RenderingManager::REQUEST_UPDATE_2DWINDOWS); } void QmitkUltrasoundCalibration::SwitchFreeze() { m_Controls.m_CalibBtnAddPoint->setEnabled(false); // generally deactivate // We use the activity state of the timer to determine whether we are currently viewing images if (!m_Timer->isActive()) // Activate Imaging { // if (m_Node) m_Node->ReleaseData(); if (m_CombinedModality.IsNull()) { m_Timer->stop(); return; } m_CombinedModality->Update(); m_Image = m_CombinedModality->GetOutput(); if (m_Image.IsNotNull() && m_Image->IsInitialized()) { m_Node->SetData(m_Image); } std::vector<mitk::NavigationData::Pointer> datas; datas.push_back(m_Tracker->GetOutput()); m_Controls.m_CalibTrackingStatus->SetNavigationDatas(&datas); m_Controls.m_CalibTrackingStatus->ShowStatusLabels(); m_Controls.m_CalibTrackingStatus->Refresh(); m_Controls.m_EvalTrackingStatus->SetNavigationDatas(&datas); m_Controls.m_EvalTrackingStatus->ShowStatusLabels(); m_Controls.m_EvalTrackingStatus->Refresh(); int interval = 40; m_Timer->setInterval(interval); m_Timer->start(); m_CombinedModality->SetIsFreezed(false); } else if (this->m_Tracker->GetOutput(0)->IsDataValid()) { // deactivate Imaging m_Timer->stop(); // Remember last tracking coordinates m_FreezePoint = this->m_Tracker->GetOutput(0)->GetPosition(); m_Controls.m_CalibBtnAddPoint->setEnabled(true); // activate only, if valid point is set m_CombinedModality->SetIsFreezed(true); } } void QmitkUltrasoundCalibration::ShowNeedlePath() { // Init Filter this->m_NeedleProjectionFilter->SelectInput(0); // Create Node for Pointset mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode("Needle Path"); if (node.IsNull()) { node = mitk::DataNode::New(); node->SetName("Needle Path"); node->SetData(m_NeedleProjectionFilter->GetProjection()); node->SetBoolProperty("show contour", true); this->GetDataStorage()->Add(node); } } void QmitkUltrasoundCalibration::ClearTemporaryMembers() { m_CalibPointsTool->Clear(); m_CalibPointsImage->Clear(); m_CalibPointsCount = 0; m_EvalPointsImage->Clear(); m_EvalPointsTool->Clear(); m_EvalPointsProjected->Clear(); this->m_Controls.m_CalibPointList->clear(); m_SpacingPoints->Clear(); m_Controls.m_SpacingPointsList->clear(); m_SpacingPointsCount = 0; } vtkSmartPointer<vtkPolyData> QmitkUltrasoundCalibration::ConvertPointSetToVtkPolyData(mitk::PointSet::Pointer PointSet) { vtkSmartPointer<vtkPolyData> returnValue = vtkSmartPointer<vtkPolyData>::New(); vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New(); for (int i = 0; i < PointSet->GetSize(); i++) { double point[3] = {PointSet->GetPoint(i)[0], PointSet->GetPoint(i)[1], PointSet->GetPoint(i)[2]}; points->InsertNextPoint(point); } vtkSmartPointer<vtkPolyData> temp = vtkSmartPointer<vtkPolyData>::New(); temp->SetPoints(points); vtkSmartPointer<vtkVertexGlyphFilter> vertexFilter = vtkSmartPointer<vtkVertexGlyphFilter>::New(); vertexFilter->SetInputData(temp); vertexFilter->Update(); returnValue->ShallowCopy(vertexFilter->GetOutput()); return returnValue; } double QmitkUltrasoundCalibration::ComputeFRE(mitk::PointSet::Pointer imageFiducials, mitk::PointSet::Pointer realWorldFiducials, vtkSmartPointer<vtkLandmarkTransform> transform) { if (imageFiducials->GetSize() != realWorldFiducials->GetSize()) return -1; double FRE = 0; for (int i = 0; i < imageFiducials->GetSize(); ++i) { itk::Point<double> current_image_fiducial_point = imageFiducials->GetPoint(i); if (transform != nullptr) { current_image_fiducial_point = transform->TransformPoint( imageFiducials->GetPoint(i)[0], imageFiducials->GetPoint(i)[1], imageFiducials->GetPoint(i)[2]); } double cur_error_squared = current_image_fiducial_point.SquaredEuclideanDistanceTo(realWorldFiducials->GetPoint(i)); FRE += cur_error_squared; } FRE = sqrt(FRE / (double)imageFiducials->GetSize()); return FRE; } void QmitkUltrasoundCalibration::ApplyTransformToPointSet(mitk::PointSet::Pointer pointSet, vtkSmartPointer<vtkAbstractTransform> transform) { for (int i = 0; i < pointSet->GetSize(); ++i) { itk::Point<double> current_point_transformed = itk::Point<double>(); current_point_transformed = transform->TransformPoint(pointSet->GetPoint(i)[0], pointSet->GetPoint(i)[1], pointSet->GetPoint(i)[2]); pointSet->SetPoint(i, current_point_transformed); } } void QmitkUltrasoundCalibration::OnFreezeClicked() { if (m_CombinedModality.IsNull()) { return; } if (m_CombinedModality->GetIsFreezed()) { // device was already frozen so we need to delete all spacing points because they need to be collected all at once // no need to check if all four points are already collected, because if that's the case you can no longer click the // Freeze button m_SpacingPoints->Clear(); m_Controls.m_SpacingPointsList->clear(); m_SpacingPointsCount = 0; m_Controls.m_SpacingAddPoint->setEnabled(false); } else { m_Controls.m_SpacingAddPoint->setEnabled(true); } SwitchFreeze(); } void QmitkUltrasoundCalibration::OnAddSpacingPoint() { auto point = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetSelectedPosition(); this->m_SpacingPoints->InsertPoint(m_SpacingPointsCount, point); QString text = text.number(m_SpacingPointsCount + 1); text = "Point " + text; this->m_Controls.m_SpacingPointsList->addItem(text); m_SpacingPointsCount++; if (m_SpacingPointsCount == 4) // now we have all 4 points needed { m_Controls.m_SpacingAddPoint->setEnabled(false); m_Controls.m_CalculateSpacing->setEnabled(true); m_Controls.m_SpacingBtnFreeze->setEnabled(false); } } void QmitkUltrasoundCalibration::OnCalculateSpacing() { mitk::Point3D horizontalOne = m_SpacingPoints->GetPoint(0); mitk::Point3D horizontalTwo = m_SpacingPoints->GetPoint(1); mitk::Point3D verticalOne = m_SpacingPoints->GetPoint(2); mitk::Point3D verticalTwo = m_SpacingPoints->GetPoint(3); // Get the distances between the points in the image double xDistance = horizontalOne.EuclideanDistanceTo(horizontalTwo); double yDistance = verticalOne.EuclideanDistanceTo(verticalTwo); // Calculate the spacing of the image and fill a vector with it double xSpacing = 30 / xDistance; double ySpacing = 20 / yDistance; m_CombinedModality->GetUltrasoundDevice()->SetSpacing(xSpacing, ySpacing); // Now that the spacing is set clear all stuff and return to Calibration m_SpacingPoints->Clear(); m_Controls.m_SpacingPointsList->clear(); m_SpacingPointsCount = 0; m_CombinedModality->SetIsFreezed(false); } void QmitkUltrasoundCalibration::OnUSDepthChanged(const std::string &key, const std::string &) { // whenever depth of USImage is changed the spacing should no longer be overwritten if (key == mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH) { } } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.h index f92a943e7b..78bfc1132f 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/QmitkUltrasoundCalibration.h @@ -1,380 +1,380 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUltrasoundCalibration_h #define QmitkUltrasoundCalibration_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> // MITK #include <mitkIGTLClient.h> #include <mitkNavigationDataToIGTLMessageFilter.h> #include <mitkNeedleProjectionFilter.h> #include <mitkPointSet.h> #include <mitkPointSetDifferenceStatisticsCalculator.h> #include <mitkUSCombinedModality.h> // Microservices #include "ui_QmitkUltrasoundCalibrationControls.h" #include <vtkLandmarkTransform.h> #include <vtkPolyData.h> #include <vtkSmartPointer.h> #include <ctkServiceEvent.h> /*! \brief QmitkUltrasoundCalibration \warning This view provides a simple calibration process. \ingroup ${plugin_target}_internal */ class QmitkUltrasoundCalibration : public QmitkAbstractView { Q_OBJECT public: QmitkUltrasoundCalibration(); ~QmitkUltrasoundCalibration() override; static const std::string VIEW_ID; void CreateQtPartControl(QWidget *parent) override; void OnUSDepthChanged(const std::string &, const std::string &); protected slots: /** * \brief Triggered, whenever the user switches Tabs * */ void OnTabSwitch(int index); /** * \brief Triggered, when the user has clicked "select Devices". * */ void OnDeviceSelected(); void OnDeviceDeselected(); /** * \brief Triggered, when the user clicks "Add Point" * */ void OnAddCalibPoint(); /** * \brief Triggered, when the user clicks "Calibrate" * */ void OnCalibration(); /** * \brief Triggered, when the user clicks "Add Target Points". * * Adds an image point and an tracking point to their respective evaluation pointsets */ void OnAddEvalTargetPoint(); /** * \brief Triggered, when the user clicks "Add Point". * * Adds a projected point to the projected point evaluation set. */ void OnAddEvalProjectedPoint(); /** * \brief Triggered when the user clicks "Save Results" in the Evaluation tab. */ void OnSaveEvaluation(); /** * \brief Triggered when the user clicks "Save Calibration" in the Calibration tab. */ void OnSaveCalibration(); /** * \brief Triggered when the user clicks "Run Next Round". Also used as a reset mechanism. */ void OnReset(); /** * \brief Triggered in regular intervals by a timer, when live view is enabled. * */ void Update(); /** * \brief Freezes or unfreezes the image. */ void SwitchFreeze(); /** * */ void OnStartCalibrationProcess(); /** *\brief Method to use the PLUS-Toolkoit for Calibration of EchoTrack */ void OnStartPlusCalibration(); void OnStopPlusCalibration(); /** *\ brief Starts the Streaming of USImage and Navigation Data when PLUS is connected */ void OnStartStreaming(); void OnNewConnection(); /** \*brief Get the Calibration from the PLUS-Toolkit once Calibration with fCal is done */ void OnGetPlusCalibration(); /** - \*brief Convert the recieved igtl::Matrix into an mitk::AffineTransform3D which can be used to calibrate the + \*brief Convert the received igtl::Matrix into an mitk::AffineTransform3D which can be used to calibrate the CombinedModality */ void ProcessPlusCalibration(igtl::Matrix4x4 &imageToTracker); void OnStreamingTimerTimeout(); /** * */ void OnStopCalibrationProcess(); void OnAddCurrentTipPositionToReferencePoints(); void OnStartVerification(); void OnAddCurrentTipPositionForVerification(); void OnDeviceServiceEvent(const ctkServiceEvent event); void OnFreezeClicked(); void OnAddSpacingPoint(); void OnCalculateSpacing(); /* * \brief load the configuration of the phantom fiducials which have to be saved as points in the sensor coordinate * system of the tracking sensor attached to the phantom */ void OnLoadPhantomConfiguration(); /* * \brief match the annotation pointset with the geometry of the phantom configuration */ void OnMatchAnnotationToPhantomConfiguration(); /* * \brief move the annotation pointset up */ void OnMovePhantomAnnotationsUp(); /* * \brief move the annotation pointset down */ void OnMovePhantomAnnotationsDown(); /* * \brief move the annotation pointset left */ void OnMovePhantomAnnotationsLeft(); /* * \brief move the annotation pointset right */ void OnMovePhantomAnnotationsRight(); /* * \brief rotate the annotation pointset right */ void OnRotatePhantomAnnotationsRight(); /* * \brief rotate the annotation pointset left */ void OnRotatePhantomAnnotationsLeft(); /* * \brief add a calibration point to be used for phantom based calibration */ void OnPhantomCalibPointsChanged(); /* * \brief perform phantom based calibration */ void OnPhantomBasedCalibration(); signals: /** - * \brief used for thread seperation, the worker thread must not call OnNewConnection directly. + * \brief used for thread separation, the worker thread must not call OnNewConnection directly. * QT signals are thread safe and separate the threads */ void NewConnectionSignal(); protected: void SetFocus() override; void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList<mitk::DataNode::Pointer> &nodes) override; void UpdatePhantomAnnotationPointVisualization(int index = -1); /*! \brief translate the annotated image feature m_CalibPoints image by the specified translation vector */ void TranslatePhantomAnnotations(double tx, double ty, double tz); /*! \brief rotate the annotated image feature m_CalibPoints image by the specified angle */ void RotatePhantomAnnotations(double angle); Ui::QmitkUltrasoundCalibrationControls m_Controls; /** * \brief Internal function that activates display of the needle path. */ void ShowNeedlePath(); /** * \brief Clears all member attributes which are holding intermediate results for the calibration. */ void ClearTemporaryMembers(); void OnPlusConnected(); /** * \brief The combined modality used for imaging and tracking. */ mitk::AbstractUltrasoundTrackerDevice::Pointer m_CombinedModality; /** * \brief NavigationDataSource used for tracking data. * This will be gotten by the combined modality. */ mitk::NavigationDataSource::Pointer m_Tracker; QTimer *m_Timer; mitk::DataNode::Pointer m_Node; mitk::DataNode::Pointer m_CalibNode; mitk::DataNode::Pointer m_WorldNode; // IGTL Servers and Devices needed for the communication with PLUS mitk::IGTLServer::Pointer m_USServer; mitk::IGTLMessageProvider::Pointer m_USMessageProvider; mitk::ImageToIGTLMessageFilter::Pointer m_USImageToIGTLMessageFilter; mitk::IGTLServer::Pointer m_TrackingServer; mitk::IGTLMessageProvider::Pointer m_TrackingMessageProvider; mitk::NavigationDataToIGTLMessageFilter::Pointer m_TrackingToIGTLMessageFilter; mitk::IGTLClient::Pointer m_TransformClient; mitk::IGTLDeviceSource::Pointer m_TransformDeviceSource; QTimer *m_StreamingTimer; unsigned long m_NewConnectionObserverTag; /** * \brief The current Ultrasound Image. */ mitk::Image::Pointer m_Image; /** * \brief Current point when the image was last frozen. */ mitk::Point3D m_FreezePoint; /** * \brief Pointset containing all tool points. */ mitk::PointSet::Pointer m_CalibPointsImage; /** * \brief Pointset containing corresponding points on the image. */ mitk::PointSet::Pointer m_CalibPointsTool; mitk::PointSet::Pointer m_PhantomConfigurationPointSet; ///< pointset holding the feature position of the phantom in tool coordinates /** * \brief Pointset containing Projected Points (aka "where we thought the needle was gonna land") */ mitk::PointSet::Pointer m_EvalPointsProjected; /** * \brief Pointset containing the evaluated points on the image. */ mitk::PointSet::Pointer m_EvalPointsImage; /** * \brief Pointset containing tracked evaluation points. */ mitk::PointSet::Pointer m_EvalPointsTool; /** * \brief Pointset containing tracked evaluation points. */ mitk::PointSet::Pointer m_VerificationReferencePoints; mitk::DataNode::Pointer m_VerificationReferencePointsDataNode; int m_currentPoint; std::vector<mitk::Point3D> m_allReferencePoints; std::vector<double> m_allErrors; /** * \brief Creates a Pointset that projects the needle's path */ mitk::NeedleProjectionFilter::Pointer m_NeedleProjectionFilter; /** * \brief Total number of calibration points set. */ int m_CalibPointsCount; QString m_CurrentDepth; /** * \brief StatisticsRegarding Projection Accuracy. * (Compares m_EvalPointsProjected to m_EvalPointsImage) */ mitk::PointSetDifferenceStatisticsCalculator::Pointer m_ProjectionStatistics; /** * \brief StatisticsRegarding Evaluation Accuracy. * (Compares m_EvalPointsTool to m_EvalPointsImage) */ mitk::PointSetDifferenceStatisticsCalculator::Pointer m_EvaluationStatistics; /** * \brief StatisticsRegarding Calibration Accuracy. * (Compares m_CalibPointsTool to a transformed copy of m_CalibPointsImage). */ mitk::PointSetDifferenceStatisticsCalculator::Pointer m_CalibrationStatistics; /** * \brief Result of the Calibration. */ mitk::AffineTransform3D::Pointer m_Transformation; /** * This method is copied from PointSetModifier which is part of MBI. It should be replaced * by external method call as soon as this functionality will be available in MITK. */ vtkSmartPointer<vtkPolyData> ConvertPointSetToVtkPolyData(mitk::PointSet::Pointer PointSet); double ComputeFRE(mitk::PointSet::Pointer imageFiducials, mitk::PointSet::Pointer realWorldFiducials, vtkSmartPointer<vtkLandmarkTransform> transform = nullptr); void ApplyTransformToPointSet(mitk::PointSet::Pointer pointSet, vtkSmartPointer<vtkAbstractTransform> transform); mitk::PointSet::Pointer m_SpacingPoints; mitk::DataNode::Pointer m_SpacingNode; int m_SpacingPointsCount; private: mitk::MessageDelegate2<QmitkUltrasoundCalibration, const std::string &, const std::string &> m_USDeviceChanged; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/SettingsWidgets/QmitkUSNavigationAbstractSettingsWidget.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/SettingsWidgets/QmitkUSNavigationAbstractSettingsWidget.h index c6c03d4be2..2133f307f5 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/SettingsWidgets/QmitkUSNavigationAbstractSettingsWidget.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/SettingsWidgets/QmitkUSNavigationAbstractSettingsWidget.h @@ -1,99 +1,99 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSNavigationAbstractSettingsWidget_h #define QmitkUSNavigationAbstractSettingsWidget_h #include <QWidget> #include "mitkDataNode.h" /** * \brief Abstract class of settings widgets used by the QmitkUSNavigationProcessWidget. * This class handles the emitting of Saved(), Canceled() and SettingsChanged() * signals and provides slots for save and cancel buttons. * * The actual saving and loading of settings is delegated to concrete subclasses * which should therefore implement OnSetSettingsNode(), OnSaveProcessing(), * OnCancelProcessing(), OnLoadSettingsProcessing(). */ class QmitkUSNavigationAbstractSettingsWidget : public QWidget { Q_OBJECT signals: void Saved(); void Canceled(); void SettingsChanged(itk::SmartPointer<mitk::DataNode>); protected slots: /** * \brief Triggers the saving of the current settings. * OnSaveProcessing() is called and the Saved() signal is emitted afterwards. */ void OnSave(); /** * \brief Ends the settings changing process without saving the changes. * OnCancelProcessing() is called and the Canceled() signal is emitted * afterwards. */ void OnCancel(); public: explicit QmitkUSNavigationAbstractSettingsWidget(QWidget *parent = nullptr); ~QmitkUSNavigationAbstractSettingsWidget() override; /** * \brief Loads the settings. * The actual loading is done by calling the OnLoadSettingsProcessing() * method. */ void LoadSettings(); /** * \brief Setter for the data node in which the settings are loaded. * The settings are made available as properties of this data node. */ void SetSettingsNode(itk::SmartPointer<mitk::DataNode> settingsNode, bool overwriteValues = false); itk::SmartPointer<mitk::DataNode> GetSettingsNode(); protected: /** * \brief Method for handling the setting of a new settings node. * This method has to be implemented by a concrete subclass. */ virtual void OnSetSettingsNode(itk::SmartPointer<mitk::DataNode> settingsNode, bool overwriteValues) = 0; /** * \brief Method for actually saving the settings. * This method has to be implemented by a concrete subclass. */ virtual void OnSaveProcessing() = 0; /** * \brief Method for handling the cancel process. * This method can be implemented by a concrete subclass. An empty default * implementation exists. */ virtual void OnCancelProcessing() {} /** - * \brief Method for acutally loading the settings. + * \brief Method for actually loading the settings. * This method has to be implemented by a concrete subclass. */ virtual void OnLoadSettingsProcessing() = 0; private: mitk::DataNode::Pointer m_SettingsNode; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/USNavigationControls.ui b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/USNavigationControls.ui index 578840cd65..3e998fe46e 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/USNavigationControls.ui +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/USNavigationControls.ui @@ -1,370 +1,370 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>USNavigationControls</class> <widget class="QWidget" name="USNavigationControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>360</width> <height>330</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QTabWidget" name="m_TabWidget"> <property name="currentIndex"> <number>0</number> </property> <widget class="QWidget" name="Devices"> <attribute name="title"> <string>Devices</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QLabel" name="label_3"> <property name="font"> <weight>75</weight> <bold>true</bold> <underline>true</underline> </property> <property name="text"> <string>Step 1:</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_4"> <property name="text"> <string> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Please select an ultrasound device and a tracking device from the list above. These devices will be used to perform the procedure. Both devices must be active to appear on their respective List. Optionally, you may load a calibration file along with the ultrasound device.</body></html> </string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>10</height> </size> </property> </spacer> </item> <item> <widget class="QLabel" name="label_13"> <property name="font"> <pointsize>14</pointsize> <weight>75</weight> <bold>true</bold> </property> <property name="text"> <string>Device Selection:</string> </property> </widget> </item> <item> <widget class="QmitkUSNavigationStepCombinedModality" name="m_CombinedModalitySelectionWidget" native="true"/> </item> <item> <widget class="QPushButton" name="m_BtnSelectDevices"> <property name="enabled"> <bool>false</bool> </property> <property name="minimumSize"> <size> <width>0</width> <height>50</height> </size> </property> <property name="text"> <string>Select Combined Modality</string> </property> </widget> </item> <item> <spacer name="spacer1"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Expanding</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>220</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tab"> <attribute name="title"> <string>Zoning</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <widget class="QLabel" name="label_14"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>75</weight> <bold>true</bold> <underline>true</underline> </property> <property name="text"> <string>Step 2:</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_15"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Sans Serif'; font-size:10pt; font-weight:400; font-style:normal;"> Mark risk struktures by navigating to them with the ultrasound probe. Once located, press freeze. Mark the structures by clicking in the center, moving the mouse till the size is acceptable and clicking again to fix the size. You may then change the zone's color and size. Repeat until satisfied. </body></html> </string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <spacer name="verticalSpacer_4"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>10</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="m_BtnFreeze"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>50</height> </size> </property> <property name="text"> <string>Freeze Image</string> </property> <property name="checkable"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QLabel" name="label"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string><html><head/><body>Current Zones:</body></html></string> </property> </widget> </item> <item> <widget class="QmitkUSZoneManagementWidget" name="m_ZonesWidget" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> </widget> </item> <item> <widget class="QPushButton" name="m_BtnStartIntervention"> <property name="minimumSize"> <size> <width>0</width> <height>50</height> </size> </property> <property name="font"> <pointsize>12</pointsize> <weight>75</weight> <bold>true</bold> </property> <property name="text"> <string>Start Intervention</string> </property> </widget> </item> </layout> </widget> <widget class="QWidget" name="tab_4"> <attribute name="title"> <string>Intervention</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_4"> <item> <widget class="QLabel" name="label_10"> <property name="font"> <weight>75</weight> <bold>true</bold> <underline>true</underline> </property> <property name="text"> <string>Step 3:</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_11"> <property name="text"> <string> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> - When all the previous steps are completed, click "Start Intervention" to proceed. When done, click "Stop Intervention" to finsih. No further input is required at this stage. You may stop the intervention to go back and change parameters at any time.</body></html> + When all the previous steps are completed, click "Start Intervention" to proceed. When done, click "Stop Intervention" to finish. No further input is required at this stage. You may stop the intervention to go back and change parameters at any time.</body></html> </string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QPushButton" name="m_BtnReset"> <property name="minimumSize"> <size> <width>0</width> <height>50</height> </size> </property> <property name="text"> <string>Stop and Reset</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_BtnNeedleView"> <property name="minimumSize"> <size> <width>0</width> <height>50</height> </size> </property> <property name="text"> <string>NeedleView</string> </property> <property name="checkable"> <bool>true</bool> </property> <property name="checked"> <bool>false</bool> </property> </widget> </item> <item> <widget class="QGroupBox" name="m_RangeBox"> <property name="title"> <string>Zone Range</string> </property> </widget> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkUSZoneManagementWidget</class> <extends>QWidget</extends> <header>src/internal/Widgets/QmitkUSZoneManagementWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkUSNavigationStepCombinedModality</class> <extends>QWidget</extends> <header>src/internal/NavigationStepWidgets/QmitkUSNavigationStepCombinedModality.h</header> <container>1</container> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.h index b862ea1fd8..9e7dc059b4 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.h @@ -1,60 +1,60 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSCombinedModalityCreationWidget_h #define QmitkUSCombinedModalityCreationWidget_h #include <QWidget> #include "mitkUSCombinedModality.h" namespace Ui { class QmitkUSCombinedModalityCreationWidget; } /** * \brief Widget that enables the user to create a mitk::USCombinedModality of a mitk::NavigationDataSource and a mitk::USDevice. * A mitk::NavigationDataSource and a mitk::USDevice can be picked from two lists, showing * the corresponding micro service objects. The combined modality is registered as a micro * service as well during the creation process. */ class QmitkUSCombinedModalityCreationWidget : public QWidget { Q_OBJECT signals: - /** \brief Emmited when the user clicks the "Cancel" button. */ + /** \brief Emitted when the user clicks the "Cancel" button. */ void SignalAborted(); - /** \brief Emmited when the user clicked the "Create" button and the creation is successfull. */ + /** \brief Emitted when the user clicked the "Create" button and the creation is successful. */ void SignalCreated(mitk::USCombinedModality::Pointer combinedModality); - /** \brief Emmited when the user clicked the "Create" button and the creation is successfull. */ + /** \brief Emitted when the user clicked the "Create" button and the creation is successful. */ void SignalCreated(); protected slots: /** \brief Creates a combined modility of the selected mitk::NavigationDataSource and mitk::USDevice. **/ void OnCreation(); /** \brief Handles the enabled state of the "Create" button. **/ void OnSelectedUltrasoundOrTrackingDevice(); public: explicit QmitkUSCombinedModalityCreationWidget(QWidget *parent = nullptr); ~QmitkUSCombinedModalityCreationWidget() override; private: Ui::QmitkUSCombinedModalityCreationWidget *ui; itk::SmartPointer<mitk::AbstractUltrasoundTrackerDevice> m_CombinedModality; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.ui b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.ui index fddd41ad6f..0a5b900580 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.ui +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSCombinedModalityCreationWidget.ui @@ -1,174 +1,174 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkUSCombinedModalityCreationWidget</class> <widget class="QWidget" name="QmitkUSCombinedModalityCreationWidget"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>323</width> <height>350</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>350</height> </size> </property> <property name="windowTitle"> <string>Form</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QLabel" name="usDevicesServiceListLabel"> <property name="font"> <weight>75</weight> <bold>true</bold> </property> <property name="text"> <string>Ultrasound Devices:</string> </property> </widget> </item> <item> <widget class="QmitkServiceListWidget" name="usDevicesServiceList" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Ignored"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> </widget> </item> <item> <widget class="QLabel" name="trackingDevicesServiceListLabel"> <property name="font"> <weight>75</weight> <bold>true</bold> </property> <property name="text"> <string>Tracking Devices:</string> </property> </widget> </item> <item> <widget class="QmitkServiceListWidget" name="trackingDevicesServiceList" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Ignored"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> </widget> </item> <item> <widget class="QLabel" name="helpLabel"> <property name="text"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Sans Serif'; font-size:10pt; font-weight:400; font-style:normal;"> -Please select an ultrasound device and a tracking device from the lists above. These devices will be used to create a combined modality. Additionally, you may specifiy a vendor and a name.</body></html></string> +Please select an ultrasound device and a tracking device from the lists above. These devices will be used to create a combined modality. Additionally, you may specify a vendor and a name.</body></html></string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <layout class="QFormLayout" name="formLayout"> <item row="0" column="0"> <widget class="QLabel" name="vendorLineEditLabel"> <property name="text"> <string>Vendor</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLineEdit" name="vendorLineEdit"> <property name="text"> <string>MBI</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="nameLineEditLabel"> <property name="text"> <string>Name</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QLineEdit" name="nameLineEdit"> <property name="text"> <string>Combined Modality</string> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="activateTrackedUSCheckbox"> <property name="text"> <string>Activate Tracked Ultrasound</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QPushButton" name="createButton"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Create Combined Modality</string> </property> <property name="icon"> <iconset resource="../../../resources/USNavigation.qrc"> <normaloff>:/USNavigation/accept.png</normaloff>:/USNavigation/accept.png</iconset> </property> </widget> </item> <item> <widget class="QPushButton" name="cancelButton"> <property name="text"> <string>Cancel</string> </property> <property name="icon"> <iconset resource="../../../resources/USNavigation.qrc"> <normaloff>:/USNavigation/restart.png</normaloff>:/USNavigation/restart.png</iconset> </property> </widget> </item> </layout> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkServiceListWidget</class> <extends>QWidget</extends> <header>QmitkServiceListWidget.h</header> <container>1</container> </customwidget> </customwidgets> <resources> <include location="../../../resources/USNavigation.qrc"/> </resources> <connections/> <slots> <slot>SignalAborted()</slot> </slots> </ui> diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationFreezeButton.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationFreezeButton.h index d0552974ca..53b56553b8 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationFreezeButton.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationFreezeButton.h @@ -1,77 +1,77 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSNavigationFreezeButton_h #define QmitkUSNavigationFreezeButton_h #include <QPushButton> #include "mitkUSCombinedModality.h" /** * \brief QPushButton for freezing and unfreezing a combined modality. - * The button already has an icon and a text. On every successfull + * The button already has an icon and a text. On every successful * freeze or unfreeze the signal SignalFrezzed() is emitted. One should * listen to this signal rather than to the clicked() signal of the * QPushButton as the combined modality may not be freezed after * clicked() was emitted. */ class QmitkUSNavigationFreezeButton : public QPushButton { Q_OBJECT signals: /** * \brief Emitted every time the freeze state of the combined modality changed. * True if the combined modality is freezed now, false if it isn't. */ void SignalFreezed(bool); protected slots: void OnButtonClicked(bool checked); void OnFreezeButtonToggle(); public: explicit QmitkUSNavigationFreezeButton(QWidget* parent = nullptr); ~QmitkUSNavigationFreezeButton() override; /** * \brief Setter for the combined modality to be freezed by this button. * An index may be specified for a tracking data output. The combined * modality will only be freezed then, if the current tracking data of * this output is valid. */ void SetCombinedModality(mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality, int outputIndex = -1); /** * \brief Try to freeze the combined modality. * This does the same as clicking the button while the combined * modality isn't freezed. If the combined modality is already * freezed this method does nothing. */ void Freeze(); /** * \brief Unfreeze the combined modality. * This does the same as clicking the button while the combined * modality is freezed. If the combined modality isn't freezed * this method does nothing. */ void Unfreeze(); private: mitk::AbstractUltrasoundTrackerDevice::Pointer m_CombinedModality; int m_OutputIndex; bool m_FreezeButtonToggle; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationZoneDistancesWidget.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationZoneDistancesWidget.h index 3e5910075a..07ce78de3f 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationZoneDistancesWidget.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSNavigationZoneDistancesWidget.h @@ -1,73 +1,73 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSNavigationZoneDistancesWidget_h #define QmitkUSNavigationZoneDistancesWidget_h #include <QWidget> #include "mitkNumericTypes.h" namespace itk { template<class T> class SmartPointer; } namespace mitk { class NavigationData; class DataNode; } class QmitkZoneProgressBar; /** * \brief Widget for showing distances to given zones using instances of QmitkZoneProgressBar. * The zones can be added by AddZone() and removed by ClearZones(). To update * the progress bars, UpdateDistancesToNeedlePosition() has to be called with * a navigation data. */ class QmitkUSNavigationZoneDistancesWidget : public QWidget { Q_OBJECT signals: - /** \brief Emmited whenever a the distance to a zone falls below zero. */ + /** \brief Emitted whenever a the distance to a zone falls below zero. */ void SignalZoneViolated(const mitk::DataNode*, mitk::Point3D); public: explicit QmitkUSNavigationZoneDistancesWidget(QWidget *parent = nullptr); ~QmitkUSNavigationZoneDistancesWidget() override; /** * \brief Set the key for the data node float property holding the radius of a zone. * The default value of this attribute is "zone.size". */ void SetSizePropertyKey(const std::string& sizePropertyKey); /** \brief Get the key for the data node float property holding the radius of a zone. */ const std::string& GetSizePropertyKey() const; /** \brief Adds a zone to the widget. */ void AddZone(itk::SmartPointer<mitk::DataNode> zoneNode); /** \brief Removes all zones from the widget. */ void ClearZones(); /** \brief Updates color and label of each zone distance bar according to the given needle position. */ void UpdateDistancesToNeedlePosition(itk::SmartPointer<mitk::NavigationData> needle); protected: std::string m_SizePropertyKey; QVector<itk::SmartPointer<mitk::DataNode> > m_ZoneNodes; QVector<QmitkZoneProgressBar*> m_ZoneProgressBars; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSZoneManagementWidget.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSZoneManagementWidget.h index b87de26d5b..1302e7dd96 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSZoneManagementWidget.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkUSZoneManagementWidget.h @@ -1,150 +1,150 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUSZoneManagementWidget_h #define QmitkUSZoneManagementWidget_h #include <QWidget> #include "mitkDataStorage.h" namespace itk { template<class T> class SmartPointer; } namespace mitk { class USZonesInteractor; } namespace Ui { class QmitkUSZoneManagementWidget; } class QmitkUSZonesDataModel; class QItemSelection; class QModelIndex; /** * \brief Shows a table of the zone nodes and allows to change properties and add and delete zone nodes. * * A data node interactor (mitk::USZonesInteractor) is used for creating new zone nodes and a QTableModel * (QmitkUSZonesDataModel) is used for handling the zones data. * * When using the widget, one has to call OnStartAddingZone() every time he wants the interaction for adding * new zone nodes to be active. */ class QmitkUSZoneManagementWidget : public QWidget { Q_OBJECT signals: /** - * \brief Emmited whenever a new zone was added to the data model. + * \brief Emitted whenever a new zone was added to the data model. */ void ZoneAdded(); /** - * \brief Emmited whenever a new zone was removed from the data mode. + * \brief Emitted whenever a new zone was removed from the data mode. */ void ZoneRemoved(); public slots: /** * \brief Removes all rows from the data model which are selected in the table. */ void RemoveSelectedRows(); /** * \brief Creates a new zone node and activates the data interactor on this node. * This slot has to be called whenever a new zone should be added. Interactions are active * then, so the user can create the zone. */ void OnStartAddingZone(); /** * \brief Aborts the creation of a new zone and deletes the corresponding node. */ void OnAbortAddingZone(); /** * \brief Removes all nodes from the data model. */ void OnResetZones(); protected slots: void OnSelectionChanged(const QItemSelection& selected, const QItemSelection & deselected); /** * \brief Updates zone radius according to the value of the zone size slider. * \param value new radius of the zone */ void OnZoneSizeSliderValueChanged(int value); /** * \brief Updates maximum number of added zones and selects the last row of the table. * It is called every time a row was added to the data model. */ void OnRowInsertion(const QModelIndex& parent, int start, int end); /** * \brief Updates the zone size slider when data was changed. * It is called every time a row was changed in the data model. */ void OnDataChanged(const QModelIndex& topLeft, const QModelIndex& /*bottomRight*/); public: explicit QmitkUSZoneManagementWidget(QWidget* parent = nullptr); ~QmitkUSZoneManagementWidget() override; /** * \brief Sets the state machine file for being used by the mitk::USZonesInteractor * \param filename name of the state machine file */ void SetStateMachineFilename(const std::string& filename); /** * \brief Setter for the DataStorage where the zone nodes will be stored. * The nodes will be derivates of the node specified by the base node name. * * \param dataStorage data storage where the zone nodes will be stored * \param baseNodeName optional name of the node which will be the source node of all zone nodes (defaults "Zones") */ void SetDataStorage(mitk::DataStorage::Pointer dataStorage, const char* baseNodeName = "Zones"); /** * \brief Setter for the DataStorage where the zone nodes will be stored. * The nodes will be derivates of the base nodes. * - * \param dataStorage data storage where the zone nodes will be strored + * \param dataStorage data storage where the zone nodes will be stored * \param baseNode data node which will be the source node of all zone nodes */ void SetDataStorage(mitk::DataStorage::Pointer dataStorage, itk::SmartPointer<mitk::DataNode> baseNode); /** * \brief Get all zone nodes from the data storage. */ mitk::DataStorage::SetOfObjects::ConstPointer GetZoneNodes(); protected: QmitkUSZonesDataModel* m_ZonesDataModel; itk::SmartPointer<mitk::USZonesInteractor> m_Interactor; mitk::DataStorage::Pointer m_DataStorage; mitk::DataNode::Pointer m_BaseNode; std::string m_StateMachineFileName; private: Ui::QmitkUSZoneManagementWidget* ui; unsigned int m_CurMaxNumOfZones; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkZoneProgressBar.h b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkZoneProgressBar.h index 7e965c790c..1a40b3f20d 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkZoneProgressBar.h +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/Widgets/QmitkZoneProgressBar.h @@ -1,98 +1,98 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkZoneProgressBar_h #define QmitkZoneProgressBar_h #include <QProgressBar> /** * \brief QProgressBar for displaying distances to zones. * Colors are changed according to the distance to the zone and and the * progress will be filled more the smaller the distance to the zone * becomes. */ class QmitkZoneProgressBar : public QProgressBar { Q_OBJECT public: /** * \brief Initializes the progress bar with the given name, max range and warn range. * The colors are set to default values (color: red, warn color: red, border * color: gray). * * \param name will be shown on the progress bar * \param maxRange the progress bar will be empty for distances greater or equal to this distance - * \param warnRange the progess bar will change its color for distances smaller than this distance + * \param warnRange the progress bar will change its color for distances smaller than this distance */ explicit QmitkZoneProgressBar(QString name, int maxRange, int warnRange, QWidget *parent = nullptr); /** * @param value the current distance to the zone */ void setValue(int value); /** * \brief Can be called to indicate that there is currently no valid distance value available. * E.g. if tracking data is not available at the moment. If there is a valid * value again, the method setValue() can be called. */ void setValueInvalid(); /** * \brief Setter for the text on the progress bar. * Defaults to the string given as name to the constructor. The format string * can contain '%1' which will be replaced by the current distance value. * * \param format the text to be displayed on the progress bar */ void SetTextFormatValid(QString format); /** * \param format the text to be displayed when setValueInvalid() was called */ void SetTextFormatInvalid(QString format); /** * \param color the color for the progress bar fill */ void SetColor(float color[3]); /** * \param color the color, the progress bar fill changes to if the distance falls below the warn range */ void SetWarnColor(float color[3]); /** * @param color the color for the border of the progress bar */ void SetBorderColor(float color[3]); protected: void UpdateStyleSheet(QString startColor, QString stopColor); QString ColorToString(float color[3]); QString m_TextFormatValid; QString m_TextFormatInvalid; int m_MaxRange; int m_WarnRange; QString m_ColorString; QString m_WarnColorString; QString m_BorderColorString; QString m_StyleSheet; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/mitkUSTargetPlacementQualityCalculator.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/mitkUSTargetPlacementQualityCalculator.cpp index b35d43278e..aa13133c00 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/mitkUSTargetPlacementQualityCalculator.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/mitkUSTargetPlacementQualityCalculator.cpp @@ -1,146 +1,146 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkUSTargetPlacementQualityCalculator.h" #include "mitkDataNode.h" #include "mitkSurface.h" #include "mitkPointSet.h" #include <vtkSmartPointer.h> #include <vtkPolyData.h> #include <vtkTransformPolyDataFilter.h> #include <vtkCenterOfMass.h> #include <vtkMath.h> #include <vtkLinearTransform.h> mitk::USTargetPlacementQualityCalculator::USTargetPlacementQualityCalculator() : m_OptimalAngle(-1), m_CentersOfMassDistance(-1), m_MeanAngleDifference(-1) { } mitk::USTargetPlacementQualityCalculator::~USTargetPlacementQualityCalculator() { } void mitk::USTargetPlacementQualityCalculator::Update() { if ( m_OptimalAngle < 0 ) { mitkThrow() << "Optimal angle must be set before call of update."; } if ( m_TargetPoints.IsNull() ) { mitkThrow() << "Targets points must be set before call of update."; } vtkSmartPointer<vtkPolyData> targetSurface = this->GetTransformedPolydata(); vtkSmartPointer<vtkCenterOfMass> centerOfMass = vtkSmartPointer<vtkCenterOfMass>::New(); centerOfMass->SetUseScalarsAsWeights(false); centerOfMass->SetInputData(targetSurface); centerOfMass->Update(); double targetCenter[3]; centerOfMass->GetCenter(targetCenter); mitk::Point3D targetCenterPoint; targetCenterPoint[0] = targetCenter[0]; targetCenterPoint[1] = targetCenter[1]; targetCenterPoint[2] = targetCenter[2]; MITK_INFO("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPlacementPlanning") << "Center of mass of the target calculated as: " << targetCenterPoint; vtkSmartPointer<vtkPoints> plannedTargetsPoints = vtkSmartPointer<vtkPoints>::New(); std::vector< itk::Vector<float, 3u> > targetsToCenterOfMassVectors; for ( mitk::PointSet::PointsConstIterator it = m_TargetPoints->Begin(); it != m_TargetPoints->End(); ++it ) { // insert all planned target points into a vtkPolyData for calculating // the center of mass afterwards //mitk::Point3D origin = it->GetData()->GetGeometry()->GetOrigin(); mitk::Point3D origin = it->Value(); plannedTargetsPoints->InsertNextPoint(origin[0], origin[1], origin[2]); // define normalised vectors from each planned target point to the center // of mass of the target structure itk::Vector<float, 3u> vector = targetCenterPoint - origin; vector.Normalize(); targetsToCenterOfMassVectors.push_back(vector); } vtkSmartPointer<vtkPolyData> plannedTargetsPointSet = vtkSmartPointer<vtkPolyData>::New(); plannedTargetsPointSet->SetPoints(plannedTargetsPoints); centerOfMass->SetInputData(plannedTargetsPointSet); centerOfMass->Update(); double plannedCenter[3]; centerOfMass->GetCenter(plannedCenter); mitk::Point3D plannedTargetsCenterPoint; plannedTargetsCenterPoint[0] = plannedCenter[0]; plannedTargetsCenterPoint[1] = plannedCenter[1]; plannedTargetsCenterPoint[2] = plannedCenter[2]; MITK_INFO("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPlacementPlanning") - << "Center of mass of the planned target points caclulated as: " << plannedTargetsCenterPoint; + << "Center of mass of the planned target points calculated as: " << plannedTargetsCenterPoint; m_CentersOfMassDistance = targetCenterPoint.EuclideanDistanceTo(plannedTargetsCenterPoint); MITK_INFO("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPlacementPlanning") << "Distance between target center of mass and planned target points center of mass: " << m_CentersOfMassDistance; unsigned int numberOfAngles = targetsToCenterOfMassVectors.size() * (targetsToCenterOfMassVectors.size()-1) / 2; m_AngleDifferences.set_size(numberOfAngles); unsigned int n = 0; m_MeanAngleDifference = 0; for ( unsigned int i = 0; i < targetsToCenterOfMassVectors.size(); i++ ) { for ( unsigned int j = i+1; j < targetsToCenterOfMassVectors.size(); j++ ) { double angleDiff = acos ( targetsToCenterOfMassVectors.at(i) * targetsToCenterOfMassVectors.at(j) ) - m_OptimalAngle; if ( angleDiff < 0 ) { angleDiff = -angleDiff; } m_AngleDifferences.put(n++, angleDiff); m_MeanAngleDifference += angleDiff; } } m_MeanAngleDifference /= numberOfAngles; // calculate mean m_MeanAngleDifference = vtkMath::DegreesFromRadians(m_MeanAngleDifference); MITK_INFO("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPlacementPlanning") << "Angles between the target points: " << m_AngleDifferences; MITK_INFO("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPlacementPlanning") << "Mean difference of angles between the target points: " << m_MeanAngleDifference; } vtkSmartPointer<vtkPolyData> mitk::USTargetPlacementQualityCalculator::GetTransformedPolydata() { if ( m_TargetSurface.IsNull() || ! m_TargetSurface->GetVtkPolyData() ) { mitkThrow() << "Target surface must not be null."; } // transform vtk polydata according to mitk geometry vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New(); transformFilter->SetInputData(0, m_TargetSurface->GetVtkPolyData()); transformFilter->SetTransform(m_TargetSurface->GetGeometry()->GetVtkTransform()); transformFilter->Update(); return transformFilter->GetOutput(); } diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox index 3ab99a43a9..53abfc7575 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox +++ b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox @@ -1,92 +1,92 @@ /** \page org_imageguidedtherapytutorial The MITK-IGT Tutorial View This view is not meant as an end-user module. It contains tutorial program code that explains how to use the MITK-IGT component. It contains only two buttons. The "Start image guided therapy" button will create a virtual tracking device and a virtual tool. It will move the tool around on random paths in a tracking volume of 200x200x200 mm. The tool is visualized with a cone. If you do not see a cone moving around, you will need to initialize the rendering views correctly. Use the DataManager view to perform a global reinit. The symbol of this view is the following: \imageMacro{icon_igt_simple_example.png,"",2} and the whole view looks like this: \imageMacro{IGTExampleIGT_QT_Tutorial_PluginView.png,"",2} In this tutorial we connect to the NDI Polaris tracking system (or alternatively use a virtual tracking device) and we will show the movement of a tool as cone in the StdMultiWidget editor. First of all, you will have to add an IGT dependency to your cmake list. For this example, MitkIGTUI would be sufficient, but as the plugin contains several views, we have additional OpenIGTLink and US dependencies: \code{.cpp} project(org_mitk_gui_qt_igtexamples) mitk_create_plugin( EXPORT_DIRECTIVE IGTEXAMPLES_EXPORT EXPORTED_INCLUDE_SUFFIXES src MODULE_DEPENDS MitkQtWidgetsExt MitkIGT MitkIGTUI MitkOpenIGTLink MitkOpenIGTLinkUI MitkUS ) \endcode When clicking the start button, a cone should move in the 3D view and stop after clicking the stop button. -The view has several fuctions. Most of them deal with the basic functionality with the plugin (e.g. CreateQTPartControl or CreateConnections). For a deeper understanding, you might have a look at the files QmitkIGTTutorialView.cpp and QmitkIGTTutorialView.h +The view has several functions. Most of them deal with the basic functionality with the plugin (e.g. CreateQTPartControl or CreateConnections). For a deeper understanding, you might have a look at the files QmitkIGTTutorialView.cpp and QmitkIGTTutorialView.h For our IGT functionality, the following functions are important: \li OnStartIGT: Starts the navigation pipeline \li OnStopIGT: Disconnect the pipeline \li OnTimer: Updates the view Let's now have a deeper look at these functions. \section OnStartIGT OnStartIGT \snippet QmitkIGTTutorialView.cpp OnStart 1 -We first check in a try environment, if we should use an NDI tracking device or a virtual device. Let's start with NDI, we hardcode the parameters here and give out a warning. In your propper application, the parameters should be set via the gui aswell (see \ref org_mitk_views_igttrackingtoolbox ), but for simplicity, we just set hardcoded parameters here. If you want to try it with your own NDI device, you need to adapt these parameters here in the code: +We first check in a try environment, if we should use an NDI tracking device or a virtual device. Let's start with NDI, we hardcode the parameters here and give out a warning. In your proper application, the parameters should be set via the gui aswell (see \ref org_mitk_views_igttrackingtoolbox ), but for simplicity, we just set hardcoded parameters here. If you want to try it with your own NDI device, you need to adapt these parameters here in the code: \snippet QmitkIGTTutorialView.cpp OnStart 2 The tracking device has to be set to a source. For more information on the tracking pipeline, please have a look at the \ref IGTTutorialStepFilterPipeline. \snippet QmitkIGTTutorialView.cpp OnStart 3 Alternatively, we can setup a virtual tracking device. We create this device, set the bounds, add a tool and connect it to the source: \snippet QmitkIGTTutorialView.cpp OnStart 4 Now we need to connect the tracking system \snippet QmitkIGTTutorialView.cpp OnStart 5 For the visualisation, we need an object. Here, we create a red cone \snippet QmitkIGTTutorialView.cpp OnStart 6 The visualization filter will actually render the cone \snippet QmitkIGTTutorialView.cpp OnStart 7 For a continuous display, we need to call update, here we decide to do it every 100 ms using a timer. \snippet QmitkIGTTutorialView.cpp OnStart 8 Disable the selection of tracking devices during tracking: \snippet QmitkIGTTutorialView.cpp OnStart 8a -For propper coding, you should always catch the exceptions: +For proper coding, you should always catch the exceptions: \snippet QmitkIGTTutorialView.cpp OnStart 9 \section OnTimer OnTimer Each time, the timer is updated, the following code is executed: \snippet QmitkIGTTutorialView.cpp OnTimer \section OnStopIGT OnStopIGT This function will stop the pipeline and clean up everything: \snippet QmitkIGTTutorialView.cpp OnStop You now have a very simple plugin, which creates an own tracking device and starts or stops tracking. Of course, for your more advanced project, you could implement a new tracking device to be available in every plugin (see \ref IGTHowToImplementATrackingDevice ) or use already implemented tracking devices via the tracking toolbox and/or microservices. This small example should just show you the most simple way to start tracking. Return to the \ref IGTTutorialOverview "[IGT Tutorial Overview]" */ diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkOpenIGTLinkExample.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkOpenIGTLinkExample.dox index 76addade04..b0f9435159 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkOpenIGTLinkExample.dox +++ b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkOpenIGTLinkExample.dox @@ -1,6 +1,6 @@ /** \page org_openigtlinkexample OpenIGTLink client example -A simple OpenIGTLink client that can stream and visualize tracking data from an OpenIGTLink server. This server can be another MITK intances, e.g., running the OpenIGTLink provider example or any other OpenIGTLink server such as a PLUS server. +A simple OpenIGTLink client that can stream and visualize tracking data from an OpenIGTLink server. This server can be another MITK instances, e.g., running the OpenIGTLink provider example or any other OpenIGTLink server such as a PLUS server. */ diff --git a/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.cpp b/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.cpp index f108526e35..aed6e67a60 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.cpp +++ b/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.cpp @@ -1,728 +1,728 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkIGTTrackingLabView.h" #include <QmitkRenderWindow.h> #include <QmitkNDIConfigurationWidget.h> #include <QmitkFiducialRegistrationWidget.h> #include <QmitkUpdateTimerWidget.h> #include <QmitkToolSelectionWidget.h> #include <QmitkToolTrackingStatusWidget.h> #include <mitkStaticIGTHelperFunctions.h> #include <mitkIGTException.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateDataType.h> #include <itkVector.h> #include <vtkTransform.h> #include <vtkTransformPolyDataFilter.h> #include <vtkAppendPolyData.h> #include <vtkPoints.h> // Qt #include <QMessageBox> #include <QIcon> #include <QPushButton> // vtk #include <mitkVtkResliceInterpolationProperty.h> const std::string QmitkIGTTrackingLabView::VIEW_ID = "org.mitk.views.igttrackinglab"; QmitkIGTTrackingLabView::QmitkIGTTrackingLabView() : QmitkAbstractView() ,m_Source(nullptr) ,m_PermanentRegistrationFilter(nullptr) ,m_Visualizer(nullptr) ,m_VirtualView(nullptr) ,m_PSRecordingPointSet(nullptr) ,m_PointSetRecording(false) ,m_PermanentRegistration(false) ,m_CameraView(false) ,m_ImageFiducialsDataNode(nullptr) ,m_TrackerFiducialsDataNode(nullptr) ,m_PermanentRegistrationSourcePoints(nullptr) { } //############################################################################################### //############################################################################################### //############################## Timer method for IGT pipeline updating ######################### //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::UpdateTimer() { if (m_PermanentRegistration && m_PermanentRegistrationFilter.IsNotNull()) { if(IsTransformDifferenceHigh(m_ObjectmarkerNavigationData, m_ObjectmarkerNavigationDataLastUpdate)) { m_ObjectmarkerNavigationDataLastUpdate->Graft(m_ObjectmarkerNavigationData); m_PermanentRegistrationFilter->Update(); } } if (m_CameraView && m_VirtualView.IsNotNull()) {m_VirtualView->Update();} if(m_PointSetRecording && m_PSRecordingPointSet.IsNotNull()) { int size = m_PSRecordingPointSet->GetSize(); mitk::NavigationData::Pointer nd = m_PointSetRecordingNavigationData; if(size > 0) { mitk::Point3D p = m_PSRecordingPointSet->GetPoint(size-1); if(p.EuclideanDistanceTo(nd->GetPosition()) > (double) m_Controls.m_PSRecordingSpinBox->value()) m_PSRecordingPointSet->InsertPoint(size, nd->GetPosition()); } else m_PSRecordingPointSet->InsertPoint(size, nd->GetPosition()); } } //############################################################################################### //############################################################################################### //############################## Slots of CONFIGURATION step #################################### //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::OnSetupNavigation() { if(m_Source.IsNotNull()) if(m_Source->IsTracking()) return; mitk::DataStorage* ds = this->GetDataStorage(); if(ds == nullptr) { MITK_WARN << "IGTSurfaceTracker: Error. Cannot access DataStorage. Navigation not possible"; return; } //Building up the filter pipeline try { this->InitializeRegistration(); } catch(mitk::IGTException& e) { MITK_WARN << "Error while building the IGT-Pipeline: " << e.GetDescription(); this->DestroyIGTPipeline(); // destroy the pipeline if building is incomplete return; } catch(...) { MITK_WARN << "Unexpected error while building the IGT-Pipeline"; this->DestroyIGTPipeline(); return; } } void QmitkIGTTrackingLabView::OnInstrumentSelected() { if (m_Controls.m_TrackingDeviceSelectionWidget->GetSelectedNavigationDataSource().IsNotNull()) { m_InstrumentNavigationData = m_Controls.m_TrackingDeviceSelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_Controls.m_TrackingDeviceSelectionWidget->GetSelectedToolID()); } else { m_Controls.m_PointerNameLabel->setText("<not available>"); return; } if (m_InstrumentNavigationData.IsNotNull()) { m_Controls.m_PointerNameLabel->setText(m_InstrumentNavigationData->GetName()); } else { m_Controls.m_PointerNameLabel->setText("<not available>"); } } void QmitkIGTTrackingLabView::OnObjectmarkerSelected() { if (m_Controls.m_TrackingDeviceSelectionWidget->GetSelectedNavigationDataSource().IsNotNull()) { m_ObjectmarkerNavigationData = m_Controls.m_TrackingDeviceSelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_Controls.m_TrackingDeviceSelectionWidget->GetSelectedToolID()); MITK_INFO << "Objectmarker rotation: " << m_ObjectmarkerNavigationData->GetOrientation(); } else { m_Controls.m_ObjectmarkerNameLabel->setText("<not available>"); return; } if (m_ObjectmarkerNavigationData.IsNotNull()) { m_Controls.m_ObjectmarkerNameLabel->setText(m_ObjectmarkerNavigationData->GetName()); } else { m_Controls.m_ObjectmarkerNameLabel->setText("<not available>"); } } //############################################################################################### //############################################################################################### //####################### Slots of INITIAL REGISTRATION step #################################### //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::OnInitialRegistration() { //Check for initialization if (!CheckRegistrationInitialization()) return; mitk::PointSet::Pointer imageFiducials = dynamic_cast<mitk::PointSet*>(m_ImageFiducialsDataNode->GetData()); mitk::PointSet::Pointer trackerFiducials = dynamic_cast<mitk::PointSet*>(m_TrackerFiducialsDataNode->GetData()); //############### conversion to vtk data types (we will use the vtk landmark based transform) ########################## //convert point sets to vtk poly data vtkSmartPointer<vtkPoints> sourcePoints = vtkSmartPointer<vtkPoints>::New(); vtkSmartPointer<vtkPoints> targetPoints = vtkSmartPointer<vtkPoints>::New(); for (int i=0; i<imageFiducials->GetSize(); i++) { double point[3] = {imageFiducials->GetPoint(i)[0],imageFiducials->GetPoint(i)[1],imageFiducials->GetPoint(i)[2]}; sourcePoints->InsertNextPoint(point); double point_targets[3] = {trackerFiducials->GetPoint(i)[0],trackerFiducials->GetPoint(i)[1],trackerFiducials->GetPoint(i)[2]}; targetPoints->InsertNextPoint(point_targets); } //########################### here, the actual transform is computed ########################## //compute transform vtkSmartPointer<vtkLandmarkTransform> transform = vtkSmartPointer<vtkLandmarkTransform>::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); //compute FRE of transform double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(imageFiducials, trackerFiducials, transform); m_Controls.m_RegistrationWidget->SetQualityDisplayText("FRE: " + QString::number(FRE) + " mm"); //############################################################################################# //############### conversion back to itk/mitk data types ########################## //convert from vtk to itk data types itk::Matrix<float,3,3> rotationFloat = itk::Matrix<float,3,3>(); itk::Vector<float,3> translationFloat = itk::Vector<float,3>(); itk::Matrix<double,3,3> rotationDouble = itk::Matrix<double,3,3>(); itk::Vector<double,3> translationDouble = itk::Vector<double,3>(); vtkSmartPointer<vtkMatrix4x4> m = transform->GetMatrix(); for(int k=0; k<3; k++) for(int l=0; l<3; l++) { rotationFloat[k][l] = m->GetElement(k,l); rotationDouble[k][l] = m->GetElement(k,l); } for(int k=0; k<3; k++) { translationFloat[k] = m->GetElement(k,3); translationDouble[k] = m->GetElement(k,3); } //create affine transform 3D surface mitk::AffineTransform3D::Pointer mitkTransform = mitk::AffineTransform3D::New(); mitkTransform->SetMatrix(rotationDouble); mitkTransform->SetOffset(translationDouble); //############################################################################################# //############### object is transformed ########################## //save transform m_T_ObjectReg = mitk::NavigationData::New(mitkTransform); // this is stored in a member because it is needed for permanent registration later on //transform surface if(m_Controls.m_SurfaceActive->isChecked() && m_Controls.m_ObjectComboBox->GetSelectedNode().IsNotNull()) { m_Controls.m_ObjectComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(mitkTransform); } //################################################################ //############### if activated: ct image is also transformed ########################## //transform ct image //todo: Explain that AffineTransform3D is used, because NavigationData does not support spacing! if(m_Controls.m_ImageActive->isChecked() && m_Controls.m_ImageComboBox->GetSelectedNode().IsNotNull()) { //first we have to store the original ct image transform to compose it with the new transform later mitk::AffineTransform3D::Pointer imageTransform = m_Controls.m_ImageComboBox->GetSelectedNode()->GetData()->GetGeometry()->GetIndexToWorldTransform(); m_T_ImageGeo = mitk::AffineTransform3D::New(); // this is also stored in a member because it is needed for permanent registration later on //now the new transform of the ct image is computed m_T_ImageGeo->Compose(imageTransform); imageTransform->Compose(mitkTransform); mitk::AffineTransform3D::Pointer newImageTransform = mitk::AffineTransform3D::New(); //create new image transform... setting the composed directly leads to an error itk::Matrix<mitk::ScalarType,3,3> rotationFloatNew = imageTransform->GetMatrix(); itk::Vector<mitk::ScalarType,3> translationFloatNew = imageTransform->GetOffset(); newImageTransform->SetMatrix(rotationFloatNew); newImageTransform->SetOffset(translationFloatNew); m_Controls.m_ImageComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(newImageTransform); m_T_ImageReg = m_Controls.m_ImageComboBox->GetSelectedNode()->GetData()->GetGeometry()->GetIndexToWorldTransform(); } //################################################################ } void QmitkIGTTrackingLabView::OnAddRegistrationTrackingFiducial() { mitk::NavigationData::Pointer nd = m_InstrumentNavigationData; if( nd.IsNull() || !nd->IsDataValid()) { QMessageBox::warning( nullptr, "Invalid tracking data", "Navigation data is not available or invalid!", QMessageBox::Ok ); return; } if(m_TrackerFiducialsDataNode.IsNotNull() && m_TrackerFiducialsDataNode->GetData() != nullptr) { mitk::PointSet::Pointer ps = dynamic_cast<mitk::PointSet*>(m_TrackerFiducialsDataNode->GetData()); ps->InsertPoint(ps->GetSize(), nd->GetPosition()); } else QMessageBox::warning(nullptr, "IGTSurfaceTracker: Error", "Can not access Tracker Fiducials. Adding fiducial not possible!"); } void QmitkIGTTrackingLabView::InitializeRegistration() { mitk::DataStorage* ds = this->GetDataStorage(); if( ds == nullptr ) return; // let the registration widget know about the slice navigation controllers // in the active render window part (crosshair updates) foreach(QmitkRenderWindow* renderWindow, this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindows().values()) { m_Controls.m_RegistrationWidget->AddSliceNavigationController(renderWindow->GetSliceNavigationController()); } if(m_ImageFiducialsDataNode.IsNull()) { m_ImageFiducialsDataNode = mitk::DataNode::New(); mitk::PointSet::Pointer ifPS = mitk::PointSet::New(); m_ImageFiducialsDataNode->SetData(ifPS); mitk::Color color; color.Set(1.0f, 0.0f, 0.0f); m_ImageFiducialsDataNode->SetName("Image Fiducials"); m_ImageFiducialsDataNode->SetColor(color); m_ImageFiducialsDataNode->SetBoolProperty( "updateDataOnRender", false ); ds->Add(m_ImageFiducialsDataNode); } m_Controls.m_RegistrationWidget->SetImageFiducialsNode(m_ImageFiducialsDataNode); if(m_TrackerFiducialsDataNode.IsNull()) { m_TrackerFiducialsDataNode = mitk::DataNode::New(); mitk::PointSet::Pointer tfPS = mitk::PointSet::New(); m_TrackerFiducialsDataNode->SetData(tfPS); mitk::Color color; color.Set(0.0f, 1.0f, 0.0f); m_TrackerFiducialsDataNode->SetName("Tracking Fiducials"); m_TrackerFiducialsDataNode->SetColor(color); m_TrackerFiducialsDataNode->SetBoolProperty( "updateDataOnRender", false ); ds->Add(m_TrackerFiducialsDataNode); } m_Controls.m_RegistrationWidget->SetTrackerFiducialsNode(m_TrackerFiducialsDataNode); } //############################################################################################### //############################################################################################### //####################### Slots of PERMANENT REGISTRATION step ################################## //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::OnPermanentRegistration(bool on) { if(on) { //###################################################################### - //######################## inititalization ############################# + //######################## initialization ############################## //###################################################################### //some initial checks if(!CheckRegistrationInitialization()) { m_Controls.m_UsePermanentRegistrationToggle->setChecked(false); return; } //remember initial object transform to calculate the object to marker transform later on and convert it to navigation data mitk::AffineTransform3D::Pointer transform = this->m_Controls.m_ObjectComboBox->GetSelectedNode()->GetData()->GetGeometry()->GetIndexToWorldTransform(); mitk::NavigationData::Pointer T_Object = mitk::NavigationData::New(transform,false); //TODO: catch exception during conversion? //then reset the transform because we will now start to calculate the permanent registration this->m_Controls.m_ObjectComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIdentity(); if(m_Controls.m_ImageActive->isChecked()) {this->m_Controls.m_ImageComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(m_T_ImageGeo);} //create the permanent registration filter m_PermanentRegistrationFilter = mitk::NavigationDataObjectVisualizationFilter::New(); //###################################################################### //first: initialize permanent registration of surface (always activated) //###################################################################### //connect filter to source m_PermanentRegistrationFilter->SetInput(0,this->m_ObjectmarkerNavigationData); //set representation object m_PermanentRegistrationFilter->SetRepresentationObject(0,this->m_Controls.m_ObjectComboBox->GetSelectedNode()->GetData()); //get the marker transform out of the navigation data mitk::NavigationData::Pointer T_Marker = m_ObjectmarkerNavigationData; //compute transform from object to marker (T_MarkerRel = T_Object * T_Marker^-1) mitk::NavigationData::Pointer T_MarkerRel = mitk::NavigationData::New(); T_MarkerRel->Compose(T_Object); T_MarkerRel->Compose(T_Marker->GetInverse()); m_T_MarkerRel = T_MarkerRel; m_PermanentRegistrationFilter->SetOffset(0,m_T_MarkerRel->GetAffineTransform3D()); //###################################################################### //second: initialize permanent registration of image (if activated) //###################################################################### if (m_Controls.m_ImageActive->isChecked() && (m_Controls.m_ImageComboBox->GetSelectedNode().IsNotNull())) { mitk::DataNode::Pointer imageNode = this->m_Controls.m_ImageComboBox->GetSelectedNode(); imageNode->AddProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New(VTK_RESLICE_LINEAR) ); m_PermanentRegistrationFilter->SetInput(1,this->m_ObjectmarkerNavigationData); m_PermanentRegistrationFilter->SetRepresentationObject(1,imageNode->GetData()); //for the image we can't use NavigationData objects as transforms because an image needs additional geometry information, e.g., spacing //thus we use mitk::AffineTransform3D objects //computer transform from image to marker (T_ImageRel = T_ImageGeo * T_MarkerRel) mitk::AffineTransform3D::Pointer T_ImageRel = mitk::AffineTransform3D::New(); T_ImageRel->SetIdentity(); T_ImageRel->Compose(m_T_ImageGeo); T_ImageRel->Compose(m_T_MarkerRel->GetAffineTransform3D()); m_PermanentRegistrationFilter->SetOffset(1,T_ImageRel); } //some general stuff m_PermanentRegistration = true; m_ObjectmarkerNavigationDataLastUpdate = mitk::NavigationData::New(); } else //if off = disable the permanent registration { //stop permanent registration m_PermanentRegistration = false; //restore old registration if(m_T_ObjectReg.IsNotNull()) {this->m_Controls.m_ObjectComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(m_T_ObjectReg->GetAffineTransform3D());} if(m_T_ImageReg.IsNotNull()) {this->m_Controls.m_ImageComboBox->GetSelectedNode()->GetData()->GetGeometry()->SetIndexToWorldTransform(m_T_ImageReg);} //delete filter m_PermanentRegistrationFilter = nullptr; } } //############################################################################################### //############################################################################################### //####################### Slots of POINT SET RECORDING step ##################################### //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::OnPointSetRecording(bool record) { mitk::DataStorage* ds = this->GetDataStorage(); if(record) { if (m_Controls.m_PointSetRecordingToolSelectionWidget->GetSelectedToolID() == -1) { QMessageBox::warning(nullptr, "Error", "No tool selected for point set recording!"); m_Controls.m_PointSetRecordCheckBox->setChecked(false); return; } m_PointSetRecordingNavigationData = m_Controls.m_PointSetRecordingToolSelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_Controls.m_PointSetRecordingToolSelectionWidget->GetSelectedToolID()); //initialize point set mitk::DataNode::Pointer psRecND = ds->GetNamedNode("Recorded Points"); if(m_PSRecordingPointSet.IsNull() || psRecND.IsNull()) { m_PSRecordingPointSet = nullptr; m_PSRecordingPointSet = mitk::PointSet::New(); mitk::DataNode::Pointer dn = mitk::DataNode::New(); dn->SetName("Recorded Points"); dn->SetColor(0.,1.,0.); dn->SetData(m_PSRecordingPointSet); ds->Add(dn); } else { m_PSRecordingPointSet->Clear(); } m_PointSetRecording = true; } else { m_PointSetRecording = false; } } //############################################################################################### //############################################################################################### //####################### Slots of VIRTUAL CAMERA VIEW step ##################################### //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::OnVirtualCamera(bool on) { if (m_Controls.m_CameraViewSelection->GetSelectedToolID() == -1) { m_Controls.m_ActivateNeedleView->setChecked(false); QMessageBox::warning(nullptr, "Error", "No tool selected for camera view!"); return; } if(on) { m_VirtualView = mitk::CameraVisualization::New(); m_VirtualView->SetInput(m_Controls.m_CameraViewSelection->GetSelectedNavigationDataSource()->GetOutput(m_Controls.m_CameraViewSelection->GetSelectedToolID())); mitk::Vector3D viewDirection; viewDirection[0] = (int)(m_Controls.m_NeedleViewX->isChecked()); viewDirection[1] = (int)(m_Controls.m_NeedleViewY->isChecked()); viewDirection[2] = (int)(m_Controls.m_NeedleViewZ->isChecked()); if (m_Controls.m_NeedleViewInvert->isChecked()) viewDirection *= -1; m_VirtualView->SetDirectionOfProjectionInToolCoordinates(viewDirection); mitk::Vector3D viewUpVector; viewUpVector[0] = (int)(m_Controls.m_NeedleUpX->isChecked()); viewUpVector[1] = (int)(m_Controls.m_NeedleUpY->isChecked()); viewUpVector[2] = (int)(m_Controls.m_NeedleUpZ->isChecked()); if (m_Controls.m_NeedleUpInvert->isChecked()) viewUpVector *= -1; m_VirtualView->SetViewUpInToolCoordinates(viewUpVector); m_VirtualView->SetRenderer(this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("3d")->GetRenderer()); //next line: better code when this plugin is migrated to mitk::abstractview //m_VirtualView->SetRenderer(mitk::BaseRenderer::GetInstance(this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetRenderWindow("3d")->GetRenderWindow())); m_CameraView = true; //make pointer itself invisible m_Controls.m_CameraViewSelection->GetSelectedNavigationTool()->GetDataNode()->SetBoolProperty("visible",false); //disable UI elements m_Controls.m_ViewDirectionBox->setEnabled(false); m_Controls.m_ViewUpBox->setEnabled(false); } else { m_VirtualView = nullptr; m_CameraView = false; m_Controls.m_CameraViewSelection->GetSelectedNavigationTool()->GetDataNode()->SetBoolProperty("visible",true); m_Controls.m_ViewDirectionBox->setEnabled(true); m_Controls.m_ViewUpBox->setEnabled(true); } } //############################################################################################### //############################################################################################### //############################## some general UI methods, always needed ######################### //############################################################################################### //############################################################################################### QmitkIGTTrackingLabView::~QmitkIGTTrackingLabView() { if (m_Timer->isActive()) m_Timer->stop(); } void QmitkIGTTrackingLabView::CreateQtPartControl( QWidget *parent ) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi( parent ); this->CreateBundleWidgets(); this->CreateConnections(); } void QmitkIGTTrackingLabView::CreateBundleWidgets() { //initialize registration widget m_Controls.m_RegistrationWidget->HideStaticRegistrationRadioButton(true); m_Controls.m_RegistrationWidget->HideContinousRegistrationRadioButton(true); m_Controls.m_RegistrationWidget->HideUseICPRegistrationCheckbox(true); } void QmitkIGTTrackingLabView::CreateConnections() { //initialize timer m_Timer = new QTimer(this); //create connections connect(m_Timer, SIGNAL(timeout()), this, SLOT(UpdateTimer())); connect( m_Controls.m_UsePermanentRegistrationToggle, SIGNAL(toggled(bool)), this, SLOT(OnPermanentRegistration(bool)) ); connect( m_Controls.m_TrackingDeviceSelectionWidget, SIGNAL(NavigationDataSourceSelected(mitk::NavigationDataSource::Pointer)), this, SLOT(OnSetupNavigation()) ); connect( m_Controls.m_UseAsPointerButton, SIGNAL(clicked()), this, SLOT(OnInstrumentSelected()) ); connect( m_Controls.m_UseAsObjectmarkerButton, SIGNAL(clicked()), this, SLOT(OnObjectmarkerSelected()) ); connect( m_Controls.m_RegistrationWidget, SIGNAL(AddedTrackingFiducial()), this, SLOT(OnAddRegistrationTrackingFiducial()) ); connect( m_Controls.m_RegistrationWidget, SIGNAL(PerformFiducialRegistration()), this, SLOT(OnInitialRegistration()) ); connect( m_Controls.m_PointSetRecordCheckBox, SIGNAL(toggled(bool)), this, SLOT(OnPointSetRecording(bool)) ); connect( m_Controls.m_ActivateNeedleView, SIGNAL(toggled(bool)), this, SLOT(OnVirtualCamera(bool)) ); //start timer m_Timer->start(30); //initialize Combo Boxes m_Controls.m_ObjectComboBox->SetDataStorage(this->GetDataStorage()); m_Controls.m_ObjectComboBox->SetAutoSelectNewItems(false); m_Controls.m_ObjectComboBox->SetPredicate(mitk::NodePredicateDataType::New("Surface")); m_Controls.m_ImageComboBox->SetDataStorage(this->GetDataStorage()); m_Controls.m_ImageComboBox->SetAutoSelectNewItems(false); m_Controls.m_ImageComboBox->SetPredicate(mitk::NodePredicateDataType::New("Image")); } void QmitkIGTTrackingLabView::SetFocus() { m_Controls.m_UseAsPointerButton->setFocus(); } //############################################################################################### //############################################################################################### //####################### some additional slots and help methods ################################ //####################### for cleaner code - not that important ################################ //####################### to understand the basic functions ################################ //############################################################################################### //############################################################################################### void QmitkIGTTrackingLabView::DestroyIGTPipeline() { if(m_Source.IsNotNull()) { m_Source->StopTracking(); m_Source->Disconnect(); m_Source = nullptr; } m_PermanentRegistrationFilter = nullptr; m_Visualizer = nullptr; m_VirtualView = nullptr; } bool QmitkIGTTrackingLabView::CheckRegistrationInitialization() { // a couple of variables which we need in this method std::string warningMessage = ""; bool initializationErrorDetected = false; mitk::PointSet::Pointer imageFiducials,trackerFiducials; // check some initialization stuff if (m_ImageFiducialsDataNode.IsNull() || m_TrackerFiducialsDataNode.IsNull()) { warningMessage = "Initialization not finished!"; MITK_WARN << warningMessage; QMessageBox::warning(nullptr, "Registration not possible", warningMessage.c_str()); return false; } else { imageFiducials = dynamic_cast<mitk::PointSet*>(m_ImageFiducialsDataNode->GetData()); trackerFiducials = dynamic_cast<mitk::PointSet*>(m_TrackerFiducialsDataNode->GetData()); } // now, do a lot of other checks... if (m_Controls.m_SurfaceActive->isChecked() && m_Controls.m_ObjectComboBox->GetSelectedNode().IsNull()) { warningMessage = "No surface selected for registration.\nRegistration is not possible"; initializationErrorDetected = true; } else if (m_Controls.m_ImageActive->isChecked() && m_Controls.m_ImageComboBox->GetSelectedNode().IsNull()) { warningMessage = "No image selected for registration.\nRegistration is not possible"; initializationErrorDetected = true; } else if (imageFiducials.IsNull() || trackerFiducials.IsNull()) { warningMessage = "Fiducial data objects not found. \n" "Please set 3 or more fiducials in the image and with the tracking system.\n\n" "Registration is not possible"; initializationErrorDetected = true; } else if ((imageFiducials->GetSize() < 3) || (trackerFiducials->GetSize() < 3) || (imageFiducials->GetSize() != trackerFiducials->GetSize())) { warningMessage = "Not enough fiducial pairs found. At least 3 fiducial must exist for the image and the tracking system respectively."; initializationErrorDetected = true; } - // finaly: if an err was detected, give a warning and an error popup, then return false + // finally: if an err was detected, give a warning and an error popup, then return false if(initializationErrorDetected) { MITK_WARN << warningMessage; QMessageBox::warning(nullptr, "Registration not possible", warningMessage.c_str()); return false; } //if no error was detected simply return true else {return true;} } bool QmitkIGTTrackingLabView::IsTransformDifferenceHigh(mitk::NavigationData::Pointer transformA, mitk::NavigationData::Pointer transformB, double euclideanDistanceThreshold, double angularDifferenceThreshold) { if(transformA.IsNull() || transformA.IsNull()) {return false;} mitk::Point3D posA,posB; posA = transformA->GetPosition(); posB = transformB->GetPosition(); if(posA.EuclideanDistanceTo(posB) > euclideanDistanceThreshold) {return true;} double returnValue; mitk::Quaternion rotA,rotB; rotA = transformA->GetOrientation(); rotB = transformB->GetOrientation(); itk::Vector<double,3> point; //caution 5D-Tools: Vector must lie in the YZ-plane for a correct result. point[0] = 0.0; point[1] = 0.0; point[2] = 100000.0; rotA.normalize(); rotB.normalize(); itk::Matrix<double,3,3> rotMatrixA; for(int i=0; i<3; i++) for(int j=0; j<3; j++) rotMatrixA[i][j] = rotA.rotation_matrix_transpose().transpose()[i][j]; itk::Matrix<double,3,3> rotMatrixB; for(int i=0; i<3; i++) for(int j=0; j<3; j++) rotMatrixB[i][j] = rotB.rotation_matrix_transpose().transpose()[i][j]; itk::Vector<double,3> pt1 = rotMatrixA * point; itk::Vector<double,3> pt2 = rotMatrixB * point; returnValue = (pt1[0]*pt2[0]+pt1[1]*pt2[1]+pt1[2]*pt2[2]) / ( sqrt(pow(pt1[0],2.0)+pow(pt1[1],2.0)+pow(pt1[2],2.0)) * sqrt(pow(pt2[0],2.0)+pow(pt2[1],2.0)+pow(pt2[2],2.0))); returnValue = acos(returnValue); if(returnValue*57.3 > angularDifferenceThreshold){return true;} return false; } diff --git a/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.h b/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.h index a5c31d3f0d..fce88e2519 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.h +++ b/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTrackingLabView.h @@ -1,208 +1,208 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkIGTTrackingLabView_h #define QmitkIGTTrackingLabView_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include "ui_QmitkIGTTrackingLabViewControls.h" #include <mitkNavigationDataToPointSetFilter.h> #include <mitkNavigationDataLandmarkTransformFilter.h> #include <mitkNavigationDataReferenceTransformFilter.h> #include <mitkNavigationDataObjectVisualizationFilter.h> #include <mitkNavigationDataToPointSetFilter.h> #include <mitkTrackingDeviceSource.h> #include <mitkSurface.h> #include <mitkCameraVisualization.h> #include <QToolBox> #include <QCheckBox> #include <QComboBox> #include <QPushButton> #include <QLabel> #include <QSpinBox> #include <QTimer> #include <vtkLandmarkTransform.h> #include <vtkSmartPointer.h> /*! \brief QmitkIGTTrackingLabView \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \ingroup ${plugin_target}_internal */ class QmitkIGTTrackingLabView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; /** \brief default constructor */ QmitkIGTTrackingLabView(); /** \brief default destructor */ ~QmitkIGTTrackingLabView() override; void CreateQtPartControl(QWidget *parent) override; void SetFocus() override; protected slots: -/** This timer updates the IGT pipline, when nessecary: +/** This timer updates the IGT pipline, when necessary: * 1: if permanent registration is activated, then the permanent * registration filter has to be updated * 2: if the camera view is on it also must be updated * 3: point set recording is based on another filter which needs to be * updated when activated */ void UpdateTimer(); //############## Configuration Step ##################### /** \brief This method sets up the navigation pipeline during initialization. */ void OnSetupNavigation(); /** This method is called when the instrument is selected. * It stores the navigation data of the instrument. */ void OnInstrumentSelected(); /** This method is called when the object marker is selected. * It stores the navigation data of the object marker. */ void OnObjectmarkerSelected(); //############## Initial Registration Step ############## /** \brief This method calls the initial fiducial registration. */ void OnInitialRegistration(); /** \brief This method adds a new fiducial to the tracker fiducials PointSet. */ void OnAddRegistrationTrackingFiducial(); /** \brief This method initializes the registration for the FiducialRegistrationWidget. */ void InitializeRegistration(); //############## Permanent Registration Step ############ /** \brief This method activates the permanent registration based on one tool's position. */ void OnPermanentRegistration(bool on); //############## Pointset Recording Step ################ /** \brief This method starts the PointSet recording. */ void OnPointSetRecording(bool record); //############## Camera View Step ####################### /** \brief This method activates the virtual camera. */ void OnVirtualCamera(bool on); protected: Ui::QmitkIGTTrackingLabViewControls m_Controls; /** \brief This method creates all widgets this bundle needs. */ void CreateBundleWidgets(); /** \brief This method creates the SIGNAL SLOT connections. */ void CreateConnections(); /** * Checks if everything is initialized for registration. Gives error messages and returns false if not. */ bool CheckRegistrationInitialization(); /** \brief This method destroys the filter pipeline. */ void DestroyIGTPipeline(); //####################### Members for the IGT pipeline ###################################### // The IGT pipeline is basically initialized in the method OnSetupNavigation(). Further initialization // is done in the methods OnPermanentRegistration(), OnPointSetRecording() and OnVirtualCamera(). // The pipline is updated in the method UpdateTimer(). When the complete pipeline is active, it is // structured as follows: // ,-> m_PermanentRegistrationFilter // m_Source -> m_Visualizer // `-> m_VirtualView mitk::TrackingDeviceSource::Pointer m_Source; ///< source that connects to the tracking device mitk::NavigationDataObjectVisualizationFilter::Pointer m_PermanentRegistrationFilter; ///< this filter transforms from tracking coordinates into mitk world coordinates if needed it is interconnected before the FiducialEegistrationFilter mitk::NavigationDataObjectVisualizationFilter::Pointer m_Visualizer; ///< visualization filter mitk::CameraVisualization::Pointer m_VirtualView; ///< filter to update the vtk camera according to the reference navigation data //in addition to the pipeline objects, pointers to the navigation data objects are stored for fast access: mitk::NavigationData::Pointer m_InstrumentNavigationData; ///< navigation data of instrument mitk::NavigationData::Pointer m_ObjectmarkerNavigationData; ///< navigation data of object marker //####################### other members ###################################### QTimer* m_Timer; ///< central timer which updates the IGT pipeline //members for the point set recording mitk::NavigationData::Pointer m_PointSetRecordingNavigationData; mitk::PointSet::Pointer m_PSRecordingPointSet; bool m_PointSetRecording; bool m_PermanentRegistration; bool m_CameraView; //members for initial registration mitk::DataNode::Pointer m_ImageFiducialsDataNode; mitk::DataNode::Pointer m_TrackerFiducialsDataNode; //members for permanent registration mitk::PointSet::Pointer m_PermanentRegistrationSourcePoints; mitk::NavigationData::Pointer m_T_MarkerRel; mitk::NavigationData::Pointer m_T_ObjectReg; mitk::AffineTransform3D::Pointer m_T_ImageReg; mitk::AffineTransform3D::Pointer m_T_ImageGeo; mitk::NavigationData::Pointer m_ObjectmarkerNavigationDataLastUpdate; ///< this is the position of the object marker from the last call of update(); it is used to check the difference and decide if the visualization must be updated //######################## some internal help methods ############################ /** * Checks if the difference between two given transformations is high which means the method returns -* true if the difference exeeds the given position and angular threshold. +* true if the difference exceeds the given position and angular threshold. */ bool IsTransformDifferenceHigh(mitk::NavigationData::Pointer transformA, mitk::NavigationData::Pointer transformB, double euclideanDistanceThreshold = .8, double angularDifferenceThreshold = .8); }; #endif diff --git a/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTutorialView.cpp b/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTutorialView.cpp index f5412b58bd..2404b52536 100644 --- a/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTutorialView.cpp +++ b/Plugins/org.mitk.gui.qt.igtexamples/src/internal/QmitkIGTTutorialView.cpp @@ -1,257 +1,257 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkIGTTutorialView.h" #include "mitkNDIPassiveTool.h" #include "mitkNDITrackingDevice.h" #include "mitkVirtualTrackingDevice.h" #include "mitkStandardFileLocations.h" #include "mitkSerialCommunication.h" #include "mitkCone.h" #include <QTimer> #include <QMessageBox> #include "mitkNDIPolarisTypeInformation.h" const std::string QmitkIGTTutorialView::VIEW_ID = "org.mitk.views.igttutorial"; QmitkIGTTutorialView::QmitkIGTTutorialView() : QmitkAbstractView(), m_Controls(nullptr), m_Source(nullptr), m_Visualizer(nullptr), m_Timer(nullptr) { } QmitkIGTTutorialView::~QmitkIGTTutorialView() { } void QmitkIGTTutorialView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widget m_Controls = new Ui::QmitkIGTTutorialViewControls; m_Controls->setupUi(parent); this->CreateConnections(); } } void QmitkIGTTutorialView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_StartButton), SIGNAL(clicked()),(QObject*) this, SLOT(OnStartIGT())); connect( (QObject*)(m_Controls->m_StopButton), SIGNAL(clicked()),(QObject*) this, SLOT(OnStopIGT())); } } void QmitkIGTTutorialView::SetFocus() { m_Controls->m_virtualTrackingRadioButton->setFocus(); } //The next line starts a snippet to display this code in the documentation. If you don't revise the documentation, don't remove it! //! [OnStart 1] void QmitkIGTTutorialView::OnStartIGT() { //This method is called when the "Start Image Guided Therapy" button is pressed. Any kind of navigation application will //start with the connection to a tracking system and as we do image guided procedures we want to show //something on the screen. In this tutorial we connect to the NDI Polaris tracking system pr a virtual tracking device and we will //show the movement of a tool as cone in MITK. //! [OnStart 1] //! [OnStart 2] try { if(m_Controls->m_NDITrackingRadioButton->isChecked()) { /**************** Variant 1: Use a NDI Polaris Tracking Device ****************/ //Here we want to use the NDI Polaris tracking device. Therefore we instantiate a object of the class //NDITrackingDevice and make some settings which are necessary for a proper connection to the device. MITK_INFO << "NDI tracking"; QMessageBox::warning ( nullptr, "Warning", "You have to set the parameters for the NDITracking device inside the code (QmitkIGTTutorialView::OnStartIGT()) before you can use it."); mitk::NDITrackingDevice::Pointer tracker = mitk::NDITrackingDevice::New(); //instantiate tracker->SetPortNumber(mitk::SerialCommunication::COM4); //set the comport tracker->SetBaudRate(mitk::SerialCommunication::BaudRate115200); //set the baud rate tracker->SetType(mitk::NDIPolarisTypeInformation::GetTrackingDeviceName()); //set the type there you can choose between Polaris and Aurora //The tools represent the sensors of the tracking device. In this case we have one pointer tool. //The TrackingDevice object it self fills the tool with data. So we have to add the tool to the //TrackingDevice object. // The Polaris system needs a ".rom" file which describes the geometry of the markers related to the tool tip. //NDI provides an own software (NDI architect) to generate those files. tracker->AddTool("MyInstrument", "c:\\myinstrument.rom"); //! [OnStart 2] /**************** End of Variant 1 ****************/ //! [OnStart 3] //The tracking device object is used for the physical connection to the device. To use the //data inside of our tracking pipeline we need a source. This source encapsulate the tracking device //and provides objects of the type mitk::NavigationData as output. The NavigationData objects stores - //position, orientation, if the data is valid or not and special error informations in a covariance + //position, orientation, if the data is valid or not and special error information in a covariance //matrix. // //Typically the start of a pipeline is a TrackingDeviceSource. To work correct we have to set a //TrackingDevice object. Attention you have to set the tools before you set the whole TrackingDevice //object to the TrackingDeviceSource because the source need to know how many outputs should be //generated. m_Source = mitk::TrackingDeviceSource::New(); //We need the filter objects to stay alive, //therefore they must be members. m_Source->SetTrackingDevice(tracker); //Here we set the tracking device to the source of the pipeline. //! [OnStart 3] } //! [OnStart 4] else { /**************** Variant 2: Emulate a Tracking Device with mitk::VirtualTrackingDevice ****************/ // For tests, it is useful to simulate a tracking device in software. This is what mitk::VirtualTrackingDevice does. // It will produce random position, orientation and error values for each tool that is added. MITK_INFO << "virtual tracking"<<endl; mitk::VirtualTrackingDevice::Pointer tracker = mitk::VirtualTrackingDevice::New(); // create virtual tracker mitk::ScalarType bounds[] = {0.0, 200.0, 0.0, 200.0, 0.0, 200.0}; tracker->SetBounds(bounds); tracker->AddTool("MyInstrument"); // add a tool to tracker //The tracking device object is used for the physical connection to the device. To use the //data inside of our tracking pipeline we need a source. This source encapsulate the tracking device //and provides objects of the type mitk::NavigationData as output. The NavigationData objects stores - //position, orientation, if the data is valid or not and special error informations in a covariance + //position, orientation, if the data is valid or not and special error information in a covariance //matrix. // //Typically the start of a pipeline is a TrackingDeviceSource. To work correct we have to set a //TrackingDevice object. Attention you have to set the tools before you set the whole TrackingDevice //object to the TrackingDeviceSource because the source need to know how many outputs should be //generated. m_Source = mitk::TrackingDeviceSource::New(); //We need the filter objects to stay alive, //therefore they must be members. m_Source->SetTrackingDevice(tracker); //Here we set the tracking device to the source of the pipeline. /**************** End of Variant 2 ****************/ } //! [OnStart 4] //! [OnStart 5] m_Source->Connect(); //Now we connect to the tracking system. //Note we do not call this on the TrackingDevice object //! [OnStart 5] //! [OnStart 6] //As we wish to visualize our tool we need to have a PolyData which shows us the movement of our tool. //Here we take a cone shaped PolyData. In MITK you have to add the PolyData as a node into the DataStorage //to show it inside of the rendering windows. After that you can change the properties of the cone //to manipulate rendering, e.g. the position and orientation as in our case. mitk::Cone::Pointer cone = mitk::Cone::New(); //instantiate a new cone double scale[] = {10.0, 10.0, 10.0}; cone->GetGeometry()->SetSpacing(scale); //scale it a little that so we can see something mitk::DataNode::Pointer node = mitk::DataNode::New(); //generate a new node to store the cone into //the DataStorage. node->SetData(cone); //The data of that node is our cone. node->SetName("My tracked object"); //The node has additional properties like a name node->SetColor(1.0, 0.0, 0.0); //or the color. Here we make it red. this->GetDataStorage()->Add(node); //After adding the Node with the cone in it to the //DataStorage, MITK will show the cone in the //render windows. //! [OnStart 6] //! [OnStart 7] //For updating the render windows we use another filter of the MITK-IGT pipeline concept. The //NavigationDataObjectVisualizationFilter needs as input a NavigationData and a //PolyData. In our case the input is the source and the PolyData our cone. //First we create a new filter for the visualization update. m_Visualizer = mitk::NavigationDataObjectVisualizationFilter::New(); m_Visualizer->SetInput(0, m_Source->GetOutput()); //Then we connect to the pipeline. m_Visualizer->SetRepresentationObject(0, cone.GetPointer()); // After that we have to assign the cone to the input //Now this simple pipeline is ready, so we can start the tracking. Here again: We do not call the //StartTracking method from the tracker object itself. Instead we call this method from our source. m_Source->StartTracking(); //! [OnStart 7] //! [OnStart 8] //Now every call of m_Visualizer->Update() will show us the cone at the position and orientation //given from the tracking device. //We use a QTimer object to call this Update() method in a fixed interval. if (m_Timer == nullptr) { m_Timer = new QTimer(this); //create a new timer } connect(m_Timer, SIGNAL(timeout()), this, SLOT(OnTimer())); //connect the timer to the method OnTimer() m_Timer->start(100); //Every 100ms the method OnTimer() is called. -> 10fps //! [OnStart 8] //! [OnStart 8a] //disable the tracking device selection this->m_Controls->m_NDITrackingRadioButton->setDisabled(true); this->m_Controls->m_virtualTrackingRadioButton->setDisabled(true); //! [OnStart 8a] } //! [OnStart 9] catch (std::exception& e) { // add cleanup MITK_INFO << "Error in QmitkIGTTutorial::OnStartIGT():" << e.what(); } //! [OnStart 9] } //![OnTimer] void QmitkIGTTutorialView::OnTimer() { //Here we call the Update() method from the Visualization Filter. Internally the filter checks if //new NavigationData is available. If we have a new NavigationData the cone position and orientation //will be adapted. m_Visualizer->Update(); auto geo = this->GetDataStorage()->ComputeBoundingGeometry3D(this->GetDataStorage()->GetAll()); mitk::RenderingManager::GetInstance()->InitializeViews( geo ); this->RequestRenderWindowUpdate(); } //![OnTimer] //![OnStop] void QmitkIGTTutorialView::OnStopIGT() { //This method is called when the Stop button is pressed. Here we disconnect the pipeline. if (m_Timer == nullptr) { MITK_INFO << "No Timer was set yet!"; return; } //To disconnect the pipeline in a save way we first stop the timer than we disconnect the tracking device. //After that we destroy all filters with changing them to nullptr. m_Timer->stop(); disconnect(m_Timer, SIGNAL(timeout()), this, SLOT(OnTimer())); m_Timer = nullptr; m_Source->StopTracking(); m_Source->Disconnect(); m_Source = nullptr; m_Visualizer = nullptr; m_Source = nullptr; this->GetDataStorage()->Remove(this->GetDataStorage()->GetNamedNode("My tracked object")); //enable the tracking device selection this->m_Controls->m_NDITrackingRadioButton->setEnabled(true); this->m_Controls->m_virtualTrackingRadioButton->setEnabled(true); } //![OnStop] diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox index c31bc51829..e1c8507387 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkIGTTracking.dox @@ -1,20 +1,20 @@ /** \page org_mitk_gui_qt_igttracking The IGT Tracking Plugin This plugin offers basic tracking functionalities. This includes connecting to a tracking system, logging and recording of tracking data, managing tracking tools and playing recorded tracking data. The plugin includes different views, which are described on different pages in detail. As part of the tutorial, it is recommended to get familiar with each of the following views as they lead you through the main functionality of the IGT plugin. Please read the following pages to get familiar with them: <ul> <li> \subpage org_mitk_views_igttrackingtoolbox : Allows for connecting a tracking system and logging/recording the tracked data. -<li> \subpage org_mitk_views_igtnavigationtoolmanager : This view offers functionality to manage tool storages. Each tool storage holds a preconfigured tool collection. Once saved you can load a tool storage in the Tracking Toolbox and don't need to add every tool seperately. +<li> \subpage org_mitk_views_igtnavigationtoolmanager : This view offers functionality to manage tool storages. Each tool storage holds a preconfigured tool collection. Once saved you can load a tool storage in the Tracking Toolbox and don't need to add every tool separately. <li> \subpage org_mitk_views_navigationdataplayer : Plays navigation data which was recorded with the Tracking Toolbox for example. <li> \subpage org_mitk_views_calibrationtoolmanager Calibration Tool Manager. This view offers functionality to calibrate navigation tools. <li> \subpage org_mitk_views_igtregistrationview : The IGTFiducialRegistration view allows the recording of real world landmarks and corresponding landmarks on a virtual object. </ul> Return to the \ref TrackingPlugins "[IGT Tutorial Overview]" */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolCalibration.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolCalibration.dox index 079e6d0673..b380197a0f 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolCalibration.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolCalibration.dox @@ -1,85 +1,85 @@ /** \page org_mitk_views_calibrationtoolmanager The MITK-IGT Navigation Tool Calibration \imageMacro{iconTrackingToolCalibration.png,"Icon of the MITK-IGT Tracking Toolbox",2.00} \tableofcontents \section QmitkMITKIGTNavigationToolCalibrationIntroduction Introduction This view allows the calibration of navigation tools. The calibrated tools can be saved permanently and later be used for any other IGT application. The following coordinate transforms are associated with tracking of a tool: <ul> <li> The sensor transformation from the global tracking coordinate system to the local coordinate system of the tracked sensor (m_Position, m_Orientation). <li> The tool tip transformation from the local sensor coordinate system to a tool tip coordinate system defined by a tool tip position and a main tool axis (m_ToolTipPosition, m_ToolAxisOrientation). The tool axis is defined as the negative z-axis of the tool tip coordinate system. <li> The main axis of the representation object of the tool (e.g. a surface) has to be defined along the negative z-axis. </ul> \imageMacro{TrackingTool.png,"Coordinate transforms associated to the tracking tool.",5.00} \section QmitkMITKIGTNavigationToolCalibrationPrerequisities Prerequisites In the IGT Tracking Toolbox configure your tracking device with at least two tools. The tool you wish to calibrate and one tool used as a pointer during the calibration process. For details on how to configure your tracking device and your tools have a look at \ref org_mitk_views_igttrackingtoolbox . After you configured your device and your tools connect your device and start tracking. Now switch to the IGT Navigation Tool Calibration for the calibration process. \section QmitkMITKIGTNavigationToolCalibrationInitialization Initialization On the tab Initialization choose the tracking device you configured in the prevois step by clicking on it in the box "Available Navigation Data Sources". Then in the box "Tools" the tools you configured for this device should appear. Click on the tool that needs to be calibrated and then on the button "Use as Tool to Calibrate". On top of the view under the headline "Tool To calibrate" you now see the tool information for the chosen tool. For the tool used as a pointer do the same. Click on it, then click on the button "Use as Calibration Pointer" and on top of the view under the headline "Calibration pointer you should see the tool information for the pointer tool. \imageMacro{QmitkIGTTracking_ToolCalibration_Initialization.png,"MITK Screenshot with the initialized tools for calibration",5.00} \section QmitkMITKIGTNavigationToolCalibrationToolTipCalibration Tool Tip Calibration After you finished the initialization of your tracking device you can proceed on to the tab Tool Tip Calibration to calibrate your tool. For the Tool Tip Calibration you have four different options: <ul> <li> Manual: Enter the known Translation and Rotation for the Tool Tip manually <li> Single Reference Tool: Use a calibrated tool as a reference to calibrate the non-calibrated tool <li> Multiple Tools Reference: Not implemented yet <li> Pivoting: Calibrate the tool by pivoting it around its tip. (Not fully implemented yet) </ul> \subsection QmitkMITKIGTNavigationToolCalibrationManual Manual Tool Tip Calibration Use this method to calibrate a navigation tool, of which you already know the translation and rotation that determine the tool tip calibration. Click on Start Edit Tooltip and in the new window you can enter the values for the translation and the rotation. Either by using the sliders or by entering the values into the boxes. \imageMacro{QmitkIGTTracking_ToolCalibration_Manual_EditingWindow.png,"MITK Screenshot of the window for manual tool calibration",5.00} After you entered the values you can click "Use Manipulated ToolTip" to perform the Calibration on the Tool to calibrate. The box "Current Tool Tip Orientation" will show you the results. It will list the resulting values of the Quaternion, the Euler Angles and the Matrix. \imageMacro{QmitkIGTTracking_ToolCalibration_Manual_After.png,"MITK Screenshot of the Current Tool Tip Orientation Box after the tool was manually calibrated",5.00} To save the result permanently just click "Save Calibrated Navigation Tool" and you can save the calibrated tool as an IGTTool for later use with your tracking device in a navigation application. -If you are not satisfied with the results you can click "Start Edit Tooltip" again and either change the values for the rotation and translation again or just reset everything by clicking on "Reset to Identity". To write the new values or reseted values into the tool just click "Use Manipulated Tool Tip" again. Now you can save your relust just as described above. +If you are not satisfied with the results you can click "Start Edit Tooltip" again and either change the values for the rotation and translation again or just reset everything by clicking on "Reset to Identity". To write the new values or resetted values into the tool just click "Use Manipulated Tool Tip" again. Now you can save your relust just as described above. \subsection QmitkMITKIGTNavigationToolCalibrationReference Tool Tip Calibration with a single Reference Tool Use this method to calibrate a navigation tool using a tool as pointer that is already calibrated. First choose the number of tracking data you wish to collect. It is 100 by default but you may choose as many as you wish. Now place your tool to calibrate in a fixed position where it is tracked. Next place your pointing tool in a manner that its tip touches the tip and is tracked too. Fix it in this position. For a good calibration it is important that the tools move the least possible. After you placed the tools click on the "Collect Navigation Data" Button and wait until all the data is gathered. Now you have several options to adjust the calibration to your needs. You can calibrate the position and/or the orientation or even invert the calibration transform. Calibrating the position will translate the position of the tool to calibrate to the position of the calibration pointer. The orientation calibration will copy the mean orientation of the calibration pointer to the tool the calibrate. Choose the options needed for your tool and tracker and then click on "Run Calibration". The new Tool Tip Position and Orientation will be displayed und you can now apply them onto your tool by clicking on "Set New Tool Tip Position and/or Tool Orientation". To finally save the calibrated tool for later use just click on "Save Calibrated Navigation Tool". If you are not satisfied with the result of the calibration just repeat the steps described above. \imageMacro{QmitkIGTTracking_ToolCalibration_Reference.png,"MITK Screenshot of the Tool Tip Calibration Widget after a fully performed Tool Calibration using a single reference tool ",5.00} \subsection QmitkMITKIGTNavigationToolCalibrationPivot Tool Tip Calibration via Pivoting -To calibrate your tool via pivoting place it on its tip an pivot it around its tip. Be careful not to move the tip otherwise the calibration result will be inaccurate. You can define the number of poses that should be collected. After starting the collecting process pivote the tool to different poses until the collection ends. Then click on "Comute Pivot Point" to compute the pivot point. Finally you can use the pivot result as tooltip transformation and save the calibrated tool to the hard disc for later use. +To calibrate your tool via pivoting place it on its tip an pivot it around its tip. Be careful not to move the tip otherwise the calibration result will be inaccurate. You can define the number of poses that should be collected. After starting the collecting process pivote the tool to different poses until the collection ends. Then click on "Compute Pivot Point" to compute the pivot point. Finally you can use the pivot result as tooltip transformation and save the calibrated tool to the hard disc for later use. \subsection QmitkMITKIGTNavigationToolCalibration Tool Landmark Calibration Two types of landmarks can be defined for each tool: <ul> <li> Control points for a later point-based registration <li> Tool landmarks that represents features on the tool which are e.g. visible in a CT image </ul> Both sets of landmarks are defined in the tool coordinate space. Control points are virtual and can only defined manually. These landmarks clearly define the tools pose only by using landmarks in the tool coordinate system. E.g., two landmarks for a 5DoF tool and three landmarks for a 6DoF tool. They may be used, e.g., for a point based registration of a tool from image space to tracking space. A typical set of three control points for a 6 DoF tool might be [1;0;0], [0;1;0], [0;0;1]. -Tool landmarks are designed for representing defined landmarks on a tool. The number of these landmarks might exeed the number of control points for reasons of redundancy and averaging. They are used for, e.g., manually registering the pose of a tool by visual markers in a CT scan. If you would use these landmarks to do a point based registration from image space to tracking space later, you might overweight the tool because of two many landmarks compared to other markers. The tool landmarks can be calibrated manually or by using a second tracked pointer, move it to each landmark and press "Add Pointer Position". +Tool landmarks are designed for representing defined landmarks on a tool. The number of these landmarks might exceed the number of control points for reasons of redundancy and averaging. They are used for, e.g., manually registering the pose of a tool by visual markers in a CT scan. If you would use these landmarks to do a point based registration from image space to tracking space later, you might overweight the tool because of two many landmarks compared to other markers. The tool landmarks can be calibrated manually or by using a second tracked pointer, move it to each landmark and press "Add Pointer Position". Return to the overview of the IGT Tracking Plugin views: \ref org_mitk_gui_qt_igttracking */ diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox index dfff505877..34c22b8c4d 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox @@ -1,53 +1,53 @@ /** \page org_mitk_views_igtnavigationtoolmanager The MITK-IGT Navigation Tool Manager \imageMacro{iconTrackingToolManager.png,"Icon of the Navigation Tool Manager",2.00} \section QmitkMITKIGTNavigationToolManager Introduction -This view allows for creating and editing NavigationToolStorages. These storages contains naviagtion tools of a tracking device, can be saved permanently and used later for any other IGT application. +This view allows for creating and editing NavigationToolStorages. These storages contains navigation tools of a tracking device, can be saved permanently and used later for any other IGT application. \tableofcontents \section QmitkMITKIGTNavigationToolManagerToolOverview Navigation Tools Overview A navigation tool of MITK-IGT represents a tracking tool (e.g. an emt sensor or an optically tracked tool) and it's corresponding data, like it's name and it's surface. A navigation tool is a generalized container for any trackable object in combination with it's additional information. Every navigation tool has different properties which are: <ul> <li> Name <li> Unique identifier <li> Tool definition file <li> Serial number <li> Surface for visualization <li> Type of tracking device <li> Type of the tool <li> Tool landmarks </ul> Note that not all properties are needed for all types of tools. A tool definition file, for example, is only needed by optical tracking tools (e.g. a .rom file for Polaris or a toolfile for the MicronTracker). A tool associated with the aurora system is alwalys identified by it's serial number. You can also detect Aurora tools automatically with the TrackingToolbox view and edit the automatically detected tool storage later with this view. \section QmitkMITKIGTNavigationToolManagerManagingNavigationToolStorage Managing Navigation Tool Storage -In order to create edit a tool storage container, you can select one of the available tool storages listed in the upper part of the UI. The list shows all tool storages which are available throug the micro services concept of MITK. The list also shows the current tool storage of the IGT tracking toolbox view if it is active. In addition to the listed tool storages, you can load new storages from the hard disc which will then appear in the list and might be edited as all other storage by simply selecting it in the list. You may also save a selected tool storage to the hard disc or create a new one. +In order to create edit a tool storage container, you can select one of the available tool storages listed in the upper part of the UI. The list shows all tool storages which are available through the micro services concept of MITK. The list also shows the current tool storage of the IGT tracking toolbox view if it is active. In addition to the listed tool storages, you can load new storages from the hard disc which will then appear in the list and might be edited as all other storage by simply selecting it in the list. You may also save a selected tool storage to the hard disc or create a new one. In the lower part of the UI you always see the list of tools of the tool storage which is currently selected in the upper part. Use the buttons "add", "edit" and "delete" to manage the contained navigation tools. If you click "edit" or "delete" the operation is applied on the currently selected tool, as shown in the screenshot below. \imageMacro{QmitkIGTTracking_NavigationToolManagemantStartScreen.png,"Screenshot of the main view of NavigationToolManagent",10.90} \section QmitkMITKIGTNavigationToolManagerAddingEditingNavigationTools Adding / Editing Navigation Tools -If you add or edit a navigation tool, an input mask, as shown in the screenshot below, appears. The tool identifier is filled automatically, if you change it, remember that it is unique in the current storage. Also, choose a valid surface for every tool, this is nessesary for correct tool visualization. By default, a cone is displayed. The other information depends on the tracking system type, e.g. choose a tool file for the Polaris or the MicronTracker system and type in a serial number for the Aurora system. Two identical tools with the same serial number are also possible, they are assigned by the order in which they are attached to the device. As long as they also have the same surface as representation, this should not be a problem for most of the use cases. +If you add or edit a navigation tool, an input mask, as shown in the screenshot below, appears. The tool identifier is filled automatically, if you change it, remember that it is unique in the current storage. Also, choose a valid surface for every tool, this is necessary for correct tool visualization. By default, a cone is displayed. The other information depends on the tracking system type, e.g. choose a tool file for the Polaris or the MicronTracker system and type in a serial number for the Aurora system. Two identical tools with the same serial number are also possible, they are assigned by the order in which they are attached to the device. As long as they also have the same surface as representation, this should not be a problem for most of the use cases. The tool type is additional information which is not needed by the tracking device but might be needed by further IGT applications. The same applies to the tool landmarks which might be defined for a tool. There are two different types of landmarks which are designed as described here: <ul> <li> Tool Calibration Landmarks: These landmarks may be used clearly define the tools pose only by using landmarks in the tool coordinate system. E.g., two landmarks for a 5DoF tool and three landmarks for a 6DoF tool. These landmarks may be used, e.g., for a point based registration of a tool from image space to tracking space. -<li> Tool Registration Landmarks: These landmarks are designed for representing defined landmarks on a tools surface. The number of these landmarks might exeed the number of tool calibration landmarks for reasons of redundancy and averaging. They are used for, e.g., manually registering the pose of a tool by visual markers in a CT scan. If you would use these landmarks to do a point based registration from image space to tracking space later, you might overweight the tool because of two many landmarks compared to other markers. +<li> Tool Registration Landmarks: These landmarks are designed for representing defined landmarks on a tools surface. The number of these landmarks might exceed the number of tool calibration landmarks for reasons of redundancy and averaging. They are used for, e.g., manually registering the pose of a tool by visual markers in a CT scan. If you would use these landmarks to do a point based registration from image space to tracking space later, you might overweight the tool because of two many landmarks compared to other markers. </ul> \imageMacro{QmitkIGTTracking_NavigationToolManagementAddTool.png,"Screenshot of add/edit navigation tool screen",9.19} Return to the overview of the IGT Tracking Plugin views: \ref org_mitk_gui_qt_igttracking */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox index 1e80ec7f9f..a97d92c6c8 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox @@ -1,93 +1,93 @@ /** \page org_mitk_views_igttrackingtoolbox The MITK-IGT Tracking Toolbox \imageMacro{iconTrackingToolbox.png,"Icon of the MITK-IGT Tracking Toolbox",2.00} \tableofcontents \section QmitkMITKIGTTrackingToolboxIntroduction Introduction The MITK-IGT Tracking Toolbox is a view which allows you to connect to a tracking device, track and visualize navigation tools and write the tracked data into a log file. This page gives an overview of the view and is at the same time part of the IGT tutorial step \ref org_mitk_gui_qt_igttracking. All parts containing instructions for the tutorial begin with the bold printed label Tutorial. \imageMacro{QmitkIGTTracking_ScreenshotMitk.png,"MITK Screenshot with the TrackingToolbox activated",16.00} \section QmitkMITKIGTTrackingToolboxWorkflow General workflow Introduction Currently the devices Polaris, Aurora (both Northern Digital Inc. (NDI); Waterloo, Ontario, Canada), MicronTracker (Claron Technology, Inc.; Toronto, Ontario, Canada) and Optitrack (NaturalPoint) are supported (see <a href="https://www.mitk.org/wiki/Mitk-Tracking-Device_Support_Levels"> Hardware Tracking Device Support</a>). Different tracking hardware can be used via OpenIGTLink connections (see \ref IGTTutorialStepOpenIGTLink "Open IGT Link tutorial" ). For this Tracking Toolbox tutorial, we will use a virtual tracking device, which allows you to use simulated tracking data. This is very helpful if you want to test or implement some tracking application and don't have the hardware always available. A general Workflow with the Tracking Toolbox may be: <ul> <li> Configuration of a tracking device <li> Adding or loading a toolfile which holds tool definitions <li> Start tracking <li> Logging tracked data </ul> Tutorial: In the following sections, we will get familiar with each of these points using the Virtual Tracking Device. \section QmitkMITKIGTTrackingToolboxConnecting Tracking Device Configuration The tracking device can be specified in the tracking device configuration section located in the upper area of the tracking tab. As shown in the screenshot below, you choose your tracking device in the drop down menu. -If you use a real tracking system, you might need to set some parameters like the serial port for Aurora or Polaris or the host name for your OpenIGTLink connection. Most implemented tracking device include an option to test your conection. Therefore you just need to press the button "test connection". The results are displayed in the small black box on the right. +If you use a real tracking system, you might need to set some parameters like the serial port for Aurora or Polaris or the host name for your OpenIGTLink connection. Most implemented tracking device include an option to test your connection. Therefore you just need to press the button "test connection". The results are displayed in the small black box on the right. Tutorial: For a first introduction, please select the virtual tracking device in the drop-down-menu. You should see an option to add some jittering to the simulated data. \imageMacro{QmitkIGTTracking_ConfigurationWidget.png,"Tracking Device Configuration",8.55} \section Tracking Tools For tracking, you need information about your tools. You can either add single tools, load previously created tool storages or for some devices auto-detect all available tools. The best way to edit tools after creation/loading is \ref org_mitk_views_igtnavigationtoolmanager view. Creation of new tools or loading of existing tool storages can be done within the Tracking Tool Widget. \imageMacro{QmitkIGTTracking_NavigationToolManagement_TrackingTools.png, "The tracking tool widget for adding or loading tools.",9.00} All added or loaded tools will then be displayed in grey as shown in the screenshot below. If you start tracking they will become green if the tools were found and red if they were not found inside the tracking volume. \imageMacro{QmitkIGTTracking_TrackingToolsWidget.png,"Added Tracking Tools",9.08} \subsection QmitkMITKIGTTrackingToolboxAddingTools Adding tools The most simple step to begin with is to add new tools with this widget. The same widget is also available within \ref org_mitk_views_igtnavigationtoolmanager view and the single parameters are explained there in more detail. \imageMacro{QmitkIGTTracking_NavigationToolManagementAddTool.png,"Adding a new tool", 9.00} Tutorial: Please click the "Add single tool" button and make sure, that the Virtual Tracker is selected in the drop-down-menu (the tracking device configured in the first step must always match your tools!). You might want to give your tool a new name in the "Basic Information" section and load a surface for visualization in the "Tool Visualization" section (a surface file can be found in your binary folder if you did compile MITK by yourself: MITK-superbuild\MITK-Data\IGT-Data\ClaronTool.stl). If you don't have any surface data, you can just select "use simple cone". Click on "Finished" and repeat this step to add a second tool. \subsection QmitkMITKIGTTrackingToolboxLoadingTools Loading tools To load tools which can be tracked you need a predefined tracking tool storage. You can use the MITK \ref org_mitk_views_igtnavigationtoolmanager view to define a navigation tool storage or to save the tools created within the last step in a toolstorage. Navigation tool storages can be loaded by pressing the button "Load Tools". Please ensure that the tracking device type of the tools matches the chosen tracking device, otherwise you will get an error message if you try to start tracking. \subsection QmitkMITKIGTTrackingToolboxAutoDetection Auto detection of tools (only Aurora) If you use the Aurora system you also have the possibility to automatically detect the connected tools. In this case a tracking tool storage is created by the software. In the Tracking Device Configuration widget, a button "Auto Detection" appears. If you press this button the software connects to the system and automatically detects all connected tools. You will then be asked whether you want to save the detected tools as a tool storage to the hard drive. You might want to do this if you want to use or modify this tool storage later. In the automatically detected tool storage the tools are named AutoDetectedTools1, AutoDetectedTools2, and so on. Small spheres are used as tool surfaces. After autodetection the detected tools are loaded automatically even if you did not save them. \section QmitkMITKIGTTrackingToolboxStartTracking Start/stop tracking To start tracking, you first need to connect to your tracking device ("connect" button). If your tools or tool storage don't match the tracking device or if no connection can be established, this might give an error message here. \imageMacro{QmitkIGTTracking_TrackingControl.png,"Tracking Control to start tracking.", 9.00} -If connected succesfully, the start tracking button is enabled. As soon as you clicked this button, the tool information and tools will be highlighted red or green (un-/successful tracking) and in case of successful tracking, it's position will be updated and the tools are visualized in the 3D view of MITK. +If connected successfully, the start tracking button is enabled. As soon as you clicked this button, the tool information and tools will be highlighted red or green (un-/successful tracking) and in case of successful tracking, it's position will be updated and the tools are visualized in the 3D view of MITK. Note that options may not be changed after connecting the tracking device. You can start, freeze, unfreeze and stop the tracking as long as you are connected. If you want to finish your tracking, please stop an disconnect your tracking device. Tutorial: Please click "connect" and "start tracking". Both tools should move within the tracking volume, the position data should be updated in the tool widget and be highlighted green. You can freeze, unfreeze and stop/restart the tracking as often as you like. When finished, please stop and disconnect. \section QmitkMITKIGTTrackingOptions Options -In the options tab you can enable or disable the visualization of the tracking volume and of the tool quaternions. If enabled, the tool quaternions are shown in the tool information. You can also define the update rate of the tracking data. The update rate should not be set higher than the update rate of the tracking system. Other options might be available here depending on the newest developement within MITK-IGT. +In the options tab you can enable or disable the visualization of the tracking volume and of the tool quaternions. If enabled, the tool quaternions are shown in the tool information. You can also define the update rate of the tracking data. The update rate should not be set higher than the update rate of the tracking system. Other options might be available here depending on the newest development within MITK-IGT. \imageMacro{QmitkIGTTracking_Options.png,"Recorded logging data.", 9.00} \section QmitkMITKIGTTrackingToolboxLogging Logging features The logging feature of the Tracking Toolbox supports logging in XML or CSV format. -If your device is tracking, you are able to log the tracking data by using the logging tab. You first must define a file name. You can then choose whether you want comma seperated (csv) or xml format. Press "Start Logging" to start logging. You can also limit the number of logged frames, which will cause the logging to stop automatically after the given number. +If your device is tracking, you are able to log the tracking data by using the logging tab. You first must define a file name. You can then choose whether you want comma separated (csv) or xml format. Press "Start Logging" to start logging. You can also limit the number of logged frames, which will cause the logging to stop automatically after the given number. \imageMacro{QmitkIGTTracking_LoggingWidget.png,"Tracking options.", 9.00} Tutorial: Please connect and start tracking as you already did in the last step, switch to the logging tab, specify a csv file and start logging for a view seconds. Stop the tracking after a short period of time. You should now find the specified file which should look similar to the following screenshot and contain position data for both tools: \imageMacro{QmitkIGTTracking_LogFile.png,"Recorded logging data.", 9.00} Return to the overview of the IGT Tracking Plugin views: \ref org_mitk_gui_qt_igttracking */ diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox index 89ef20256f..0878386ff1 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox +++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox @@ -1,29 +1,29 @@ /** \page org_mitk_views_navigationdataplayer The NavigationData Player \imageMacro{iconTrackingDataPlayer.png,"Icon of the NavigationData Player",2.00} \tableofcontents \section NavigationDataPlayerOverview -The navigation data player plays recorded or artificial navigation data of one ore more tracking tools and visualizes their trajectory. -It can also make the data available als a NavigationDataSource to Plugins that require a stream of tracking data, without having to create a tracking device. +The navigation data player plays recorded or artificial navigation data of one or more tracking tools and visualizes their trajectory. +It can also make the data available as a NavigationDataSource to Plugins that require a stream of tracking data, without having to create a tracking device. \imageMacro{QmitkIGTTracking_NavigationDataPlayer.png, "The Navigation Data Player", 7} To use it, select a set of recorded navigation data using the "Open File" button. The Player will show the number of tools and the number of frames in the file. Select the sequential player if you want to play the data with a specified tempo (set the update Interval accordingly). Use the Time-based player to play the data in the speed they were originally acquired in. <ul> <li>Check "Repeat" to repeat the data as a loop indefinitely. <li>Check "Register as Microservice" to make the data available as a microservice TrackingDataSource. Other Filters can then be connected to it from other plugins. This is useful for development purposes or to replay previously recorded Situations. <li> Check "Display" to render the data in the render Window. </ul> Tutorial: As part of the IGT tutorial, you might try to replay your recorded data from step \ref org_mitk_views_igttrackingtoolbox. You should see two spheric tools moving within the tracking volume. Note that the tool storage is not included in the navigation data player at the moment, and hence all tools are represented as spheres. Return to the overview of the IGT Tracking Plugin views: \ref org_mitk_gui_qt_igttracking */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp index 74ac043b7c..8f50df4c2c 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp @@ -1,756 +1,756 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include <numeric> // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkIGTNavigationToolCalibration.h" // mitk #include <mitkNavigationToolWriter.h> #include <mitkTrackingDeviceSource.h> #include <mitkTrackingDevice.h> #include <mitkTrackingTool.h> #include <mitkQuaternionAveraging.h> #include <mitkPivotCalibration.h> #include <mitkNavigationData.h> // Qt #include <QMessageBox> #include <QFileDialog> #include <QFileInfo> // vtk #include <vtkSphereSource.h> const std::string QmitkIGTNavigationToolCalibration::VIEW_ID = "org.mitk.views.igtnavigationtoolcalibration"; QmitkIGTNavigationToolCalibration::QmitkIGTNavigationToolCalibration() { m_ToolTransformationWidget = new QmitkInteractiveTransformationWidget(); } QmitkIGTNavigationToolCalibration::~QmitkIGTNavigationToolCalibration() { //The following code is required due to a bug in the point list widget. //If this is removed, MITK crashes when closing the view: m_Controls.m_RegistrationLandmarkWidget->SetPointSetNode(nullptr); m_Controls.m_CalibrationLandmarkWidget->SetPointSetNode(nullptr); //clean up data storage this->GetDataStorage()->Remove(m_ToolTipPointPreview); delete m_ToolTransformationWidget; } void QmitkIGTNavigationToolCalibration::SetFocus() { } void QmitkIGTNavigationToolCalibration::OnToolCalibrationMethodChanged(int index) { //if pivot calibration (3) or manual(0) is chosen only calibration pointer is needed if (index == 0 || index == 3) { if (!CheckInitialization(false)) { return; } } else{ if (!CheckInitialization()) { return; } } UpdateManualToolTipCalibrationView(); m_Controls.m_CalibrationMethodsWidget->setCurrentIndex(index); m_IndexCurrentCalibrationMethod = index; } void QmitkIGTNavigationToolCalibration::CreateQtPartControl(QWidget *parent) { m_TrackingTimer = new QTimer(this); // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect(m_Controls.m_SetToolToCalibrate, SIGNAL(clicked()), this, SLOT(SetToolToCalibrate())); connect(m_Controls.m_SetPointer, SIGNAL(clicked()), this, SLOT(SetCalibrationPointer())); connect(m_TrackingTimer, SIGNAL(timeout()), this, SLOT(UpdateTrackingTimer())); connect(m_Controls.m_AddLandmark, SIGNAL(clicked()), this, SLOT(AddLandmark())); connect(m_Controls.m_SaveCalibratedTool, SIGNAL(clicked()), this, SLOT(SaveCalibratedTool())); connect(m_Controls.m_AddPivotPose, SIGNAL(clicked()), this, SLOT(OnAddPivotPose())); connect(m_Controls.m_ComputePivot, SIGNAL(clicked()), this, SLOT(OnComputePivot())); connect(m_Controls.m_UseComputedPivotPoint, SIGNAL(clicked()), this, SLOT(OnUseComputedPivotPoint())); connect(m_Controls.m_StartEditTooltipManually, SIGNAL(clicked()), this, SLOT(OnStartManualToolTipCalibration())); connect(m_Controls.m_GetPositions, SIGNAL(clicked()), this, SLOT(OnGetPositions())); connect(m_Controls.m_ToolAxis_X, SIGNAL(valueChanged(double)), this, SLOT(OnToolAxisSpinboxChanged())); connect(m_Controls.m_ToolAxis_Y, SIGNAL(valueChanged(double)), this, SLOT(OnToolAxisSpinboxChanged())); connect(m_Controls.m_ToolAxis_Z, SIGNAL(valueChanged(double)), this, SLOT(OnToolAxisSpinboxChanged())); connect(m_Controls.m_CalibrateToolAxis, SIGNAL(clicked()), this, SLOT(OnCalibrateToolAxis())); connect((QObject*)(m_ToolTransformationWidget), SIGNAL(EditToolTipFinished(mitk::AffineTransform3D::Pointer)), this, SLOT(OnManualEditToolTipFinished(mitk::AffineTransform3D::Pointer))); connect(m_Controls.m_CalibrationMethodComboBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnToolCalibrationMethodChanged(int))); connect((QObject*)(m_Controls.m_RunCalibrationButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnRunSingleRefToolCalibrationClicked())); connect((QObject*)(m_Controls.m_CollectNavigationDataButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnLoginSingleRefToolNavigationDataClicked())); connect((QObject*)(m_Controls.m_SetNewToolTipPosButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnSetNewToolTipPosButtonClicked())); m_IDToolToCalibrate = -1; m_IDCalibrationPointer = -1; m_IndexCurrentCalibrationMethod = -1; m_OnLoginSingleRefToolNavigationDataClicked = false; m_NumberOfNavigationDataCounter = 0; m_NumberOfNavigationData = -1; //for pivot calibration m_OnAddPivotPoseClicked = false; PivotCount = 0; m_PivotPoses = std::vector<mitk::NavigationData::Pointer>(); m_CalibrationLandmarks = mitk::PointSet::New(); m_CalibrationLandmarksNode = mitk::DataNode::New(); m_CalibrationLandmarksNode->SetData(m_CalibrationLandmarks); m_Controls.m_CalibrationLandmarkWidget->SetPointSetNode(m_CalibrationLandmarksNode); m_RegistrationLandmarks = mitk::PointSet::New(); m_RegistrationLandmarksNode = mitk::DataNode::New(); m_RegistrationLandmarksNode->SetData(m_RegistrationLandmarks); m_Controls.m_RegistrationLandmarkWidget->SetPointSetNode(m_RegistrationLandmarksNode); m_ToolSurfaceInToolCoordinatesDataNode = mitk::DataNode::New(); m_ToolSurfaceInToolCoordinatesDataNode->SetName("ToolSurface(ToolCoordinates)"); m_LoggedNavigationDataDifferences = std::vector< mitk::NavigationData::Pointer >(); } void QmitkIGTNavigationToolCalibration::OnRunSingleRefToolCalibrationClicked() { if (!CheckInitialization()) { return; } mitk::NavigationData::Pointer ToolTipTransform = mitk::NavigationData::New(); if (m_Controls.m_CalibratePosition->isChecked()) { //1: Compute mean translational offset vector m_ResultOffsetVector.Fill(0); for (std::vector<mitk::Point3D>::iterator vecIter = m_LoggedNavigationDataOffsets.begin(); vecIter != m_LoggedNavigationDataOffsets.end(); vecIter++) { m_ResultOffsetVector[0] = m_ResultOffsetVector[0] + (*vecIter)[0]; m_ResultOffsetVector[1] = m_ResultOffsetVector[1] + (*vecIter)[1]; m_ResultOffsetVector[2] = m_ResultOffsetVector[2] + (*vecIter)[2]; } m_ResultOffsetVector[0] = m_ResultOffsetVector[0] / m_LoggedNavigationDataOffsets.size(); m_ResultOffsetVector[1] = m_ResultOffsetVector[1] / m_LoggedNavigationDataOffsets.size(); m_ResultOffsetVector[2] = m_ResultOffsetVector[2] / m_LoggedNavigationDataOffsets.size(); this->m_Controls.m_ResultOfCalibration->setText( QString("x: ") + QString(QString::number(m_ResultOffsetVector[0], 103, 3)) + QString("; y: ") + (QString::number(m_ResultOffsetVector[1], 103, 3)) + QString("; z: ") + (QString::number(m_ResultOffsetVector[2], 103, 3))); ToolTipTransform->SetPosition(m_ResultOffsetVector); } if (m_Controls.m_CalibrateOrientation->isChecked()) { //2: Compute mean orientation mitk::Quaternion meanOrientation; std::vector <mitk::Quaternion> allOrientations = std::vector <mitk::Quaternion>(); for (std::size_t i = 0; i < m_LoggedNavigationDataDifferences.size(); i++) { allOrientations.push_back(m_LoggedNavigationDataDifferences.at(i)->GetOrientation()); } meanOrientation = mitk::QuaternionAveraging::CalcAverage(allOrientations); this->m_Controls.m_ResultOfCalibrationOrientation->setText( QString("qx: ") + QString(QString::number(meanOrientation.x(), 103, 3)) + QString("; qy: ") + (QString::number(meanOrientation.y(), 103, 3)) + QString("; qz: ") + (QString::number(meanOrientation.z(), 103, 3)) + QString("; qr: ") + (QString::number(meanOrientation.r(), 103, 3))); ToolTipTransform->SetOrientation(meanOrientation); } MITK_INFO << "Computed calibration: "; MITK_INFO << "Translation Vector: " << ToolTipTransform->GetPosition(); MITK_INFO << "Quaternion: (" << ToolTipTransform->GetOrientation() << ")"; MITK_INFO << "Euler Angles [rad]: (" << ToolTipTransform->GetOrientation().rotation_euler_angles() << ")"; MITK_INFO << "Matrix:"; vnl_matrix_fixed<double, 3, 3> rotMatrix = ToolTipTransform->GetOrientation().rotation_matrix_transpose(); MITK_INFO << rotMatrix[0][0] << " " << rotMatrix[0][1] << " " << rotMatrix[0][2] << std::endl; MITK_INFO << rotMatrix[1][0] << " " << rotMatrix[1][1] << " " << rotMatrix[1][2] << std::endl; MITK_INFO << rotMatrix[2][0] << " " << rotMatrix[2][1] << " " << rotMatrix[2][2] << std::endl; //3: write everything into the final tool tip transform and save it as member (it will be written to the tool later on) mitk::NavigationData::Pointer ToolTipInTrackingCoordinates = mitk::NavigationData::New(); ToolTipInTrackingCoordinates->Compose(ToolTipTransform); ToolTipInTrackingCoordinates->Compose(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)); ShowToolTipPreview(ToolTipInTrackingCoordinates); m_Controls.m_SetNewToolTipPosButton->setEnabled(true); m_ComputedToolTipTransformation = ToolTipTransform; } void QmitkIGTNavigationToolCalibration::OnLoginSingleRefToolNavigationDataClicked() { if (!CheckInitialization()) { return; } //reset old data m_LoggedNavigationDataOffsets.clear(); m_LoggedNavigationDataDifferences.clear(); m_OnLoginSingleRefToolNavigationDataClicked = true; m_Controls.m_CollectNavigationDataButton->setEnabled(false); m_NumberOfNavigationData = m_Controls.m_NumberOfNavigationDataToCollect->value(); MITK_INFO << "Collecting " << m_NumberOfNavigationData << " NavigationData ... " << endl; } void QmitkIGTNavigationToolCalibration::LoginSingleRefToolNavigationData() { if (!CheckInitialization()) { return; } if (m_NumberOfNavigationDataCounter < m_NumberOfNavigationData) { //update label text QString labelText = "Collecting Data: " + QString::number(m_NumberOfNavigationDataCounter); m_Controls.m_CollectionStatus->setText(labelText); mitk::NavigationData::Pointer referenceTool = m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer); mitk::NavigationData::Pointer toolToCalibrate = m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate); //compute difference: // differenceND = toolToCalibrate^-1 * referenceTool mitk::NavigationData::Pointer differenceND = mitk::NavigationData::New(); differenceND->Compose(referenceTool); differenceND->Compose(toolToCalibrate->GetInverse()); //inverse mode... if (m_Controls.m_InvertQuaternions->isChecked()) { // negate identity matrix to directly show parameters that will set up in NDI 6D Software Architect differenceND = differenceND->GetInverse(); } //save difference in member m_LoggedNavigationDataOffsets.push_back(differenceND->GetPosition()); m_LoggedNavigationDataDifferences.push_back(differenceND); m_NumberOfNavigationDataCounter++; } if (m_NumberOfNavigationDataCounter == m_NumberOfNavigationData) { m_NumberOfNavigationDataCounter = 0; m_OnLoginSingleRefToolNavigationDataClicked = false; m_Controls.m_CollectNavigationDataButton->setEnabled(true); m_Controls.m_RunCalibrationButton->setEnabled(true); MITK_INFO << "Collecting " << m_NumberOfNavigationData << " NavigationData ... Finished" << endl; QString labelText = "Collected " + QString::number(m_NumberOfNavigationData) + " data samples!"; m_Controls.m_CollectionStatus->setText(labelText); } } void QmitkIGTNavigationToolCalibration::OnSetNewToolTipPosButtonClicked() { ApplyToolTipTransform(m_ComputedToolTipTransformation); RemoveToolTipPreview(); } void QmitkIGTNavigationToolCalibration::ClearOldPivot() { mitk::NavigationData::Pointer tempND = mitk::NavigationData::New(); this->ApplyToolTipTransform(tempND); UpdateManualToolTipCalibrationView(); //m_ManualToolTipEditWidget->hide(); //TODO this->GetDataStorage()->Remove(m_ToolSurfaceInToolCoordinatesDataNode); } void QmitkIGTNavigationToolCalibration::OnAddPivotPose() { ClearOldPivot(); //When the collect Poses Button is Clicked m_OnAddPivotPoseClicked = true; m_NumberOfNavigationData = m_Controls.m_PosesToCollect->value(); } void QmitkIGTNavigationToolCalibration::AddPivotPose() { //Save the poses to be used in computation if (PivotCount < m_NumberOfNavigationData) { mitk::NavigationData::Pointer currentPose = mitk::NavigationData::New(); currentPose->Graft(m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_IDToolToCalibrate)); m_PivotPoses.push_back(currentPose); m_Controls.m_PoseNumber->setText(QString::number(m_PivotPoses.size())); PivotCount++; } if (PivotCount == m_NumberOfNavigationData) { m_OnAddPivotPoseClicked = false; } } void QmitkIGTNavigationToolCalibration::OnComputePivot() { mitk::PivotCalibration::Pointer myPivotCalibration = mitk::PivotCalibration::New(); for (std::size_t i = 0; i < this->m_PivotPoses.size(); i++) { myPivotCalibration->AddNavigationData(m_PivotPoses.at(i)); } QString resultString; if (myPivotCalibration->ComputePivotResult()) { mitk::NavigationData::Pointer markerTransformationTrackingCoordinates = m_PivotPoses.at(0); - //Get computed pivot transfromation in tool coordinates + //Get computed pivot transformation in tool coordinates mitk::NavigationData::Pointer ToolTipToTool = mitk::NavigationData::New(); ToolTipToTool->SetPosition(myPivotCalibration->GetResultPivotPoint()); ToolTipToTool->SetOrientation(mitk::Quaternion(0,0,0,1)); mitk::NavigationData::Pointer TrackerToTool = mitk::NavigationData::New(); TrackerToTool->SetOrientation(markerTransformationTrackingCoordinates->GetOrientation()); TrackerToTool->SetPosition(markerTransformationTrackingCoordinates->GetPosition()); TrackerToTool->Compose(ToolTipToTool); // Compute pivot point in relation to marker transformation for preview mitk::NavigationData::Pointer ToolTipToTracker = mitk::NavigationData::New(); ToolTipToTracker->Compose(ToolTipToTool); ToolTipToTracker->Compose(markerTransformationTrackingCoordinates); //add the preview node to the data storage ShowToolTipPreview(ToolTipToTracker); //parse result string resultString = QString("Pivot computation succeeded!\n") + QString("RMS Error: ") + QString::number(myPivotCalibration->GetResultRMSError()) + QString("\n") + QString("Pivot Point: ") + QString::number(myPivotCalibration->GetResultPivotPoint()[0]) + ";" + QString::number(myPivotCalibration->GetResultPivotPoint()[1]) + ";" + QString::number(myPivotCalibration->GetResultPivotPoint()[2]) + QString("\n"); //finally: save results to member variable m_ComputedToolTipTransformation = ToolTipToTool; //enable button to use the computed point with the tool m_Controls.m_UseComputedPivotPoint->setEnabled(true); } else { resultString = "Pivot computation failed!"; } MITK_INFO << resultString.toStdString().c_str(); m_Controls.m_ResultText->setText(resultString); } void QmitkIGTNavigationToolCalibration::UpdatePivotCount() { PivotCount = 0; while (!m_PivotPoses.empty()) { m_PivotPoses.pop_back(); } m_Controls.m_PoseNumber->setText(QString::number(PivotCount)); } void QmitkIGTNavigationToolCalibration::OnUseComputedPivotPoint() { RemoveToolTipPreview(); QString resultString = QString("Pivoted tool tip transformation was written to the tool ") + m_ToolToCalibrate->GetToolName().c_str(); ApplyToolTipTransform(m_ComputedToolTipTransformation, resultString.toStdString()); m_Controls.m_ResultText->setText(resultString); UpdatePivotCount(); } void QmitkIGTNavigationToolCalibration::ApplyToolTipTransform(mitk::NavigationData::Pointer ToolTipTransformInToolCoordinates, std::string message) { if (!CheckInitialization(false)) { return; } //Update tool in tool storage m_ToolToCalibrate->SetToolTipPosition(ToolTipTransformInToolCoordinates->GetPosition()); m_ToolToCalibrate->SetToolAxisOrientation(ToolTipTransformInToolCoordinates->GetOrientation()); //And also update tracking device, so the transform is directly used mitk::TrackingDeviceSource::Pointer trackingDeviceSource; try { trackingDeviceSource = dynamic_cast<mitk::TrackingDeviceSource*>(m_NavigationDataSourceOfToolToCalibrate.GetPointer()); mitk::TrackingTool::Pointer TrackingToolToCalibrate = trackingDeviceSource->GetTrackingDevice()->GetTool(m_IDToolToCalibrate); TrackingToolToCalibrate->SetToolTipPosition(ToolTipTransformInToolCoordinates->GetPosition(), ToolTipTransformInToolCoordinates->GetOrientation()); } catch (std::exception& e) { MITK_ERROR << "Error while trying to set the tool tip to the running tracking device. Aborting! (" << e.what() << ")"; } MITK_INFO << message; } void QmitkIGTNavigationToolCalibration::ShowToolTipPreview(mitk::NavigationData::Pointer ToolTipInTrackingCoordinates) { if(m_ToolTipPointPreview.IsNull()) { m_ToolTipPointPreview = mitk::DataNode::New(); m_ToolTipPointPreview->SetName("Modified Tool Tip Preview"); mitk::Color blue; blue.SetBlue(1); m_ToolTipPointPreview->SetColor(blue); mitk::Surface::Pointer mySphere = mitk::Surface::New(); vtkSmartPointer<vtkSphereSource> vtkData = vtkSmartPointer<vtkSphereSource>::New(); vtkData->SetRadius(3.0f); vtkData->SetCenter(0.0, 0.0, 0.0); vtkData->Update(); mySphere->SetVtkPolyData(vtkData->GetOutput()); m_ToolTipPointPreview->SetData(mySphere); this->GetDataStorage()->Add(m_ToolTipPointPreview); } m_ToolTipPointPreview->GetData()->GetGeometry()->SetIndexToWorldTransform(ToolTipInTrackingCoordinates->GetAffineTransform3D()); } void QmitkIGTNavigationToolCalibration::RemoveToolTipPreview() { this->GetDataStorage()->Remove(m_ToolTipPointPreview.GetPointer()); } void QmitkIGTNavigationToolCalibration::UpdateManualToolTipCalibrationView() { if (m_ToolToCalibrate.IsNull()) { return; } //parse human readable transformation data and display it std::stringstream translation; std::stringstream orientation; translation << m_ToolToCalibrate->GetToolTipPosition(); orientation << "Quaternion: (" << m_ToolToCalibrate->GetToolAxisOrientation() << ")" << std::endl; orientation << std::endl; orientation << "Euler Angles [rad]: (" << m_ToolToCalibrate->GetToolAxisOrientation().rotation_euler_angles() << ")" << std::endl; orientation << std::endl; orientation << "Matrix:" << std::endl; vnl_matrix_fixed<double, 3, 3> rotMatrix = m_ToolToCalibrate->GetToolAxisOrientation().rotation_matrix_transpose(); orientation << rotMatrix[0][0] << " " << rotMatrix[0][1] << " " << rotMatrix[0][2] << std::endl; orientation << rotMatrix[1][0] << " " << rotMatrix[1][1] << " " << rotMatrix[1][2] << std::endl; orientation << rotMatrix[2][0] << " " << rotMatrix[2][1] << " " << rotMatrix[2][2] << std::endl; m_Controls.m_ManualCurrentTranslation->setText(translation.str().c_str()); m_Controls.m_ManualCurrentOrientation->setPlainText(orientation.str().c_str()); } void QmitkIGTNavigationToolCalibration::OnStartManualToolTipCalibration() { if (!CheckInitialization(false)) { return; } m_ToolTransformationWidget->SetToolToEdit(m_ToolToCalibrate); m_ToolTransformationWidget->SetDefaultOffset(m_ToolToCalibrate->GetToolTipPosition()); m_ToolTransformationWidget->SetDefaultRotation(m_ToolToCalibrate->GetToolAxisOrientation()); m_ToolTransformationWidget->open(); } void QmitkIGTNavigationToolCalibration::OnManualEditToolTipFinished(mitk::AffineTransform3D::Pointer toolTip) { //This function is called, when the toolTipEdit view is closed. - //if user pressed cancle, nullptr is returned. Do nothing. Else, set values. + //if user pressed cancel, nullptr is returned. Do nothing. Else, set values. if (toolTip) { mitk::NavigationData::Pointer tempND = mitk::NavigationData::New(toolTip);//Convert to Navigation data for simple transversion to quaternion QString resultString = QString("Manual edited values are written to ") + m_ToolToCalibrate->GetToolName().c_str(); ApplyToolTipTransform(tempND, resultString.toStdString()); m_Controls.m_ResultText->setText(resultString); m_ComputedToolTipTransformation = tempND; } UpdateManualToolTipCalibrationView(); } void QmitkIGTNavigationToolCalibration::OnGetPositions() { if (!CheckInitialization(true)) { return; } //Navigation Data from Tool which should be calibrated if (!m_AxisCalibration_ToolToCalibrate) m_AxisCalibration_ToolToCalibrate = mitk::NavigationData::New(); m_AxisCalibration_ToolToCalibrate->Graft(m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_IDToolToCalibrate)); //Navigation Data from calibration pointer tool if (!m_AxisCalibration_NavDataCalibratingTool) m_AxisCalibration_NavDataCalibratingTool = mitk::NavigationData::New(); m_AxisCalibration_NavDataCalibratingTool->Graft(m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_IDCalibrationPointer)); MITK_DEBUG << "Positions for tool axis calibration:"; MITK_DEBUG << " ToolTip: " << m_AxisCalibration_ToolToCalibrate->GetPosition() << ","; MITK_DEBUG << " Rotation: \n" << m_AxisCalibration_ToolToCalibrate->GetRotationMatrix(); MITK_DEBUG << " End of the tool: " << m_AxisCalibration_NavDataCalibratingTool->GetPosition(); QString _label = "Position recorded: " + QString::number(m_AxisCalibration_NavDataCalibratingTool->GetPosition()[0], 'f', 1) + ", " + QString::number(m_AxisCalibration_NavDataCalibratingTool->GetPosition()[1], 'f', 1) + ", " + QString::number(m_AxisCalibration_NavDataCalibratingTool->GetPosition()[2], 'f', 1); m_Controls.m_ToolAxisPositionLabel->setText(_label); } void QmitkIGTNavigationToolCalibration::OnCalibrateToolAxis() { if (!m_ComputedToolTipTransformation) { MITK_ERROR << "Please compute tool tip first."; - QMessageBox::information(nullptr, "Error", "Please compute / specifiy tool tip first"); + QMessageBox::information(nullptr, "Error", "Please compute / specify tool tip first"); return; } if (!m_AxisCalibration_ToolToCalibrate || !m_AxisCalibration_NavDataCalibratingTool) { MITK_ERROR << "Please record position first."; QMessageBox::information(nullptr, "Error", "Please record position first"); return; } //Calculate the tool tip //here is an explanation, what is happening here: /* The axis is equal to the (tool tip) minus the (end of the tool) in tool coordinates of the tool which should be calibrated. The tool tip is defined as the origin of the tool coordinate system. The end of the tool is recorded by the calibration pointer's position and is transformed into the coordinate system of the tool to be calibrated Normalize it. */ //m_CalibratedToolAxis = -m_AxisCalibration_ToolToCalibrate->TransformPoint(m_AxisCalibration_NavDataCalibratingTool->GetPosition()).GetVectorFromOrigin(); m_CalibratedToolAxis = -m_AxisCalibration_ToolToCalibrate->GetInverse()->TransformPoint(m_AxisCalibration_NavDataCalibratingTool->GetPosition()).GetVectorFromOrigin(); MITK_DEBUG << "Tool Endpoint in Tool coordinates: " << m_CalibratedToolAxis; m_CalibratedToolAxis.Normalize(); MITK_DEBUG << "Tool Axis: " << m_CalibratedToolAxis; m_ToolToCalibrate->SetToolAxis(mitk::Point3D(m_CalibratedToolAxis)); // Update TrackingTool m_ComputedToolTipTransformation->SetPosition(m_ToolToCalibrate->GetToolTipPosition()); m_ComputedToolTipTransformation->SetOrientation(m_ToolToCalibrate->GetToolAxisOrientation()); ApplyToolTipTransform(m_ComputedToolTipTransformation); //Update GUI QString calibratedToolAxisString = "Tool Axis: " + QString::number(m_CalibratedToolAxis.GetElement(0), 'f', 3) + ", " + QString::number(m_CalibratedToolAxis.GetElement(1), 'f', 3) + ", " + QString::number(m_CalibratedToolAxis.GetElement(2), 'f', 3); m_Controls.m_ToolAxisCalibrationLabel->setText(calibratedToolAxisString); //Block QT signals, we don't want to emit SpinboxChanged on the first value to overwrite the next ones m_Controls.m_ToolAxis_X->blockSignals(true); m_Controls.m_ToolAxis_Y->blockSignals(true); m_Controls.m_ToolAxis_Z->blockSignals(true); m_Controls.m_ToolAxis_X->setValue(m_CalibratedToolAxis[0]); m_Controls.m_ToolAxis_Y->setValue(m_CalibratedToolAxis[1]); m_Controls.m_ToolAxis_Z->setValue(m_CalibratedToolAxis[2]); m_Controls.m_ToolAxis_X->blockSignals(false); m_Controls.m_ToolAxis_Y->blockSignals(false); m_Controls.m_ToolAxis_Z->blockSignals(false); } void QmitkIGTNavigationToolCalibration::OnToolAxisSpinboxChanged() { m_CalibratedToolAxis.SetElement(0, m_Controls.m_ToolAxis_X->value()); m_CalibratedToolAxis.SetElement(1, m_Controls.m_ToolAxis_Y->value()); m_CalibratedToolAxis.SetElement(2, m_Controls.m_ToolAxis_Z->value()); m_ToolToCalibrate->SetToolAxis(mitk::Point3D(m_CalibratedToolAxis)); // Update TrackingTool if (m_ComputedToolTipTransformation.IsNull()) { m_ComputedToolTipTransformation = mitk::NavigationData::New(); } m_ComputedToolTipTransformation->SetPosition(m_ToolToCalibrate->GetToolTipPosition()); m_ComputedToolTipTransformation->SetOrientation(m_ToolToCalibrate->GetToolAxisOrientation()); ApplyToolTipTransform(m_ComputedToolTipTransformation); MITK_INFO << "Tool axis changed to " << m_CalibratedToolAxis; } void QmitkIGTNavigationToolCalibration::SetToolToCalibrate() { m_IDToolToCalibrate = m_Controls.m_SelectionWidget->GetSelectedToolID(); if (m_IDToolToCalibrate == -1) //no valid tool to calibrate { m_Controls.m_CalToolLabel->setText("<none>"); m_Controls.m_StatusWidgetToolToCalibrate->RemoveStatusLabels(); m_TrackingTimer->stop(); } else { m_ToolToCalibrate = m_Controls.m_SelectionWidget->GetSelectedNavigationTool(); m_NavigationDataSourceOfToolToCalibrate = m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource(); m_Controls.m_CalToolLabel->setText(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)->GetName()); //initialize widget m_Controls.m_StatusWidgetToolToCalibrate->RemoveStatusLabels(); m_Controls.m_StatusWidgetToolToCalibrate->SetShowPositions(true); m_Controls.m_StatusWidgetToolToCalibrate->SetTextAlignment(Qt::AlignLeft); m_Controls.m_StatusWidgetToolToCalibrate->AddNavigationData(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)); m_Controls.m_StatusWidgetToolToCalibrate->ShowStatusLabels(); //initialize manual tool tip calibration view UpdateManualToolTipCalibrationView(); //save tool surface in tool coordinates for further editing mitk::Surface::Pointer ToolSurface = dynamic_cast<mitk::Surface*>(m_ToolToCalibrate->GetDataNode()->GetData())->Clone(); m_ToolSurfaceInToolCoordinatesDataNode->SetData(ToolSurface); m_ToolSurfaceInToolCoordinatesDataNode->GetData()->GetGeometry()->SetIdentity(); // update tool tip and rotation information for tool tip calibration tab UpdateManualToolTipCalibrationView(); // update tool axis information for tool axis calibration tab mitk::Point3D toolAxis = m_ToolToCalibrate->GetToolAxis(); m_CalibratedToolAxis[0] = toolAxis[0]; m_CalibratedToolAxis[1] = toolAxis[1]; m_CalibratedToolAxis[2] = toolAxis[2]; m_Controls.m_ToolAxis_X->blockSignals(true); m_Controls.m_ToolAxis_Y->blockSignals(true); m_Controls.m_ToolAxis_Z->blockSignals(true); m_Controls.m_ToolAxis_X->setValue(m_CalibratedToolAxis[0]); m_Controls.m_ToolAxis_Y->setValue(m_CalibratedToolAxis[1]); m_Controls.m_ToolAxis_Z->setValue(m_CalibratedToolAxis[2]); m_Controls.m_ToolAxis_X->blockSignals(false); m_Controls.m_ToolAxis_Y->blockSignals(false); m_Controls.m_ToolAxis_Z->blockSignals(false); //start updating timer for status widgets, etc. if (!m_TrackingTimer->isActive()) m_TrackingTimer->start(100); } } void QmitkIGTNavigationToolCalibration::SetCalibrationPointer() { m_IDCalibrationPointer = m_Controls.m_SelectionWidget->GetSelectedToolID(); if (m_IDCalibrationPointer == -1) { m_Controls.m_PointerLabel->setText("<none>"); m_Controls.m_StatusWidgetCalibrationPointer->RemoveStatusLabels(); m_TrackingTimer->stop(); } else { m_NavigationDataSourceOfCalibrationPointer = m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource(); m_Controls.m_PointerLabel->setText(m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer)->GetName()); //initialize widget m_Controls.m_StatusWidgetCalibrationPointer->RemoveStatusLabels(); m_Controls.m_StatusWidgetCalibrationPointer->SetShowPositions(true); m_Controls.m_StatusWidgetCalibrationPointer->SetTextAlignment(Qt::AlignLeft); m_Controls.m_StatusWidgetCalibrationPointer->AddNavigationData(m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer)); m_Controls.m_StatusWidgetCalibrationPointer->ShowStatusLabels(); if (!m_TrackingTimer->isActive()) m_TrackingTimer->start(100); } } void QmitkIGTNavigationToolCalibration::UpdateOffsetCoordinates() { if (m_NavigationDataSourceOfCalibrationPointer.IsNull() || m_NavigationDataSourceOfToolToCalibrate.IsNull()) { return; } mitk::NavigationData::Pointer referenceToolND = m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer); mitk::NavigationData::Pointer toolToCalibrateND = m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate); if (referenceToolND->IsDataValid() && toolToCalibrateND->IsDataValid()) { //computation: difference between both tools (in tool coordinates) //differenceND = toolToCalibrateND^-1 * referenceToolND mitk::NavigationData::Pointer differenceND = mitk::NavigationData::New(); differenceND->Compose(referenceToolND); differenceND->Compose(toolToCalibrateND->GetInverse()); //display this orientation in the UI m_Controls.m_OffsetCoordinates->setText( QString("x: ") + QString(QString::number(differenceND->GetPosition()[0], 103, 3)) + QString("; y: ") + (QString::number(differenceND->GetPosition()[1], 103, 3)) + QString("; z: ") + (QString::number(differenceND->GetPosition()[2], 103, 3))); m_Controls.m_OrientationOffsetCoordinates->setText( QString("qx: ") + QString(QString::number(differenceND->GetOrientation().x(), 103, 3)) + QString("; qy: ") + (QString::number(differenceND->GetOrientation().y(), 103, 3)) + QString("; qz: ") + (QString::number(differenceND->GetOrientation().z(), 103, 3)) + QString("; qr: ") + (QString::number(differenceND->GetOrientation().r(), 103, 3))); //also update preview if active if (m_ToolTipPointPreview.IsNotNull()) //NOT WORKING! TODO: fix or remove! { mitk::NavigationData::Pointer ToolTipTransform = mitk::NavigationData::New(); ToolTipTransform->SetPosition(m_ResultOffsetVector); - mitk::NavigationData::Pointer ToolTipInTrackingCoordinates = mitk::NavigationData::New(); //maybe store as for better peformance... + mitk::NavigationData::Pointer ToolTipInTrackingCoordinates = mitk::NavigationData::New(); //maybe store as for better performance... ToolTipInTrackingCoordinates->Compose(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)); ToolTipInTrackingCoordinates->Compose(ToolTipTransform); m_ToolTipPointPreview->GetData()->GetGeometry()->SetIndexToWorldTransform(ToolTipInTrackingCoordinates->GetAffineTransform3D()); } } } void QmitkIGTNavigationToolCalibration::UpdateTrackingTimer() { m_Controls.m_StatusWidgetToolToCalibrate->Refresh(); m_Controls.m_StatusWidgetCalibrationPointer->Refresh(); if (m_OnLoginSingleRefToolNavigationDataClicked) LoginSingleRefToolNavigationData(); if (m_OnAddPivotPoseClicked) AddPivotPose(); // 1 == Single Reference Calibration Method if (m_IndexCurrentCalibrationMethod == 1) UpdateOffsetCoordinates(); } void QmitkIGTNavigationToolCalibration::AddLandmark() { if (!CheckInitialization()) { return; } mitk::NavigationData::Pointer navDataTool = m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate); mitk::Point3D landmark = m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer)->GetPosition(); //convert to itk transform itk::Vector<double, 3> translation; for (int k = 0; k < 3; k++) translation[k] = navDataTool->GetPosition()[k]; itk::Matrix<double, 3, 3> rotation; for (int k = 0; k < 3; k++) for (int l = 0; l < 3; l++) rotation[k][l] = navDataTool->GetOrientation().rotation_matrix_transpose()[k][l]; rotation = rotation.GetTranspose(); itk::Vector<double> landmarkItk; landmarkItk[0] = landmark[0]; landmarkItk[1] = landmark[1]; landmarkItk[2] = landmark[2]; //compute landmark in tool coordinates itk::Matrix<double, 3, 3> rotationInverse; for (int k = 0; k < 3; k++) for (int l = 0; l < 3; l++) rotationInverse[k][l] = rotation.GetInverse()[k][l]; landmarkItk = rotationInverse * (landmarkItk - translation); //convert back and add landmark to pointset landmark[0] = landmarkItk[0]; landmark[1] = landmarkItk[1]; landmark[2] = landmarkItk[2]; m_RegistrationLandmarks->InsertPoint(m_RegistrationLandmarks->GetSize(), landmark); } void QmitkIGTNavigationToolCalibration::SaveCalibratedTool() { if (m_ToolToCalibrate.IsNotNull()) { mitk::NavigationTool::Pointer calibratedTool = m_ToolToCalibrate; calibratedTool->SetToolControlPoints(this->m_CalibrationLandmarks); calibratedTool->SetToolLandmarks(this->m_RegistrationLandmarks); mitk::NavigationToolWriter::Pointer myWriter = mitk::NavigationToolWriter::New(); QString filename = QFileDialog::getSaveFileName(nullptr,tr("Save Navigation Tool"), "/", "*.IGTTool"); if (filename.isEmpty()) return; // ensure that file suffix is set QFileInfo file(filename); if (file.suffix().isEmpty()) { filename += ".IGTTool"; } if (myWriter->DoWrite(filename.toStdString(), calibratedTool)) MITK_INFO << "Saved calibrated tool to file " << filename; else MITK_WARN << "Can't write tool to file " << filename; } else { MITK_ERROR << "Did not find navigation tool storage of calibrated tool, aborting!"; } } bool QmitkIGTNavigationToolCalibration::CheckInitialization(bool CalibrationPointerRequired) { if ((m_IDToolToCalibrate == -1) || ((CalibrationPointerRequired) && (m_IDCalibrationPointer == -1) ) ) { QMessageBox msgBox; msgBox.setText("Tool to calibrate and/or calibration pointer not initialized, cannot proceed!"); msgBox.exec(); return false; } else { return true; } } diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.h b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.h index 00c3e4c14c..8bb0f43f75 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.h +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.h @@ -1,139 +1,139 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkIGTNavigationToolCalibration_h #define QmitkIGTNavigationToolCalibration_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include <mitkNavigationData.h> #include "QmitkInteractiveTransformationWidget.h" #include "ui_QmitkIGTNavigationToolCalibrationControls.h" #include <mitkNavigationDataRecorder.h> //QT headers #include <QTimer> /*! \brief IGTNavigationToolCalibration \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \ingroup ${plugin_target}_internal */ class QmitkIGTNavigationToolCalibration : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: QmitkIGTNavigationToolCalibration(); ~QmitkIGTNavigationToolCalibration() override; static const std::string VIEW_ID; void CreateQtPartControl(QWidget *parent) override; protected slots: void OnAddPivotPose(); void OnComputePivot(); void OnUseComputedPivotPoint(); void SetToolToCalibrate(); void SetCalibrationPointer(); void UpdateTrackingTimer(); void AddLandmark(); void SaveCalibratedTool(); void OnToolCalibrationMethodChanged(int index); void OnStartManualToolTipCalibration(); void OnRunSingleRefToolCalibrationClicked(); void OnLoginSingleRefToolNavigationDataClicked(); void OnSetNewToolTipPosButtonClicked(); void OnGetPositions(); void OnCalibrateToolAxis(); void OnToolAxisSpinboxChanged(); void OnManualEditToolTipFinished(mitk::AffineTransform3D::Pointer toolTip); protected: void SetFocus() override; void UpdateOffsetCoordinates(); int m_IndexCurrentCalibrationMethod; Ui::IGTNavigationToolCalibrationControls m_Controls; //some general members mitk::NavigationTool::Pointer m_ToolToCalibrate; //<<< tool that will be calibrated int m_IDToolToCalibrate; //<<< id of tool that will be calibrated (of the navigation data source) mitk::NavigationDataSource::Pointer m_NavigationDataSourceOfToolToCalibrate; //<<< navigation data source of the tool that will be calibrated mitk::NavigationDataSource::Pointer m_NavigationDataSourceOfCalibrationPointer; //<<< navigation data source of the calibration pointer mitk::DataNode::Pointer m_ToolSurfaceInToolCoordinatesDataNode; //<<< holds the tool surface in tool coordinates (for preview purposes) int m_IDCalibrationPointer; //<<< id of the calibration pointer (of the corresponding navigation data source) QTimer* m_TrackingTimer; //<<< tracking timer that updates the status widgets - void ApplyToolTipTransform(mitk::NavigationData::Pointer ToolTipTransformInToolCoordinates, std::string message = "Tool was updated with the calibrated tool tip!"); //<<< applys the given tool tip transform to the tool to calibrate + void ApplyToolTipTransform(mitk::NavigationData::Pointer ToolTipTransformInToolCoordinates, std::string message = "Tool was updated with the calibrated tool tip!"); //<<< applies the given tool tip transform to the tool to calibrate bool CheckInitialization(bool CalibrationPointerRequired = true); //<<< checks if the tool to calibrate and (if required) the calibration pointer is initialized. Displays a warning and returns false if not. mitk::NavigationData::Pointer m_ComputedToolTipTransformation; //<<< holds the new tooltip transformation after it was computed to write it into the tool later // members and helper methods for pivot tool calibration std::vector<mitk::NavigationData::Pointer> m_PivotPoses; void AddPivotPose(); void ClearOldPivot(); void UpdatePivotCount(); bool m_OnAddPivotPoseClicked; int PivotCount; // members and helper methods for manual tool calibration void UpdateManualToolTipCalibrationView(); QmitkInteractiveTransformationWidget* m_ToolTransformationWidget; // members and helper methods for single reference tool calibration void LoginSingleRefToolNavigationData(); std::vector< mitk::Point3D > m_LoggedNavigationDataOffsets; std::vector< mitk::NavigationData::Pointer > m_LoggedNavigationDataDifferences; bool m_OnLoginSingleRefToolNavigationDataClicked; int m_NumberOfNavigationData; int m_NumberOfNavigationDataCounter; mitk::Point3D m_ResultOffsetVector; // members and helper methods for tool tip preview mitk::DataNode::Pointer m_ToolTipPointPreview; //<<< Data node of the tool tip preview void ShowToolTipPreview(mitk::NavigationData::Pointer ToolTipInTrackingCoordinates); //<<< Adds a preview of the tool tip into the data storage void RemoveToolTipPreview(); //<<< Removes the preview // members for the tool landmark calibration mitk::PointSet::Pointer m_CalibrationLandmarks; mitk::DataNode::Pointer m_CalibrationLandmarksNode; mitk::PointSet::Pointer m_RegistrationLandmarks; mitk::DataNode::Pointer m_RegistrationLandmarksNode; //members and helper methods for tool axis calibration mitk::Vector3D m_CalibratedToolAxis; mitk::NavigationData::Pointer m_AxisCalibration_ToolToCalibrate; mitk::NavigationData::Pointer m_AxisCalibration_NavDataCalibratingTool; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.cpp b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.cpp index 82feb76914..cae308e21e 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.cpp +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.cpp @@ -1,1437 +1,1437 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkMITKIGTTrackingToolboxView.h" // Qt #include <QMessageBox> #include <QSettings> #include <QFileDialog> // MITK #include <mitkNavigationToolStorageDeserializer.h> #include <mitkTrackingVolumeGenerator.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkNavigationToolStorageSerializer.h> #include <mitkIOUtil.h> #include <mitkLogBackend.h> #include <mitkTrackingDeviceTypeCollection.h> #include <mitkUnspecifiedTrackingTypeInformation.h> #include <mitkNeedleProjectionFilter.h> //for exceptions #include <mitkIGTException.h> #include <mitkIGTIOException.h> #include "mitkPluginActivator.h" const std::string QmitkMITKIGTTrackingToolboxView::VIEW_ID = "org.mitk.views.mitkigttrackingtoolbox"; QmitkMITKIGTTrackingToolboxView::QmitkMITKIGTTrackingToolboxView() : QmitkAbstractView() , m_Controls(nullptr) , m_DeviceTypeCollection(nullptr) , m_ToolProjectionNode(nullptr) { m_TrackingLoggingTimer = new QTimer(this); m_TrackingRenderTimer = new QTimer(this); m_TimeoutTimer = new QTimer(this); m_tracking = false; m_connected = false; m_logging = false; m_ShowHideToolAxis = false; m_loggedFrames = 0; m_SimpleModeEnabled = false; m_NeedleProjectionFilter = mitk::NeedleProjectionFilter::New(); //create filename for autosaving of tool storage auto loggingPathWithoutFilename = QString::fromStdString(mitk::LogBackend::GetLogFile()); if (!loggingPathWithoutFilename.isEmpty()) //if there already is a path for the MITK logging file use this one { //extract path from path+filename (if someone knows a better way to do this feel free to change it) int lengthOfFilename = QFileInfo(QString::fromStdString(mitk::LogBackend::GetLogFile())).fileName().size(); loggingPathWithoutFilename.resize(loggingPathWithoutFilename.size() - lengthOfFilename); m_AutoSaveFilename = loggingPathWithoutFilename + "TrackingToolboxAutoSave.IGTToolStorage"; } else //if not: use a temporary path from IOUtil { m_AutoSaveFilename = QString(mitk::IOUtil::GetTempPath().c_str()) + "TrackingToolboxAutoSave.IGTToolStorage"; } MITK_INFO("IGT Tracking Toolbox") << "Filename for auto saving of IGT ToolStorages: " << m_AutoSaveFilename.toStdString(); //! [Thread 1] //initialize worker thread m_WorkerThread = new QThread(); m_Worker = new QmitkMITKIGTTrackingToolboxViewWorker(); //! [Thread 1] ctkPluginContext* pluginContext = mitk::PluginActivator::GetContext(); if (pluginContext) { QString interfaceName = QString::fromStdString(us_service_interface_iid<mitk::TrackingDeviceTypeCollection>()); QList<ctkServiceReference> serviceReference = pluginContext->getServiceReferences(interfaceName); if (serviceReference.size() > 0) { m_DeviceTypeServiceReference = serviceReference.at(0); const ctkServiceReference& r = serviceReference.at(0); m_DeviceTypeCollection = pluginContext->getService<mitk::TrackingDeviceTypeCollection>(r); } else { MITK_INFO << "No Tracking Device Collection!"; } } } QmitkMITKIGTTrackingToolboxView::~QmitkMITKIGTTrackingToolboxView() { this->StoreUISettings(); m_TrackingLoggingTimer->stop(); m_TrackingRenderTimer->stop(); m_TimeoutTimer->stop(); delete m_TrackingLoggingTimer; delete m_TrackingRenderTimer; delete m_TimeoutTimer; try { //! [Thread 2] // wait for thread to finish m_WorkerThread->terminate(); m_WorkerThread->wait(); //clean up worker thread if (m_WorkerThread) { delete m_WorkerThread; } if (m_Worker) { delete m_Worker; } //! [Thread 2] //remove the tracking volume this->GetDataStorage()->Remove(m_TrackingVolumeNode); //unregister microservices if (m_toolStorage) { m_toolStorage->UnRegisterMicroservice(); } if (m_IGTLMessageProvider.IsNotNull()){ m_IGTLMessageProvider->UnRegisterMicroservice(); } } catch (std::exception& e) { MITK_WARN << "Unexpected exception during clean up of tracking toolbox view: " << e.what(); } catch (...) { MITK_WARN << "Unexpected unknown error during clean up of tracking toolbox view!"; } //store tool storage and UI settings for persistence this->AutoSaveToolStorage(); this->StoreUISettings(); m_DeviceTypeCollection = nullptr; mitk::PluginActivator::GetContext()->ungetService(m_DeviceTypeServiceReference); } void QmitkMITKIGTTrackingToolboxView::CreateQtPartControl(QWidget *parent) { // build up qt view, unless already done if (!m_Controls) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkMITKIGTTrackingToolboxViewControls; m_Controls->setupUi(parent); //create connections connect(m_Controls->m_LoadTools, SIGNAL(clicked()), this, SLOT(OnLoadTools())); connect(m_Controls->m_ConnectDisconnectButton, SIGNAL(clicked()), this, SLOT(OnConnectDisconnect())); connect(m_Controls->m_StartStopTrackingButton, SIGNAL(clicked()), this, SLOT(OnStartStopTracking())); connect(m_Controls->m_ConnectSimpleMode, SIGNAL(clicked()), this, SLOT(OnConnectDisconnect())); connect(m_Controls->m_StartTrackingSimpleMode, SIGNAL(clicked()), this, SLOT(OnStartStopTracking())); connect(m_Controls->m_FreezeUnfreezeTrackingButton, SIGNAL(clicked()), this, SLOT(OnFreezeUnfreezeTracking())); connect(m_TrackingLoggingTimer, SIGNAL(timeout()), this, SLOT(UpdateLoggingTrackingTimer())); connect(m_TrackingRenderTimer, SIGNAL(timeout()), this, SLOT(UpdateRenderTrackingTimer())); connect(m_TimeoutTimer, SIGNAL(timeout()), this, SLOT(OnTimeOut())); connect(m_Controls->m_ChooseFile, SIGNAL(clicked()), this, SLOT(OnChooseFileClicked())); connect(m_Controls->m_StartLogging, SIGNAL(clicked()), this, SLOT(StartLogging())); connect(m_Controls->m_StopLogging, SIGNAL(clicked()), this, SLOT(StopLogging())); connect(m_Controls->m_VolumeSelectionBox, SIGNAL(currentIndexChanged(QString)), this, SLOT(OnTrackingVolumeChanged(QString))); connect(m_Controls->m_ShowTrackingVolume, SIGNAL(clicked()), this, SLOT(OnShowTrackingVolumeChanged())); connect(m_Controls->m_AutoDetectTools, SIGNAL(clicked()), this, SLOT(OnAutoDetectTools())); connect(m_Controls->m_ResetTools, SIGNAL(clicked()), this, SLOT(OnResetTools())); connect(m_Controls->m_AddSingleTool, SIGNAL(clicked()), this, SLOT(OnAddSingleTool())); connect(m_Controls->m_NavigationToolCreationWidget, SIGNAL(NavigationToolFinished()), this, SLOT(OnAddSingleToolFinished())); connect(m_Controls->m_NavigationToolCreationWidget, SIGNAL(Canceled()), this, SLOT(OnAddSingleToolCanceled())); connect(m_Controls->m_CsvFormat, SIGNAL(clicked()), this, SLOT(OnToggleFileExtension())); connect(m_Controls->m_XmlFormat, SIGNAL(clicked()), this, SLOT(OnToggleFileExtension())); connect(m_Controls->m_UseDifferentUpdateRates, SIGNAL(clicked()), this, SLOT(OnToggleDifferentUpdateRates())); connect(m_Controls->m_RenderUpdateRate, SIGNAL(valueChanged(int)), this, SLOT(OnChangeRenderUpdateRate())); connect(m_Controls->m_DisableAllTimers, SIGNAL(stateChanged(int)), this, SLOT(EnableDisableTimerButtons(int))); connect(m_Controls->m_advancedUI, SIGNAL(clicked()), this, SLOT(OnToggleAdvancedSimpleMode())); connect(m_Controls->m_SimpleUI, SIGNAL(clicked()), this, SLOT(OnToggleAdvancedSimpleMode())); connect(m_Controls->showHideToolProjectionCheckBox, SIGNAL(clicked()), this, SLOT(OnShowHideToolProjectionClicked())); connect(m_Controls->showHideToolAxisCheckBox, SIGNAL(clicked()), this, SLOT(OnShowHideToolAxisClicked())); connect(m_Controls->m_toolselector, SIGNAL(currentIndexChanged(int)), this, SLOT(SelectToolProjection(int))); //connections for the tracking device configuration widget connect(m_Controls->m_ConfigurationWidget, SIGNAL(TrackingDeviceSelectionChanged()), this, SLOT(OnTrackingDeviceChanged())); //! [Thread 3] //connect worker thread connect(m_Worker, SIGNAL(AutoDetectToolsFinished(bool, QString)), this, SLOT(OnAutoDetectToolsFinished(bool, QString))); connect(m_Worker, SIGNAL(ConnectDeviceFinished(bool, QString)), this, SLOT(OnConnectFinished(bool, QString))); connect(m_Worker, SIGNAL(StartTrackingFinished(bool, QString)), this, SLOT(OnStartTrackingFinished(bool, QString))); connect(m_Worker, SIGNAL(StopTrackingFinished(bool, QString)), this, SLOT(OnStopTrackingFinished(bool, QString))); connect(m_Worker, SIGNAL(DisconnectDeviceFinished(bool, QString)), this, SLOT(OnDisconnectFinished(bool, QString))); connect(m_WorkerThread, SIGNAL(started()), m_Worker, SLOT(ThreadFunc())); connect(m_Worker, SIGNAL(ConnectDeviceFinished(bool, QString)), m_Controls->m_ConfigurationWidget, SLOT(OnConnected(bool))); connect(m_Worker, SIGNAL(DisconnectDeviceFinished(bool, QString)), m_Controls->m_ConfigurationWidget, SLOT(OnDisconnected(bool))); connect(m_Worker, SIGNAL(StartTrackingFinished(bool, QString)), m_Controls->m_ConfigurationWidget, SLOT(OnStartTracking(bool))); connect(m_Worker, SIGNAL(StopTrackingFinished(bool, QString)), m_Controls->m_ConfigurationWidget, SLOT(OnStopTracking(bool))); //Add Listener, so that we know when the toolStorage changed. std::string m_Filter = "(" + us::ServiceConstants::OBJECTCLASS() + "=" + "org.mitk.services.NavigationToolStorage" + ")"; mitk::PluginActivator::GetContext()->connectServiceListener(this, "OnToolStorageChanged", QString(m_Filter.c_str())); //move the worker to the thread m_Worker->moveToThread(m_WorkerThread); //! [Thread 3] //initialize widgets m_Controls->m_TrackingToolsStatusWidget->SetShowPositions(true); m_Controls->m_TrackingToolsStatusWidget->SetTextAlignment(Qt::AlignLeft); m_Controls->m_simpleWidget->setVisible(false); //initialize tracking volume node m_TrackingVolumeNode = mitk::DataNode::New(); m_TrackingVolumeNode->SetName("TrackingVolume"); m_TrackingVolumeNode->SetBoolProperty("Backface Culling", true); mitk::Color red; red.SetRed(1); m_TrackingVolumeNode->SetColor(red); //initialize buttons m_Controls->m_AutoDetectTools->setVisible(false); //only visible if supported by tracking device m_Controls->m_StartStopTrackingButton->setEnabled(false); m_Controls->m_StartTrackingSimpleMode->setEnabled(false); m_Controls->m_FreezeUnfreezeTrackingButton->setEnabled(false); //initialize warning labels m_Controls->m_RenderWarningLabel->setVisible(false); m_Controls->m_TrackingFrozenLabel->setVisible(false); //initialize projection buttons //first it is disabled when the tool is connected check box for projection and axis is enabled m_Controls->showHideToolAxisCheckBox->setEnabled(false); m_Controls->showHideToolProjectionCheckBox->setEnabled(false); m_Controls->m_toolselector->setEnabled(false); //Update List of available models for selected tool. std::vector<mitk::TrackingDeviceData> Compatibles; if ((m_Controls == nullptr) || //check all these stuff for NULL, latterly this causes crashes from time to time (m_Controls->m_ConfigurationWidget == nullptr) || (m_Controls->m_ConfigurationWidget->GetTrackingDevice().IsNull())) { MITK_ERROR << "Couldn't get current tracking device or an object is nullptr, something went wrong!"; return; } else { Compatibles = m_DeviceTypeCollection->GetDeviceDataForLine(m_Controls->m_ConfigurationWidget->GetTrackingDevice()->GetType()); } m_Controls->m_VolumeSelectionBox->clear(); for (std::size_t i = 0; i < Compatibles.size(); i++) { m_Controls->m_VolumeSelectionBox->addItem(Compatibles[i].Model.c_str()); } //initialize tool storage m_toolStorage = mitk::NavigationToolStorage::New(GetDataStorage()); m_toolStorage->SetName("TrackingToolbox Default Storage"); m_toolStorage->RegisterAsMicroservice(); //set home directory as default path for logfile m_Controls->m_LoggingFileName->setText(QDir::toNativeSeparators(QDir::homePath()) + QDir::separator() + "logfile.csv"); //tracking device may be changed already by the persistence of the //QmitkTrackingDeciveConfigurationWidget this->OnTrackingDeviceChanged(); this->LoadUISettings(); //add tracking volume node only to data storage this->GetDataStorage()->Add(m_TrackingVolumeNode); if (!m_Controls->m_ShowTrackingVolume->isChecked()) m_TrackingVolumeNode->SetOpacity(0.0); else m_TrackingVolumeNode->SetOpacity(0.25); //Update List of available models for selected tool. m_Controls->m_VolumeSelectionBox->clear(); for (std::size_t i = 0; i < Compatibles.size(); i++) { m_Controls->m_VolumeSelectionBox->addItem(Compatibles[i].Model.c_str()); } } } void QmitkMITKIGTTrackingToolboxView::OnLoadTools() { //read in filename QString filename = QFileDialog::getOpenFileName(nullptr, tr("Open Tool Storage"), "/", tr("Tool Storage Files (*.IGTToolStorage)")); if (filename.isNull()) return; //read tool storage from disk std::string errorMessage = ""; mitk::NavigationToolStorageDeserializer::Pointer myDeserializer = mitk::NavigationToolStorageDeserializer::New(GetDataStorage()); // try-catch block for exceptions try { this->ReplaceCurrentToolStorage(myDeserializer->Deserialize(filename.toStdString()), filename.toStdString()); } catch (mitk::IGTException&) { std::string errormessage = "Error during loading the tool storage file. Please only load tool storage files created with the NavigationToolManager view."; QMessageBox::warning(nullptr, "Tool Storage Loading Error", errormessage.c_str()); return; } if (m_toolStorage->isEmpty()) { errorMessage = myDeserializer->GetErrorMessage(); MessageBox(errorMessage); return; } //update label UpdateToolStorageLabel(filename); //update tool preview m_Controls->m_TrackingToolsStatusWidget->RemoveStatusLabels(); m_Controls->m_TrackingToolsStatusWidget->PreShowTools(m_toolStorage); //save filename for persistent storage m_ToolStorageFilename = filename; } void QmitkMITKIGTTrackingToolboxView::OnResetTools() { //remove data nodes of surfaces from data storage to clean up for (unsigned int i = 0; i < m_toolStorage->GetToolCount(); i++) { this->GetDataStorage()->Remove(m_toolStorage->GetTool(i)->GetDataNode()); } this->ReplaceCurrentToolStorage(mitk::NavigationToolStorage::New(GetDataStorage()), "TrackingToolbox Default Storage"); m_Controls->m_TrackingToolsStatusWidget->RemoveStatusLabels(); QString toolLabel = QString("<none>"); m_Controls->m_ToolLabel->setText(toolLabel); m_ToolStorageFilename = ""; RemoveAllToolProjections(); } void QmitkMITKIGTTrackingToolboxView::OnStartStopTracking() { if (!m_connected) { MITK_WARN << "Can't start tracking if no device is connected. Aborting"; return; } if (m_tracking) { OnStopTracking(); } else { OnStartTracking(); } } void QmitkMITKIGTTrackingToolboxView::OnFreezeUnfreezeTracking() { if (m_Controls->m_FreezeUnfreezeTrackingButton->text() == "Freeze Tracking") { m_Worker->GetTrackingDeviceSource()->Freeze(); m_Controls->m_FreezeUnfreezeTrackingButton->setText("Unfreeze Tracking"); m_Controls->m_TrackingFrozenLabel->setVisible(true); } else if (m_Controls->m_FreezeUnfreezeTrackingButton->text() == "Unfreeze Tracking") { m_Worker->GetTrackingDeviceSource()->UnFreeze(); m_Controls->m_FreezeUnfreezeTrackingButton->setText("Freeze Tracking"); m_Controls->m_TrackingFrozenLabel->setVisible(false); } } void QmitkMITKIGTTrackingToolboxView::ShowToolProjection(int index) { mitk::DataNode::Pointer toolnode = m_toolStorage->GetTool(index)->GetDataNode(); QString ToolProjectionName = "ToolProjection" + QString::number(index); m_ToolProjectionNode = this->GetDataStorage()->GetNamedNode(ToolProjectionName.toStdString()); //If node does not exist, create the node for the Pointset if (m_ToolProjectionNode.IsNull()) { m_ToolProjectionNode = mitk::DataNode::New(); m_ToolProjectionNode->SetName(ToolProjectionName.toStdString()); if (index < static_cast<int>(m_NeedleProjectionFilter->GetNumberOfInputs())) { m_NeedleProjectionFilter->SelectInput(index); m_NeedleProjectionFilter->Update(); m_ToolProjectionNode->SetData(m_NeedleProjectionFilter->GetProjection()); m_ToolProjectionNode->SetBoolProperty("show contour", true); this->GetDataStorage()->Add(m_ToolProjectionNode, toolnode); } // this->FireNodeSelected(node); } else { m_ToolProjectionNode->SetBoolProperty("show contour", true); } } void QmitkMITKIGTTrackingToolboxView::RemoveAllToolProjections() { for (size_t i = 0; i < m_toolStorage->GetToolCount(); i++) { QString toolProjectionName = "ToolProjection" + QString::number(i); mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode(toolProjectionName.toStdString()); //Deactivate and hide the tool projection if (!node.IsNull()) { this->GetDataStorage()->Remove(node); } } } void QmitkMITKIGTTrackingToolboxView::SelectToolProjection(int idx) { if (m_Controls->showHideToolProjectionCheckBox->isChecked()) { //Deactivate and hide the tool projection if (!m_ToolProjectionNode.IsNull()) { this->GetDataStorage()->Remove(m_ToolProjectionNode); } if (m_NeedleProjectionFilter.IsNotNull()) { m_NeedleProjectionFilter->Update(); } //Refresh the view and the status widget mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // Show the tool projection for the currently selected tool ShowToolProjection(idx); } } void QmitkMITKIGTTrackingToolboxView::OnShowHideToolProjectionClicked() { int index = m_Controls->m_toolselector->currentIndex(); //Activate and show the tool projection if (m_Controls->showHideToolProjectionCheckBox->isChecked()) { ShowToolProjection(index); m_Controls->showHideToolAxisCheckBox->setEnabled(true); } else { RemoveAllToolProjections(); m_Controls->showHideToolAxisCheckBox->setEnabled(false); } if(m_NeedleProjectionFilter->GetNumberOfInputs()) { m_NeedleProjectionFilter->Update(); } //Refresh the view and the status widget mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // m_Controls->m_TrackingToolsStatusWidget->Refresh(); } void QmitkMITKIGTTrackingToolboxView::OnShowHideToolAxisClicked() { if( !m_ShowHideToolAxis ) { //Activate and show the tool axis m_NeedleProjectionFilter->ShowToolAxis(true); m_ShowHideToolAxis = true; } else { //Deactivate and hide the tool axis m_NeedleProjectionFilter->ShowToolAxis(false); m_NeedleProjectionFilter->GetProjection()->RemovePointIfExists(2); m_ShowHideToolAxis = false; } //Update the filter if(m_NeedleProjectionFilter->GetNumberOfInputs()) { m_NeedleProjectionFilter->Update(); } //Refresh the view and the status widget mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // m_Controls->m_TrackingToolsStatusWidget->Refresh(); } void QmitkMITKIGTTrackingToolboxView::OnConnectDisconnect() { if (m_connected) { OnDisconnect(); } else { OnConnect(); } } void QmitkMITKIGTTrackingToolboxView::OnConnect() { MITK_DEBUG << "Connect Clicked"; //check if everything is ready to start tracking if (this->m_toolStorage.IsNull()) { MessageBox("Error: No Tools Loaded Yet!"); return; } else if (this->m_toolStorage->GetToolCount() == 0) { MessageBox("Error: No Way To Track Without Tools!"); return; } //parse tracking device data mitk::TrackingDeviceData data = mitk::UnspecifiedTrackingTypeInformation::GetDeviceDataUnspecified(); QString qstr = m_Controls->m_VolumeSelectionBox->currentText(); if ((!qstr.isNull()) || (!qstr.isEmpty())) { std::string str = qstr.toStdString(); data = m_DeviceTypeCollection->GetDeviceDataByName(str); //Data will be set later, after device generation } //! [Thread 4] //initialize worker thread m_Worker->SetWorkerMethod(QmitkMITKIGTTrackingToolboxViewWorker::eConnectDevice); m_Worker->SetTrackingDevice(this->m_Controls->m_ConfigurationWidget->GetTrackingDevice()); m_Worker->SetInverseMode(m_Controls->m_InverseMode->isChecked()); m_Worker->SetNavigationToolStorage(this->m_toolStorage); m_Worker->SetTrackingDeviceData(data); //start worker thread m_WorkerThread->start(); //! [Thread 4] //enable checkboxes for projection and tool axis m_Controls->showHideToolAxisCheckBox->setEnabled(true); m_Controls->showHideToolProjectionCheckBox->setEnabled(true); m_Controls->m_toolselector->setEnabled(true); //disable buttons this->m_Controls->m_MainWidget->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::EnableDisableTimerButtons(int enable) { bool enableBool = enable; m_Controls->m_UpdateRateOptionsGroupBox->setEnabled(!enableBool); m_Controls->m_RenderWarningLabel->setVisible(enableBool); } void QmitkMITKIGTTrackingToolboxView::OnConnectFinished(bool success, QString errorMessage) { m_WorkerThread->quit(); m_WorkerThread->wait(); //enable buttons this->m_Controls->m_MainWidget->setEnabled(true); if (!success) { MITK_WARN << errorMessage.toStdString(); MessageBox(errorMessage.toStdString()); return; } //! [Thread 6] //get data from worker thread m_TrackingDeviceData = m_Worker->GetTrackingDeviceData(); m_ToolVisualizationFilter = m_Worker->GetToolVisualizationFilter(); if( m_ToolVisualizationFilter.IsNotNull() ) { //Connect the NeedleProjectionFilter to the ToolVisualizationFilter as third filter of the IGT pipeline m_NeedleProjectionFilter->ConnectTo(m_ToolVisualizationFilter); if (m_Controls->showHideToolProjectionCheckBox->isChecked()) { ShowToolProjection(m_Controls->m_toolselector->currentIndex()); } } //! [Thread 6] //enable/disable Buttons DisableOptionsButtons(); DisableTrackingConfigurationButtons(); m_Controls->m_TrackingControlLabel->setText("Status: connected"); m_Controls->m_ConnectDisconnectButton->setText("Disconnect"); m_Controls->m_ConnectSimpleMode->setText("Disconnect"); m_Controls->m_StartStopTrackingButton->setEnabled(true); m_Controls->m_StartTrackingSimpleMode->setEnabled(true); m_connected = true; - //During connection, thi sourceID of the tool storage changed. However, Microservice can't be updated on a different thread. + //During connection, the sourceID of the tool storage changed. However, Microservice can't be updated on a different thread. //UpdateMicroservice is necessary to use filter to get the right storage belonging to a source. //Don't do it before m_connected is true, as we don't want to call content of OnToolStorageChanged. m_toolStorage->UpdateMicroservice(); } void QmitkMITKIGTTrackingToolboxView::OnDisconnect() { m_Worker->SetWorkerMethod(QmitkMITKIGTTrackingToolboxViewWorker::eDisconnectDevice); m_WorkerThread->start(); m_Controls->m_MainWidget->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::OnDisconnectFinished(bool success, QString errorMessage) { m_WorkerThread->quit(); m_WorkerThread->wait(); m_Controls->m_MainWidget->setEnabled(true); if (!success) { MITK_WARN << errorMessage.toStdString(); MessageBox(errorMessage.toStdString()); return; } //enable/disable Buttons m_Controls->m_StartStopTrackingButton->setEnabled(false); m_Controls->m_StartTrackingSimpleMode->setEnabled(false); EnableOptionsButtons(); EnableTrackingConfigurationButtons(); m_Controls->m_TrackingControlLabel->setText("Status: disconnected"); m_Controls->m_ConnectDisconnectButton->setText("Connect"); m_Controls->m_ConnectSimpleMode->setText("Connect"); m_Controls->m_FreezeUnfreezeTrackingButton->setText("Freeze Tracking"); m_Controls->m_TrackingFrozenLabel->setVisible(false); m_connected = false; } void QmitkMITKIGTTrackingToolboxView::OnStartTracking() { //show tracking volume this->OnTrackingVolumeChanged(m_Controls->m_VolumeSelectionBox->currentText()); //Reset the view to a defined start. Do it here and not in OnStartTrackingFinished, to give other tracking devices the chance to reset the view to a different direction. this->GlobalReinit(); m_Worker->SetWorkerMethod(QmitkMITKIGTTrackingToolboxViewWorker::eStartTracking); m_WorkerThread->start(); this->m_Controls->m_MainWidget->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::OnStartTrackingFinished(bool success, QString errorMessage) { //! [Thread 5] m_WorkerThread->quit(); m_WorkerThread->wait(); //! [Thread 5] this->m_Controls->m_MainWidget->setEnabled(true); if (!success) { MessageBox(errorMessage.toStdString()); MITK_WARN << errorMessage.toStdString(); return; } if (!(m_Controls->m_DisableAllTimers->isChecked())) { if (m_Controls->m_UseDifferentUpdateRates->isChecked()) { if (m_Controls->m_RenderUpdateRate->value() != 0) m_TrackingRenderTimer->start(1000 / (m_Controls->m_RenderUpdateRate->value())); m_TrackingLoggingTimer->start(1000 / (m_Controls->m_LogUpdateRate->value())); } else { m_TrackingRenderTimer->start(1000 / (m_Controls->m_UpdateRate->value())); m_TrackingLoggingTimer->start(1000 / (m_Controls->m_UpdateRate->value())); } } m_Controls->m_TrackingControlLabel->setText("Status: tracking"); //connect the tool visualization widget for (std::size_t i = 0; i < m_Worker->GetTrackingDeviceSource()->GetNumberOfOutputs(); i++) { m_Controls->m_TrackingToolsStatusWidget->AddNavigationData(m_Worker->GetTrackingDeviceSource()->GetOutput(i)); } m_Controls->m_TrackingToolsStatusWidget->ShowStatusLabels(); if (m_Controls->m_ShowToolQuaternions->isChecked()) { m_Controls->m_TrackingToolsStatusWidget->SetShowQuaternions(true); } else { m_Controls->m_TrackingToolsStatusWidget->SetShowQuaternions(false); } //if activated enable open IGT link microservice if (m_Controls->m_EnableOpenIGTLinkMicroService->isChecked()) { - //create convertion filter + //create conversion filter m_IGTLConversionFilter = mitk::NavigationDataToIGTLMessageFilter::New(); m_IGTLConversionFilter->SetName("IGT Tracking Toolbox"); QString dataModeSelection = this->m_Controls->m_OpenIGTLinkDataFormat->currentText(); if (dataModeSelection == "TDATA") { m_IGTLConversionFilter->SetOperationMode(mitk::NavigationDataToIGTLMessageFilter::ModeSendTDataMsg); } else if (dataModeSelection == "TRANSFORM") { m_IGTLConversionFilter->SetOperationMode(mitk::NavigationDataToIGTLMessageFilter::ModeSendTransMsg); } else if (dataModeSelection == "QTDATA") { m_IGTLConversionFilter->SetOperationMode(mitk::NavigationDataToIGTLMessageFilter::ModeSendQTDataMsg); } else if (dataModeSelection == "POSITION") { m_IGTLConversionFilter->SetOperationMode(mitk::NavigationDataToIGTLMessageFilter::ModeSendQTransMsg); } m_IGTLConversionFilter->ConnectTo(m_ToolVisualizationFilter); m_IGTLConversionFilter->RegisterAsMicroservice(); //create server and message provider m_IGTLServer = mitk::IGTLServer::New(false); m_IGTLServer->SetName("Tracking Toolbox IGTL Server"); m_IGTLMessageProvider = mitk::IGTLMessageProvider::New(); m_IGTLMessageProvider->SetIGTLDevice(m_IGTLServer); m_IGTLMessageProvider->RegisterAsMicroservice(); } m_tracking = true; m_Controls->m_ConnectDisconnectButton->setEnabled(false); m_Controls->m_StartStopTrackingButton->setText("Stop Tracking"); m_Controls->m_StartTrackingSimpleMode->setText("Stop\nTracking"); m_Controls->m_FreezeUnfreezeTrackingButton->setEnabled(true); } void QmitkMITKIGTTrackingToolboxView::OnStopTracking() { if (!m_tracking) return; for (unsigned int i = 0; i < m_ToolVisualizationFilter->GetNumberOfIndexedOutputs(); i++) { mitk::NavigationData::Pointer currentTool = m_ToolVisualizationFilter->GetOutput(i); if (currentTool->IsDataValid()) { this->m_toolStorage->GetTool(i)->GetDataNode()->SetColor(mitk::IGTColor_INVALID); } } //refresh view and status widget mitk::RenderingManager::GetInstance()->RequestUpdateAll(); m_TrackingRenderTimer->stop(); m_TrackingLoggingTimer->stop(); m_Worker->SetWorkerMethod(QmitkMITKIGTTrackingToolboxViewWorker::eStopTracking); m_WorkerThread->start(); m_Controls->m_MainWidget->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::OnStopTrackingFinished(bool success, QString errorMessage) { m_WorkerThread->quit(); m_WorkerThread->wait(); m_Controls->m_MainWidget->setEnabled(true); if (!success) { MessageBox(errorMessage.toStdString()); MITK_WARN << errorMessage.toStdString(); return; } m_Controls->m_TrackingControlLabel->setText("Status: connected"); if (m_logging) StopLogging(); m_Controls->m_TrackingToolsStatusWidget->RemoveStatusLabels(); m_Controls->m_TrackingToolsStatusWidget->PreShowTools(m_toolStorage); m_tracking = false; m_Controls->m_StartStopTrackingButton->setText("Start Tracking"); m_Controls->m_StartTrackingSimpleMode->setText("Start\nTracking"); m_Controls->m_ConnectDisconnectButton->setEnabled(true); m_Controls->m_FreezeUnfreezeTrackingButton->setEnabled(false); //unregister open IGT link micro service if (m_Controls->m_EnableOpenIGTLinkMicroService->isChecked()) { m_IGTLConversionFilter->UnRegisterMicroservice(); m_IGTLMessageProvider->UnRegisterMicroservice(); } } void QmitkMITKIGTTrackingToolboxView::OnTrackingDeviceChanged() { mitk::TrackingDeviceType Type; if (m_Controls->m_ConfigurationWidget->GetTrackingDevice().IsNotNull()) { Type = m_Controls->m_ConfigurationWidget->GetTrackingDevice()->GetType(); //enable controls because device is valid m_Controls->m_TrackingToolsFrame->setEnabled(true); m_Controls->m_TrackingControlsFrame->setEnabled(true); } else { Type = mitk::UnspecifiedTrackingTypeInformation::GetTrackingDeviceName(); MessageBox("Error: This tracking device is not included in this project. Please make sure that the device is installed and activated in your MITK build."); m_Controls->m_TrackingToolsFrame->setEnabled(false); m_Controls->m_TrackingControlsFrame->setEnabled(false); return; } // Code to enable/disable device specific buttons if (m_Controls->m_ConfigurationWidget->GetTrackingDevice()->AutoDetectToolsAvailable()) { m_Controls->m_AutoDetectTools->setVisible(true); } else { m_Controls->m_AutoDetectTools->setVisible(false); } m_Controls->m_AddSingleTool->setEnabled(this->m_Controls->m_ConfigurationWidget->GetTrackingDevice()->AddSingleToolIsAvailable()); // Code to select appropriate tracking volume for current type std::vector<mitk::TrackingDeviceData> Compatibles = m_DeviceTypeCollection->GetDeviceDataForLine(Type); m_Controls->m_VolumeSelectionBox->clear(); for (std::size_t i = 0; i < Compatibles.size(); i++) { m_Controls->m_VolumeSelectionBox->addItem(Compatibles[i].Model.c_str()); } } void QmitkMITKIGTTrackingToolboxView::OnTrackingVolumeChanged(QString qstr) { if (qstr.isNull()) return; if (qstr.isEmpty()) return; mitk::TrackingVolumeGenerator::Pointer volumeGenerator = mitk::TrackingVolumeGenerator::New(); std::string str = qstr.toStdString(); mitk::TrackingDeviceData data = m_DeviceTypeCollection->GetDeviceDataByName(str); m_TrackingDeviceData = data; volumeGenerator->SetTrackingDeviceData(data); volumeGenerator->Update(); mitk::Surface::Pointer volumeSurface = volumeGenerator->GetOutput(); m_TrackingVolumeNode->SetData(volumeSurface); if (!m_Controls->m_ShowTrackingVolume->isChecked()) m_TrackingVolumeNode->SetOpacity(0.0); else m_TrackingVolumeNode->SetOpacity(0.25); GlobalReinit(); } void QmitkMITKIGTTrackingToolboxView::OnShowTrackingVolumeChanged() { if (m_Controls->m_ShowTrackingVolume->isChecked()) { OnTrackingVolumeChanged(m_Controls->m_VolumeSelectionBox->currentText()); m_TrackingVolumeNode->SetOpacity(0.25); } else { m_TrackingVolumeNode->SetOpacity(0.0); } } void QmitkMITKIGTTrackingToolboxView::OnAutoDetectTools() { if (m_Controls->m_ConfigurationWidget->GetTrackingDevice()->AutoDetectToolsAvailable()) { DisableTrackingConfigurationButtons(); m_Worker->SetWorkerMethod(QmitkMITKIGTTrackingToolboxViewWorker::eAutoDetectTools); m_Worker->SetTrackingDevice(m_Controls->m_ConfigurationWidget->GetTrackingDevice().GetPointer()); m_Worker->SetDataStorage(this->GetDataStorage()); m_WorkerThread->start(); m_TimeoutTimer->start(30000); //disable controls until worker thread is finished this->m_Controls->m_MainWidget->setEnabled(false); } } void QmitkMITKIGTTrackingToolboxView::OnAutoDetectToolsFinished(bool success, QString errorMessage) { - //Check, if the thread is running. There might have been a timeOut inbetween and this causes crashes... + //Check, if the thread is running. There might have been a timeOut in between and this causes crashes... if (m_WorkerThread->isRunning()) { m_TimeoutTimer->stop(); m_WorkerThread->quit(); m_WorkerThread->wait(); } //enable controls again this->m_Controls->m_MainWidget->setEnabled(true); EnableTrackingConfigurationButtons(); if (!success) { MITK_WARN << errorMessage.toStdString(); MessageBox(errorMessage.toStdString()); EnableTrackingConfigurationButtons(); return; } mitk::NavigationToolStorage::Pointer autoDetectedStorage = m_Worker->GetNavigationToolStorage(); //save detected tools std::string _autoDetectText; _autoDetectText = "Autodetected "; _autoDetectText.append(this->m_TrackingDeviceData.Line); //This is the device name as string of the current TrackingDevice. _autoDetectText.append(" Storage"); this->ReplaceCurrentToolStorage(autoDetectedStorage, _autoDetectText); //auto save the new storage to hard disc (for persistence) AutoSaveToolStorage(); //update label QString toolLabel = QString("Loaded Tools: ") + QString::number(m_toolStorage->GetToolCount()) + " Tools (Auto Detected)"; m_Controls->m_ToolLabel->setText(toolLabel); //update tool preview m_Controls->m_TrackingToolsStatusWidget->RemoveStatusLabels(); m_Controls->m_TrackingToolsStatusWidget->PreShowTools(m_toolStorage); EnableTrackingConfigurationButtons(); //print a logging message about the detected tools switch (m_toolStorage->GetToolCount()) { case 0: MITK_INFO("IGT Tracking Toolbox") << "Found no tools. Empty ToolStorage was autosaved to " << m_ToolStorageFilename.toStdString(); break; case 1: MITK_INFO("IGT Tracking Toolbox") << "Found one tool. ToolStorage was autosaved to " << m_ToolStorageFilename.toStdString(); break; default: MITK_INFO("IGT Tracking Toolbox") << "Found " << m_toolStorage->GetToolCount() << " tools. ToolStorage was autosaved to " << m_ToolStorageFilename.toStdString(); } } void QmitkMITKIGTTrackingToolboxView::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkMITKIGTTrackingToolboxView::UpdateRenderTrackingTimer() { //update filter m_ToolVisualizationFilter->Update(); MITK_DEBUG << "Number of outputs ToolVisualizationFilter: " << m_ToolVisualizationFilter->GetNumberOfIndexedOutputs(); MITK_DEBUG << "Number of inputs ToolVisualizationFilter: " << m_ToolVisualizationFilter->GetNumberOfIndexedInputs(); //update tool colors to show tool status for (unsigned int i = 0; i < m_ToolVisualizationFilter->GetNumberOfIndexedOutputs(); i++) { mitk::NavigationData::Pointer currentTool = m_ToolVisualizationFilter->GetOutput(i); if (currentTool->IsDataValid()) { this->m_toolStorage->GetTool(i)->GetDataNode()->SetColor(mitk::IGTColor_VALID); } else { this->m_toolStorage->GetTool(i)->GetDataNode()->SetColor(mitk::IGTColor_WARNING); } } //Update the NeedleProjectionFilter if( m_NeedleProjectionFilter.IsNotNull() ) { m_NeedleProjectionFilter->Update(); } //refresh view and status widget mitk::RenderingManager::GetInstance()->RequestUpdateAll(); m_Controls->m_TrackingToolsStatusWidget->Refresh(); } void QmitkMITKIGTTrackingToolboxView::UpdateLoggingTrackingTimer() { //update logging if (m_logging) { this->m_loggingFilter->Update(); m_loggedFrames = this->m_loggingFilter->GetNumberOfRecordedSteps(); this->m_Controls->m_LoggedFramesLabel->setText("Logged Frames: " + QString::number(m_loggedFrames)); //check if logging stopped automatically if ((m_loggedFrames > 1) && (!m_loggingFilter->GetRecording())){ StopLogging(); } } //refresh status widget m_Controls->m_TrackingToolsStatusWidget->Refresh(); } void QmitkMITKIGTTrackingToolboxView::OnChooseFileClicked() { QDir currentPath = QFileInfo(m_Controls->m_LoggingFileName->text()).dir(); // if no path was selected (QDir would select current working dir then) or the // selected path does not exist -> use home directory if (currentPath == QDir() || !currentPath.exists()) { currentPath = QDir(QDir::homePath()); } QString filename = QFileDialog::getSaveFileName(nullptr, tr("Choose Logging File"), currentPath.absolutePath(), "*.*"); if (filename == "") return; this->m_Controls->m_LoggingFileName->setText(filename); this->OnToggleFileExtension(); } // bug-16470: toggle file extension after clicking on radio button void QmitkMITKIGTTrackingToolboxView::OnToggleFileExtension() { QString currentInputText = this->m_Controls->m_LoggingFileName->text(); QString currentFile = QFileInfo(currentInputText).baseName(); QDir currentPath = QFileInfo(currentInputText).dir(); if (currentFile.isEmpty()) { currentFile = "logfile"; } // Setting currentPath to default home path when currentPath is empty or it does not exist if (currentPath == QDir() || !currentPath.exists()) { currentPath = QDir::homePath(); } // check if csv radio button is clicked if (this->m_Controls->m_CsvFormat->isChecked()) { - // you needn't add a seperator to the input text when currentpath is the rootpath + // you needn't add a separator to the input text when currentpath is the rootpath if (currentPath.isRoot()) { this->m_Controls->m_LoggingFileName->setText(QDir::toNativeSeparators(currentPath.absolutePath()) + currentFile + ".csv"); } else { this->m_Controls->m_LoggingFileName->setText(QDir::toNativeSeparators(currentPath.absolutePath()) + QDir::separator() + currentFile + ".csv"); } } // check if xml radio button is clicked else if (this->m_Controls->m_XmlFormat->isChecked()) { - // you needn't add a seperator to the input text when currentpath is the rootpath + // you needn't add a separator to the input text when currentpath is the rootpath if (currentPath.isRoot()) { this->m_Controls->m_LoggingFileName->setText(QDir::toNativeSeparators(currentPath.absolutePath()) + currentFile + ".xml"); } else { this->m_Controls->m_LoggingFileName->setText(QDir::toNativeSeparators(currentPath.absolutePath()) + QDir::separator() + currentFile + ".xml"); } } } void QmitkMITKIGTTrackingToolboxView::OnToggleAdvancedSimpleMode() { if (m_SimpleModeEnabled) { m_Controls->m_simpleWidget->setVisible(false); m_Controls->m_MainWidget->setVisible(true); m_Controls->m_SimpleUI->setChecked(false); m_SimpleModeEnabled = false; } else { m_Controls->m_simpleWidget->setVisible(true); m_Controls->m_MainWidget->setVisible(false); m_SimpleModeEnabled = true; } } void QmitkMITKIGTTrackingToolboxView::OnToggleDifferentUpdateRates() { if (m_Controls->m_UseDifferentUpdateRates->isChecked()) { if (m_Controls->m_RenderUpdateRate->value() == 0) m_Controls->m_RenderWarningLabel->setVisible(true); else m_Controls->m_RenderWarningLabel->setVisible(false); m_Controls->m_UpdateRate->setEnabled(false); m_Controls->m_OptionsUpdateRateLabel->setEnabled(false); m_Controls->m_RenderUpdateRate->setEnabled(true); m_Controls->m_OptionsRenderUpdateRateLabel->setEnabled(true); m_Controls->m_LogUpdateRate->setEnabled(true); m_Controls->m_OptionsLogUpdateRateLabel->setEnabled(true); } else { m_Controls->m_RenderWarningLabel->setVisible(false); m_Controls->m_UpdateRate->setEnabled(true); m_Controls->m_OptionsUpdateRateLabel->setEnabled(true); m_Controls->m_RenderUpdateRate->setEnabled(false); m_Controls->m_OptionsRenderUpdateRateLabel->setEnabled(false); m_Controls->m_LogUpdateRate->setEnabled(false); m_Controls->m_OptionsLogUpdateRateLabel->setEnabled(false); } } void QmitkMITKIGTTrackingToolboxView::OnChangeRenderUpdateRate() { if (m_Controls->m_RenderUpdateRate->value() == 0) m_Controls->m_RenderWarningLabel->setVisible(true); else m_Controls->m_RenderWarningLabel->setVisible(false); } void QmitkMITKIGTTrackingToolboxView::StartLogging() { if (m_ToolVisualizationFilter.IsNull()) { MessageBox("Cannot activate logging without a connected device. Configure and connect a tracking device first."); return; } if (!m_logging) { //initialize logging filter m_loggingFilter = mitk::NavigationDataRecorder::New(); m_loggingFilter->SetRecordOnlyValidData(m_Controls->m_SkipInvalidData->isChecked()); m_loggingFilter->ConnectTo(m_ToolVisualizationFilter); if (m_Controls->m_LoggingLimit->isChecked()){ m_loggingFilter->SetRecordCountLimit(m_Controls->m_LoggedFramesLimit->value()); } //start filter with try-catch block for exceptions try { m_loggingFilter->StartRecording(); } catch (mitk::IGTException&) { std::string errormessage = "Error during start recording. Recorder already started recording?"; QMessageBox::warning(nullptr, "IGTPlayer: Error", errormessage.c_str()); m_loggingFilter->StopRecording(); return; } //update labels / logging variables this->m_Controls->m_LoggingLabel->setText("Logging ON"); this->m_Controls->m_LoggedFramesLabel->setText("Logged Frames: 0"); m_loggedFrames = 0; m_logging = true; DisableLoggingButtons(); } } void QmitkMITKIGTTrackingToolboxView::StopLogging() { if (m_logging) { //stop logging m_loggingFilter->StopRecording(); m_logging = false; //update GUI this->m_Controls->m_LoggingLabel->setText("Logging OFF"); EnableLoggingButtons(); //write the results to a file if (m_Controls->m_CsvFormat->isChecked()) { mitk::IOUtil::Save(m_loggingFilter->GetNavigationDataSet(), this->m_Controls->m_LoggingFileName->text().toStdString()); } else if (m_Controls->m_XmlFormat->isChecked()) { mitk::IOUtil::Save(m_loggingFilter->GetNavigationDataSet(), this->m_Controls->m_LoggingFileName->text().toStdString()); } } } void QmitkMITKIGTTrackingToolboxView::SetFocus() { } void QmitkMITKIGTTrackingToolboxView::OnAddSingleTool() { QString Identifier = "Tool#"; QString Name = "NewTool"; if (m_toolStorage.IsNotNull()) { Identifier += QString::number(m_toolStorage->GetToolCount()); Name += QString::number(m_toolStorage->GetToolCount()); } else { Identifier += "0"; Name += "0"; } m_Controls->m_NavigationToolCreationWidget->Initialize(GetDataStorage(), Identifier.toStdString(), Name.toStdString()); m_Controls->m_NavigationToolCreationWidget->SetTrackingDeviceType(m_Controls->m_ConfigurationWidget->GetTrackingDevice()->GetType(), false); m_Controls->m_TrackingToolsWidget->setCurrentIndex(1); //disable tracking volume during tool editing lastTrackingVolumeState = m_Controls->m_ShowTrackingVolume->isChecked(); if (lastTrackingVolumeState) m_Controls->m_ShowTrackingVolume->click(); GlobalReinit(); } void QmitkMITKIGTTrackingToolboxView::OnAddSingleToolFinished() { m_Controls->m_TrackingToolsWidget->setCurrentIndex(0); if (this->m_toolStorage.IsNull()) { //this shouldn't happen! MITK_WARN << "No ToolStorage available, cannot add tool, aborting!"; return; } m_toolStorage->AddTool(m_Controls->m_NavigationToolCreationWidget->GetCreatedTool()); m_Controls->m_TrackingToolsStatusWidget->PreShowTools(m_toolStorage); m_Controls->m_ToolLabel->setText("<manually added>"); //displya in tool selector // m_Controls->m_toolselector->addItem(QString::fromStdString(m_Controls->m_NavigationToolCreationWidget->GetCreatedTool()->GetToolName())); //auto save current storage for persistence MITK_INFO << "Auto saving manually added tools for persistence."; AutoSaveToolStorage(); //enable tracking volume again if (lastTrackingVolumeState) m_Controls->m_ShowTrackingVolume->click(); GlobalReinit(); } void QmitkMITKIGTTrackingToolboxView::OnAddSingleToolCanceled() { m_Controls->m_TrackingToolsWidget->setCurrentIndex(0); //enable tracking volume again if (lastTrackingVolumeState) m_Controls->m_ShowTrackingVolume->click(); GlobalReinit(); } void QmitkMITKIGTTrackingToolboxView::GlobalReinit() { // get all nodes that have not set "includeInBoundingBox" to false mitk::NodePredicateNot::Pointer pred = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("includeInBoundingBox", mitk::BoolProperty::New(false))); mitk::DataStorage::SetOfObjects::ConstPointer rs = this->GetDataStorage()->GetSubset(pred); // calculate bounding geometry of these nodes auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(rs, "visible"); // initialize the views to the bounding geometry mitk::RenderingManager::GetInstance()->InitializeViews(bounds); } void QmitkMITKIGTTrackingToolboxView::DisableLoggingButtons() { m_Controls->m_StartLogging->setEnabled(false); m_Controls->m_LoggingFileName->setEnabled(false); m_Controls->m_ChooseFile->setEnabled(false); m_Controls->m_LoggingLimit->setEnabled(false); m_Controls->m_LoggedFramesLimit->setEnabled(false); m_Controls->m_CsvFormat->setEnabled(false); m_Controls->m_XmlFormat->setEnabled(false); m_Controls->m_SkipInvalidData->setEnabled(false); m_Controls->m_StopLogging->setEnabled(true); } void QmitkMITKIGTTrackingToolboxView::EnableLoggingButtons() { m_Controls->m_StartLogging->setEnabled(true); m_Controls->m_LoggingFileName->setEnabled(true); m_Controls->m_ChooseFile->setEnabled(true); m_Controls->m_LoggingLimit->setEnabled(true); m_Controls->m_LoggedFramesLimit->setEnabled(true); m_Controls->m_CsvFormat->setEnabled(true); m_Controls->m_XmlFormat->setEnabled(true); m_Controls->m_SkipInvalidData->setEnabled(true); m_Controls->m_StopLogging->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::DisableOptionsButtons() { m_Controls->m_ShowTrackingVolume->setEnabled(false); m_Controls->m_UseDifferentUpdateRates->setEnabled(false); m_Controls->m_UpdateRate->setEnabled(false); m_Controls->m_OptionsUpdateRateLabel->setEnabled(false); m_Controls->m_RenderUpdateRate->setEnabled(false); m_Controls->m_OptionsRenderUpdateRateLabel->setEnabled(false); m_Controls->m_LogUpdateRate->setEnabled(false); m_Controls->m_OptionsLogUpdateRateLabel->setEnabled(false); m_Controls->m_DisableAllTimers->setEnabled(false); m_Controls->m_OtherOptionsGroupBox->setEnabled(false); m_Controls->m_EnableOpenIGTLinkMicroService->setEnabled(false); m_Controls->m_OpenIGTLinkDataFormat->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::EnableOptionsButtons() { m_Controls->m_ShowTrackingVolume->setEnabled(true); m_Controls->m_UseDifferentUpdateRates->setEnabled(true); m_Controls->m_DisableAllTimers->setEnabled(true); m_Controls->m_OtherOptionsGroupBox->setEnabled(true); m_Controls->m_EnableOpenIGTLinkMicroService->setEnabled(true); m_Controls->m_OpenIGTLinkDataFormat->setEnabled(true); OnToggleDifferentUpdateRates(); } void QmitkMITKIGTTrackingToolboxView::EnableTrackingControls() { m_Controls->m_TrackingControlsFrame->setEnabled(true); } void QmitkMITKIGTTrackingToolboxView::DisableTrackingControls() { m_Controls->m_TrackingControlsFrame->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::EnableTrackingConfigurationButtons() { m_Controls->m_AutoDetectTools->setEnabled(true); m_Controls->m_AddSingleTool->setEnabled(this->m_Controls->m_ConfigurationWidget->GetTrackingDevice()->AddSingleToolIsAvailable()); m_Controls->m_LoadTools->setEnabled(true); m_Controls->m_ResetTools->setEnabled(true); } void QmitkMITKIGTTrackingToolboxView::DisableTrackingConfigurationButtons() { m_Controls->m_AutoDetectTools->setEnabled(false); m_Controls->m_AddSingleTool->setEnabled(false); m_Controls->m_LoadTools->setEnabled(false); m_Controls->m_ResetTools->setEnabled(false); } void QmitkMITKIGTTrackingToolboxView::ReplaceCurrentToolStorage(mitk::NavigationToolStorage::Pointer newStorage, std::string newStorageName) { //first: get rid of the old one //don't reset if there is no tool storage. BugFix #17793 if (m_toolStorage.IsNotNull()){ m_toolStorage->UnLockStorage(); //only to be sure... m_toolStorage->UnRegisterMicroservice(); m_toolStorage = nullptr; } //now: replace by the new one m_toolStorage = newStorage; m_toolStorage->SetName(newStorageName); m_toolStorage->RegisterAsMicroservice(); } void QmitkMITKIGTTrackingToolboxView::OnTimeOut() { MITK_WARN << "TimeOut. Quitting the thread..."; m_WorkerThread->quit(); //only if we can't quit use terminate. if (!m_WorkerThread->wait(1000)) { MITK_ERROR << "Can't quit the thread. Terminating... Might cause further problems, be careful!"; m_WorkerThread->terminate(); m_WorkerThread->wait(); } m_TimeoutTimer->stop(); } void QmitkMITKIGTTrackingToolboxView::OnToolStorageChanged(const ctkServiceEvent event) { //don't listen to any changes during connection, toolStorage is locked anyway, so this are only changes of e.g. sourceID which are not relevant for the widget. if (!m_connected && (event.getType() == ctkServiceEvent::MODIFIED)) { m_Controls->m_ConfigurationWidget->OnToolStorageChanged(); m_Controls->m_toolselector->clear(); for (size_t i = 0; i < m_toolStorage->GetToolCount(); i++) { m_Controls->m_toolselector->addItem(QString::fromStdString(m_toolStorage->GetTool(i)->GetToolName())); } } } //! [StoreUISettings] void QmitkMITKIGTTrackingToolboxView::StoreUISettings() { // persistence service does not directly work in plugins for now // -> using QSettings QSettings settings; settings.beginGroup(QString::fromStdString(VIEW_ID)); MITK_DEBUG << "Store UI settings"; - // set the values of some widgets and attrbutes to the QSettings + // set the values of some widgets and attributes to the QSettings settings.setValue("ShowTrackingVolume", QVariant(m_Controls->m_ShowTrackingVolume->isChecked())); settings.setValue("toolStorageFilename", QVariant(m_ToolStorageFilename)); settings.setValue("VolumeSelectionBox", QVariant(m_Controls->m_VolumeSelectionBox->currentIndex())); settings.setValue("SimpleModeEnabled", QVariant(m_SimpleModeEnabled)); settings.setValue("OpenIGTLinkDataFormat", QVariant(m_Controls->m_OpenIGTLinkDataFormat->currentIndex())); settings.setValue("EnableOpenIGTLinkMicroService", QVariant(m_Controls->m_EnableOpenIGTLinkMicroService->isChecked())); settings.endGroup(); } //! [StoreUISettings] //! [LoadUISettings] void QmitkMITKIGTTrackingToolboxView::LoadUISettings() { // persistence service does not directly work in plugins for now -> using QSettings QSettings settings; settings.beginGroup(QString::fromStdString(VIEW_ID)); // set some widgets and attributes by the values from the QSettings m_Controls->m_ShowTrackingVolume->setChecked(settings.value("ShowTrackingVolume", false).toBool()); m_Controls->m_EnableOpenIGTLinkMicroService->setChecked(settings.value("EnableOpenIGTLinkMicroService", true).toBool()); m_Controls->m_VolumeSelectionBox->setCurrentIndex(settings.value("VolumeSelectionBox", 0).toInt()); m_Controls->m_OpenIGTLinkDataFormat->setCurrentIndex(settings.value("OpenIGTLinkDataFormat", 0).toInt()); m_ToolStorageFilename = settings.value("toolStorageFilename", QVariant("")).toString(); if (settings.value("SimpleModeEnabled", false).toBool()) { this->OnToggleAdvancedSimpleMode(); } settings.endGroup(); //! [LoadUISettings] //! [LoadToolStorage] // try to deserialize the tool storage from the given tool storage file name if (!m_ToolStorageFilename.isEmpty()) { // try-catch block for exceptions try { mitk::NavigationToolStorageDeserializer::Pointer myDeserializer = mitk::NavigationToolStorageDeserializer::New(GetDataStorage()); m_toolStorage->UnRegisterMicroservice(); m_toolStorage = myDeserializer->Deserialize(m_ToolStorageFilename.toStdString()); m_toolStorage->RegisterAsMicroservice(); //update label UpdateToolStorageLabel(m_ToolStorageFilename); //update tool preview m_Controls->m_TrackingToolsStatusWidget->RemoveStatusLabels(); m_Controls->m_TrackingToolsStatusWidget->PreShowTools(m_toolStorage); } catch (const mitk::IGTException& e) { MITK_WARN("QmitkMITKIGTTrackingToolBoxView") << "Error during restoring tools. Problems with file (" << m_ToolStorageFilename.toStdString() << "), please check the file? Error message: "<<e.GetDescription(); this->OnResetTools(); //if there where errors reset the tool storage to avoid problems later on } } //! [LoadToolStorage] } void QmitkMITKIGTTrackingToolboxView::UpdateToolStorageLabel(QString pathOfLoadedStorage) { - QFileInfo myPath(pathOfLoadedStorage); //use this to seperate filename from path + QFileInfo myPath(pathOfLoadedStorage); //use this to separate filename from path QString toolLabel = myPath.fileName(); if (toolLabel.size() > 45) //if the tool storage name is to long trimm the string { toolLabel.resize(40); toolLabel += "[...]"; } m_Controls->m_ToolLabel->setText(toolLabel); } void QmitkMITKIGTTrackingToolboxView::AutoSaveToolStorage() { m_ToolStorageFilename = m_AutoSaveFilename; mitk::NavigationToolStorageSerializer::Pointer mySerializer = mitk::NavigationToolStorageSerializer::New(); mySerializer->Serialize(m_ToolStorageFilename.toStdString(), m_toolStorage); } diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.h b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.h index f1d4a2d830..6710d38709 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.h +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxView.h @@ -1,266 +1,266 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMITKIGTTrackingToolboxView_h #define QmitkMITKIGTTrackingToolboxView_h #include <berryISelectionListener.h> #include <ctkServiceReference.h> #include <ctkServiceEvent.h> #include <QmitkAbstractView.h> #include "ui_QmitkMITKIGTTrackingToolboxViewControls.h" //mitk headers #include <mitkNavigationToolStorage.h> #include <mitkNavigationDataObjectVisualizationFilter.h> #include <mitkNavigationDataRecorder.h> #include <mitkNavigationDataToIGTLMessageFilter.h> #include <mitkIGTLServer.h> #include <mitkIGTLMessageProvider.h> //QT headers #include <QTimer> #include "QmitkMITKIGTTrackingToolboxViewWorker.h" //Forward declaration of MITK classes namespace mitk { class NeedleProjectionFilter; } /*! \brief QmitkMITKIGTTrackingToolboxView This is the view of the bundle IGT Tracking Toolbox. The IGT Tracking Toolbox can be used to access tracking devices with MITK-IGT. The Tracking Toolbox can be used to log tracking data in XML or CSV format for measurement purposes. The Tracking Toolbox further allows for visualization of tools with given surfaces in combination with the NaviagtionToolManager. */ class QmitkMITKIGTTrackingToolboxView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkMITKIGTTrackingToolboxView(); ~QmitkMITKIGTTrackingToolboxView() override; void CreateQtPartControl(QWidget *parent) override; /// /// Sets the focus to an internal widget. /// void SetFocus() override; protected slots: /** @brief changes name of the filename when switching fileextension by radio button */ void OnToggleFileExtension(); /** @brief This slot is called if the user wants to load a new tool file. A new window opens where the user can choose a file. If the chosen file is corrupt or not valid the user gets an error message. If the file was loaded successfully the tools are show in the tool status widget. */ void OnLoadTools(); /** Starts tracking if tracking is stopped / stops tracking if tracking is started. */ void OnStartStopTracking(); /** Connects the device if it is disconnected / disconnects the device if it is connected. */ void OnConnectDisconnect(); /** Freezes the device if it is not frozen / unfreezes the device if it is frozen. */ void OnFreezeUnfreezeTracking(); /** @brief Shows or hides the tool projection of the standard tool axis. */ void OnShowHideToolProjectionClicked(); /** @brief Shows or hides the standard tool axis. */ void OnShowHideToolAxisClicked(); /** @brief This slot connects to the device. In status "connected" configuration of the device is disabled. */ void OnConnect(); /** @brief This slot disconnects from the device. */ void OnDisconnect(); /** @brief This slot tries to start tracking with the current device. If start tracking fails the user gets an error message and tracking stays off.*/ void OnStartTracking(); /** @brief This slot stops tracking. If tracking is not strated it does nothing.*/ void OnStopTracking(); - /** @brief This slot is called if the user want's to choose a file name for logging. A new windows to navigate through the file system and choose + /** @brief This slot is called if the user wants to choose a file name for logging. A new windows to navigate through the file system and choose a file opens.*/ void OnChooseFileClicked(); /** @brief This slot starts logging. Logging is only possible if a device is tracking. If not the logging mechanism start when the start tracking is called.*/ void StartLogging(); /** @brief This slot stops logging. If logging is not running it does nothing.*/ void StopLogging(); /** @brief This slot enables / disables UI elements depending on the tracking device after a device is changed.*/ void OnTrackingDeviceChanged(); /** @brief This slot selects the Tracking Volume appropriate for a given model */ void OnTrackingVolumeChanged(QString qstr); /** @brief Shows or hides the tracking volume according to the checkboxe's state */ void OnShowTrackingVolumeChanged(); /** @brief This slot auto detects tools of a NDI Aurora tracking device. If tools where found they will be stored internally as a tool storage. The user is also asked if he wants to save this tool storage to load it later. Only call it if a Aurora device was configured because other devices don't support auto detection.*/ void OnAutoDetectTools(); /** @brief Slot for tracking timer. The timer updates the IGT pipline and also the logging filter if logging is activated.*/ void UpdateRenderTrackingTimer(); void UpdateLoggingTrackingTimer(); /** @brief Slot for showing the rendering disabled warning label*/ void OnChangeRenderUpdateRate(); /** @brief Resets the Tracking Tools: this means all tools are removed. */ void OnResetTools(); /** @brief Opens a dialog where a new navigation tool can be created. */ void OnAddSingleTool(); /** @brief This slot is called if the user finishes the creation of a new tool. */ void OnAddSingleToolFinished(); /** @brief This slot is called if the user cancels the creation of a new tool. */ void OnAddSingleToolCanceled(); void OnTimeOut(); /** * \brief This function is called, when anything in the ToolStorage changed, e.g. AddTool or EditTool. * ServiceListener is connected in the QmitkMITKIGTTrackingToolboxView. */ void OnToolStorageChanged(const ctkServiceEvent event); - /* This slot enables selction of tool for projection*/ + /* This slot enables selection of tool for projection*/ void SelectToolProjection(int idx); protected slots: //help slots for enable/disable buttons void DisableLoggingButtons(); void EnableLoggingButtons(); void DisableOptionsButtons(); void EnableOptionsButtons(); void EnableTrackingConfigurationButtons(); void DisableTrackingConfigurationButtons(); void EnableTrackingControls(); void DisableTrackingControls(); void EnableDisableTimerButtons(int enable); void OnToggleAdvancedSimpleMode(); void OnToggleDifferentUpdateRates(); //slots for worker thread void OnAutoDetectToolsFinished(bool success, QString errorMessage); void OnConnectFinished(bool success, QString errorMessage); void OnStartTrackingFinished(bool success, QString errorMessage); void OnStopTrackingFinished(bool success, QString errorMessage); void OnDisconnectFinished(bool success, QString errorMessage); protected: Ui::QmitkMITKIGTTrackingToolboxViewControls* m_Controls; bool m_tracking; ///> bool which is true if tracking is running, false if not bool m_connected; ///> bool that is true when a tracking device is connected bool m_logging; ///> bool which is true if logging is running, false if not bool m_ShowHideToolAxis; ///> bool, which will be true, if the tool axis is visible during tracking int m_loggedFrames; ///> stores the current number of logged frames if logging is on mitk::NavigationToolStorage::Pointer m_toolStorage; ///>stores the loaded tools mitk::DataNode::Pointer m_TrackingVolumeNode; ///>holds the data node of the tracking volume if volume is visualized bool lastTrackingVolumeState; ///>temporary holds the state of the tracking volume (activated/not activated) during some methods QString m_ToolStorageFilename; ///>stores the filename of the current tool storage QString m_AutoSaveFilename; ///>a filename for auto saving tools if no m_ToolStorageFilename was given by the user /** @brief Shows a message box with the text given as parameter. */ void MessageBox(std::string s); /** @brief reinits the view globally. */ void GlobalReinit(); //members for the filter pipeline mitk::TrackingDeviceData m_TrackingDeviceData; ///> stores the tracking device data as long as this is not handled by the tracking device configuration widget mitk::NavigationDataObjectVisualizationFilter::Pointer m_ToolVisualizationFilter; ///> holds the tool visualization filter (second filter of the IGT pipeline) mitk::NavigationDataRecorder::Pointer m_loggingFilter; ///> holds the logging filter if logging is on (third filter of the IGT pipeline) itk::SmartPointer<mitk::NeedleProjectionFilter> m_NeedleProjectionFilter; ///> Contains the needle projection filter which is used for displaying the tool projection and the tool axis during tracking (optional third filter of the IGT pipeline). The filter is updated in the method UpdateRenderTrackingTimer(). //members for open IGT link server mitk::NavigationDataToIGTLMessageFilter::Pointer m_IGTLConversionFilter; ///> Converts the navigation data as open IGT link message and makes this filter available as microservice mitk::IGTLServer::Pointer m_IGTLServer; mitk::IGTLMessageProvider::Pointer m_IGTLMessageProvider; /** @brief This timer updates the IGT pipline and also the logging filter if logging is activated.*/ QTimer* m_TrackingRenderTimer; QTimer* m_TrackingLoggingTimer; QTimer* m_TimeoutTimer; bool m_SimpleModeEnabled; ///>Stores if simple UI mode is enabled /** Replaces the current navigation tool storage which is stored in m_toolStorage. - * Basically handles the microservice stuff: unregisteres the old storage, then + * Basically handles the microservice stuff: unregisters the old storage, then * replaces the storage and registers the new one. */ void ReplaceCurrentToolStorage(mitk::NavigationToolStorage::Pointer newStorage, std::string newStorageName); /** * \brief Stores the properties of some QWidgets (and the tool storage file name) to QSettings. */ void StoreUISettings(); /** * \brief Loads the properties of some QWidgets (and the tool storage file name) from QSettings. */ void LoadUISettings(); /** * Help method for updating the tool label */ void UpdateToolStorageLabel(QString pathOfLoadedStorage); /** - * Auto saves the current tool storage to a temporary file. This ist used for persistence. + * Auto saves the current tool storage to a temporary file. This is used for persistence. */ void AutoSaveToolStorage(); /** * Shows the projection of the tool along the tool axis for the given tool index */ void ShowToolProjection(int index); /** * Removes all the tool projections from the data storage */ void RemoveAllToolProjections(); //members for worker thread QThread* m_WorkerThread; QmitkMITKIGTTrackingToolboxViewWorker* m_Worker; private: ctkServiceReference m_DeviceTypeServiceReference; mitk::TrackingDeviceTypeCollection* m_DeviceTypeCollection; mitk::DataNode::Pointer m_ToolProjectionNode; }; #endif diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewWorker.cpp b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewWorker.cpp index 4c6ada6221..441ecefd95 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewWorker.cpp +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkMITKIGTTrackingToolboxViewWorker.cpp @@ -1,250 +1,250 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Qmitk #include "QmitkMITKIGTTrackingToolboxViewWorker.h" #include <mitkTrackingDeviceSourceConfigurator.h> QmitkMITKIGTTrackingToolboxViewWorker::QmitkMITKIGTTrackingToolboxViewWorker() { } QmitkMITKIGTTrackingToolboxViewWorker::~QmitkMITKIGTTrackingToolboxViewWorker() { } void QmitkMITKIGTTrackingToolboxViewWorker::SetWorkerMethod(WorkerMethod w) { m_WorkerMethod = w; } void QmitkMITKIGTTrackingToolboxViewWorker::SetTrackingDevice(mitk::TrackingDevice::Pointer t) { m_TrackingDevice = t; } void QmitkMITKIGTTrackingToolboxViewWorker::SetDataStorage(mitk::DataStorage::Pointer d) { m_DataStorage = d; } void QmitkMITKIGTTrackingToolboxViewWorker::SetInverseMode(bool mode) { m_InverseMode = mode; } void QmitkMITKIGTTrackingToolboxViewWorker::SetTrackingDeviceData(mitk::TrackingDeviceData d) { m_TrackingDeviceData = d; } void QmitkMITKIGTTrackingToolboxViewWorker::SetNavigationToolStorage(mitk::NavigationToolStorage::Pointer n) { m_NavigationToolStorage = n; } //! [Thread 7] void QmitkMITKIGTTrackingToolboxViewWorker::ThreadFunc() { switch (m_WorkerMethod) { case eAutoDetectTools: this->AutoDetectTools(); break; case eConnectDevice: this->ConnectDevice(); break; case eStartTracking: this->StartTracking(); break; case eStopTracking: this->StopTracking(); break; case eDisconnectDevice: this->DisconnectDevice(); break; default: MITK_WARN << "Undefined worker method was set ... something went wrong!"; break; } } //! [Thread 7] void QmitkMITKIGTTrackingToolboxViewWorker::AutoDetectTools() { mitk::NavigationToolStorage::Pointer autoDetectedStorage = mitk::NavigationToolStorage::New(m_DataStorage); try { mitk::NavigationToolStorage::Pointer tempStorage = m_TrackingDevice->AutoDetectTools(); for (unsigned int i = 0; i < tempStorage->GetToolCount(); i++) { autoDetectedStorage->AddTool(tempStorage->GetTool(i)); } } catch (mitk::Exception& e) { MITK_WARN << e.GetDescription(); emit AutoDetectToolsFinished(false, e.GetDescription()); return; } m_NavigationToolStorage = nullptr; m_NavigationToolStorage = autoDetectedStorage; emit AutoDetectToolsFinished(true, ""); MITK_INFO << "AutoDetect Tools Finished."; } void QmitkMITKIGTTrackingToolboxViewWorker::ConnectDevice() { std::string message = ""; //build the IGT pipeline mitk::TrackingDevice::Pointer trackingDevice = m_TrackingDevice; trackingDevice->SetData(m_TrackingDeviceData); - //set device to rotation mode transposed becaus we are working with VNL style quaternions + //set device to rotation mode transposed because we are working with VNL style quaternions if (m_InverseMode) { trackingDevice->SetRotationMode(mitk::TrackingDevice::RotationTransposed); } //Get Tracking Volume Data mitk::TrackingDeviceData data = m_TrackingDeviceData; //Create Navigation Data Source with the factory class mitk::TrackingDeviceSourceConfigurator::Pointer myTrackingDeviceSourceFactory = mitk::TrackingDeviceSourceConfigurator::New(m_NavigationToolStorage, trackingDevice); m_TrackingDeviceSource = myTrackingDeviceSourceFactory->CreateTrackingDeviceSource(m_ToolVisualizationFilter); if (m_TrackingDeviceSource.IsNull()) { message = std::string("Cannot connect to device: ") + myTrackingDeviceSourceFactory->GetErrorMessage(); emit ConnectDeviceFinished(false, QString(message.c_str())); return; } - //set filter to rotation mode transposed becaus we are working with VNL style quaternions + //set filter to rotation mode transposed because we are working with VNL style quaternions if (m_InverseMode) m_ToolVisualizationFilter->SetRotationMode(mitk::NavigationDataObjectVisualizationFilter::RotationTransposed); //First check if the created object is valid if (m_TrackingDeviceSource.IsNull()) { message = myTrackingDeviceSourceFactory->GetErrorMessage(); emit ConnectDeviceFinished(false, QString(message.c_str())); return; } MITK_INFO << "Connected device with " << m_TrackingDeviceSource->GetNumberOfOutputs() << " tools."; //connect to device try { m_TrackingDeviceSource->Connect(); //Microservice registration: m_TrackingDeviceSource->SetToolMetaDataCollection(m_NavigationToolStorage); m_TrackingDeviceSource->RegisterAsMicroservice(); m_NavigationToolStorage->SetSourceID(m_TrackingDeviceSource->GetMicroserviceID()); //DEPRECATED / not needed anymore because NavigationDataSource now holds a member of its tool storage. Only left for backward compatibility. m_NavigationToolStorage->LockStorage(); } catch (...) //todo: change to mitk::IGTException { message = "Error on connecting the tracking device."; emit ConnectDeviceFinished(false, QString(message.c_str())); return; } emit ConnectDeviceFinished(true, QString(message.c_str())); } mitk::TrackingDeviceSource::Pointer QmitkMITKIGTTrackingToolboxViewWorker::GetTrackingDeviceSource() { return this->m_TrackingDeviceSource; } void QmitkMITKIGTTrackingToolboxViewWorker::StartTracking() { QString errorMessage = ""; try { m_TrackingDeviceSource->StartTracking(); } catch (...) //todo: change to mitk::IGTException { errorMessage += "Error while starting the tracking device!"; emit StartTrackingFinished(false, errorMessage); return; } //remember the original colors of the tools m_OriginalColors = std::map<mitk::DataNode::Pointer, mitk::Color>(); for (unsigned int i = 0; i < this->m_NavigationToolStorage->GetToolCount(); i++) { mitk::DataNode::Pointer currentToolNode = m_NavigationToolStorage->GetTool(i)->GetDataNode(); float c[3]; currentToolNode->GetColor(c); mitk::Color color; color.SetRed(c[0]); color.SetGreen(c[1]); color.SetBlue(c[2]); m_OriginalColors[currentToolNode] = color; } emit StartTrackingFinished(true, errorMessage); } void QmitkMITKIGTTrackingToolboxViewWorker::StopTracking() { //stop tracking try { m_TrackingDeviceSource->StopTracking(); } catch (mitk::Exception& e) { emit StopTrackingFinished(false, e.GetDescription()); } //restore the original colors of the tools for (unsigned int i = 0; i < this->m_NavigationToolStorage->GetToolCount(); i++) { mitk::DataNode::Pointer currentToolNode = m_NavigationToolStorage->GetTool(i)->GetDataNode(); if (m_OriginalColors.find(currentToolNode) == m_OriginalColors.end()) { MITK_WARN << "Cannot restore original color of tool " << m_NavigationToolStorage->GetTool(i)->GetToolName(); } else { currentToolNode->SetColor(m_OriginalColors[currentToolNode]); } } // clear map m_OriginalColors m_OriginalColors.clear(); //emit signal emit StopTrackingFinished(true, ""); } void QmitkMITKIGTTrackingToolboxViewWorker::DisconnectDevice() { try { if (m_TrackingDeviceSource->IsTracking()) { m_TrackingDeviceSource->StopTracking(); } m_TrackingDeviceSource->Disconnect(); m_TrackingDeviceSource->UnRegisterMicroservice(); m_NavigationToolStorage->UnLockStorage(); m_TrackingDeviceSource = nullptr; } catch (mitk::Exception& e) { emit DisconnectDeviceFinished(false, e.GetDescription()); } emit DisconnectDeviceFinished(true, ""); } diff --git a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperViewControls.ui b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperViewControls.ui index 6afea7fa3c..75acf265a8 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperViewControls.ui +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperViewControls.ui @@ -1,311 +1,311 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkImageCropperViewControls</class> <widget class="QWidget" name="QmitkImageCropperViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>300</width> <height>600</height> </rect> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QGroupBox" name="groupBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="title"> <string>Data Selection</string> </property> <layout class="QGridLayout" name="gridLayoutDataSelection"> <item row="0" column="0"> <widget class="QLabel" name="labelImage"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Image</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QmitkSingleNodeSelectionWidget" name="imageSelectionWidget" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="labelBoundingBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Bounding Box</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QmitkSingleNodeSelectionWidget" name="boundingBoxSelectionWidget" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="1" column="2"> <widget class="QPushButton" name="buttonCreateNewBoundingBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> <property name="text"> <string>New</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBoundingObject"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>90</height> </size> </property> <property name="title"> <string>Processing</string> </property> <layout class="QGridLayout" name="gridLayoutProcessing"> <item row="0" column="0"> <widget class="QPushButton" name="buttonMasking"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Mask</string> </property> </widget> </item> <item row="" column="1"> <widget class="QPushButton" name="buttonCropping"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Crop</string> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QLabel" name="labelWarningRotation"> <property name="enabled"> <bool>true</bool> </property> <property name="text"> <string>The selected image has a rotated geometry, result won't be pixel-aligned</string> </property> <property name="textFormat"> <enum>Qt::PlainText</enum> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <widget class="ctkExpandButton" name="buttonAdvancedSettings"> <property name="sizePolicy"> <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>25</height> </size> </property> <property name="text"> <string>Advanced settings</string> </property> <property name="checkable"> <bool>false</bool> </property> <property name="autoRepeatInterval"> <number>100</number> </property> <property name="toolButtonStyle"> <enum>Qt::ToolButtonTextBesideIcon</enum> </property> <property name="autoRaise"> <bool>false</bool> </property> </widget> </item> <item> <widget class="QGroupBox" name="groupImageSettings"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>120</height> </size> </property> <property name="title"> <string>Output image settings</string> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <layout class="QHBoxLayout" name="horizontalLayoutSettings"> <item> <widget class="QLabel" name="labelOutsidePixelValue"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Outside pixel value (masking):</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="spinBoxOutsidePixelValue"> <property name="enabled"> <bool>false</bool> </property> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="checkOverwriteImage"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> - <string>Overrride original image</string> + <string>Override original image</string> </property> <property name="checked"> <bool>false</bool> </property> </widget> </item> <item> <widget class="QCheckBox" name="checkBoxCropTimeStepOnly"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Only crop current timestep / cut off other timesteps</string> </property> </widget> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> </customwidget> <customwidget> <class>ctkExpandButton</class> <extends>QToolButton</extends> <header>ctkExpandButton.h</header> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox index 5d4fcf4622..cd4556807e 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/documentation/UserManual/Manual.dox @@ -1,40 +1,40 @@ /** \page org_mitk_views_matchpoint_algorithm_control The MatchPoint Algorithm Control View \imageMacro{map_icon_run_doc.svg,"Icon of the MatchPoint Algorithm Control",3.0} \tableofcontents \section MAP_RUN_Introduction Introduction This plugin offers the user a way to register data (images or point sets) in order to establish a spatial correlation/mapping (stored as registration object in the data storage). To determine a registration the user has to select a registration algorithm. For the selection of an algorithm please see MatchPoint Algorithm Browser (\ref org_mitk_views_matchpoint_algorithm_browser). \section MAP_RUN_Usage Usage \imageMacro{map_control_example.png, "Example screenshot showing the control plugin in use.", 10} To use the plugin a registration algorithm must be loaded and moving data as well as target data must be selected. The type of data supported depends on the chosen algorithm. Basically the plugin supports the registration of images and point sets. The moving data is registered onto the target data. Thus in case of images, the result is a mapped input image in the geometry (field of view, orientation, spacing) defined by the target image.\n -All inputs that should be used for the registration are selected via the respective selection widgets shown in the image below. The box with the mask input selectors are only shown if the chosen algorithm supports masks. It is also optional to set only one ore both masks. (Remark: implications of which mask to set may depend on the specific algorithms; e.g. sometimes it is computationally more efficient to set at least the moving mask if possible.) +All inputs that should be used for the registration are selected via the respective selection widgets shown in the image below. The box with the mask input selectors are only shown if the chosen algorithm supports masks. It is also optional to set only one or both masks. (Remark: implications of which mask to set may depend on the specific algorithms; e.g. sometimes it is computationally more efficient to set at least the moving mask if possible.) \imageMacro{map_control_inputs.png, "Input selections for the registration. Moving and target inputs are mandatory. Moving and target masks are only available if the algorithm supports them and are optional.", 5} If an algorithm is loaded and inputs are selected, the plugin will automatically switch to the "Execution" tab. \subsection MAP_RUN_Usage_selection Selection tab \imageMacro{map_control_step1_selection.png, "Details of the selection tab.", 5} In this tab registration algorithms that are selected in the MatchPoint Algorithm Browser can be chosen. In the tab you see the ID of the algorithm selected by the browser and its profile information.\n If you press the button "Load selected algorithm", the algorithm will be used by the control plugin. The name of the algorithm occurs in the text field "Loaded algorithm" (at the top of the plugin view).\n At this point, it has no effect if you change the selection in the browser. The control plugin will keep the loaded algorithm until you choose to load another one. \subsection MAP_RUN_Usage_exec Execution tab \imageMacro{map_control_step2_execution.png, "Details of the execution tab.", 5} In this tab you can specify a name for the registration job (this will determine the names of the result nodes in the Data Manager View and the data selection widgets).\n You can also choose to "store registration" (which is normally the goal of the whole process, because this is the very result of the algorithm ;).\n Additionally you can choose "Generate + store mapped result". This is a convenience feature which often saves you the time to use the mapper plugin afterwards. It will do the same like using the mapper plugin with the moving and target image, setting padding value "0" and using "linear interpolation". If you need other settings, skip the convenience generation and use the MatchPoint mapper plugin directly.\n "Start" will trigger the registration process. Some algorithms can be stopped while processing takes place. In those cases, there is a "Stop" button enabled, as soon as the registration process starts. \subsection MAP_RUN_Usage_settings Settings tab \imageMacro{map_control_step3_settings.png, "Details of the settings tab.", 5} In this tab, you can change the parametrization of the loaded algorithm (before it starts), if it offers any possibility to do so. */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/src/internal/QmitkMatchPoint.h b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/src/internal/QmitkMatchPoint.h index ac11c3bf6a..85dbf7e4dd 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/src/internal/QmitkMatchPoint.h +++ b/Plugins/org.mitk.gui.qt.matchpoint.algorithm.control/src/internal/QmitkMatchPoint.h @@ -1,204 +1,204 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMatchPoint_h #define QmitkMatchPoint_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include "ui_QmitkMatchPointControls.h" #include <mitkImage.h> // MatchPoint #include <mapDeploymentDLLInfo.h> #include <mapDeploymentDLLHandle.h> #include <mapRegistrationAlgorithmBase.h> #include <mapIterativeAlgorithmInterface.h> #include <mapMultiResRegistrationAlgorithmInterface.h> #include <mapStoppableAlgorithmInterface.h> #include <mitkMAPRegistrationWrapper.h> class QmitkRegistrationJob; class QmitkMappingJob; /*! \brief MatchPoint \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \ingroup ${plugin_target}_internal */ class QmitkMatchPoint : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; /** * Creates smartpointer typedefs */ berryObjectMacro(QmitkMatchPoint); QmitkMatchPoint(); ~QmitkMatchPoint() override; protected slots: /** * @brief Connect all GUI elements to its corresponding slots */ virtual void CreateConnections(); /// \brief Called when the user clicks the GUI button void OnLoadAlgorithmButtonPushed(); void OnSelectedAlgorithmChanged(); void OnNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes); void OnStartRegBtnPushed(); void OnStopRegBtnPushed(); void OnSaveLogBtnPushed(); void OnRegJobError(QString err); void OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* pRegJob); void OnRegJobFinished(); void OnMapJobError(QString err); void OnMapResultIsAvailable(mitk::BaseData::Pointer spMappedData, const QmitkMappingJob* job); void OnAlgorithmIterated(QString info, bool hasIterationCount, unsigned long currentIteration); void OnLevelChanged(QString info, bool hasLevelCount, unsigned long currentLevel); void OnAlgorithmStatusChanged(QString info); void OnAlgorithmInfo(QString info); protected: void CreateQtPartControl(QWidget* parent) override; void SetFocus() override; private: /** * @brief Adapt the visibility of GUI elements depending on the current data loaded */ void AdaptFolderGUIElements(); void Error(QString msg); void UpdateAlgorithmList(); /** * checks if appropriated nodes are selected in the data manager. If nodes are selected, - * they are stored m_MovingData and m_TargetData. It also sets the info lables accordingly. + * they are stored m_MovingData and m_TargetData. It also sets the info labels accordingly. * @return True: All inputs are set and valid (images). False: At least one input is not set * or invalid */ bool CheckInputs(); /** * Updates the state of registration control buttons. Regarding to selected * inputs, loaded algorithm and its state.*/ void ConfigureRegistrationControls(); /** * Configures the progress bars according to the chosen algorithm. */ void ConfigureProgressInfos(); /** - Configure the node selectors predicates and informations according to the selected algorithm. + Configure the node selectors predicates and information according to the selected algorithm. */ void ConfigureNodeSelectors(); /** Methods returns a list of all nodes in the data manager containing a registration wrapper. * The list may be empty.*/ mitk::DataStorage::SetOfObjects::Pointer GetRegNodes() const; /** Returns a proposal for a (unique) default reg job name */ std::string GetDefaultRegJobName() const; /** Returns the display name of the passed node. Normally it is just node->GetName(). * if the node contains a point set it is additionally checked if the point set node * has a source node and its name will be added in parentheses.*/ std::string GetInputNodeDisplayName(const mitk::DataNode* node) const; /** Returns the Pointer to the DLL info of the algorithm currently selected by the system. The info is received via m_AlgorithmSelectionListener. @return If there is no item selected the returning pointer will be null. */ const map::deployment::DLLInfo* GetSelectedAlgorithmDLL() const; //! [Qt Selection Listener method and pointer] /** * @brief Method of berry::ISelectionListener that implements the selection listener functionality. * @param sourcepart The workbench part responsible for the selection change. * @param selection This parameter holds the current selection. * * @see ISelectionListener */ void OnAlgorithmSelectionChanged(const berry::IWorkbenchPart::Pointer& sourcepart, const berry::ISelection::ConstPointer& selection); void UpdateAlgorithmSelection(berry::ISelection::ConstPointer selection); friend struct berry::SelectionChangedAdapter<QmitkMatchPoint>; QWidget* m_Parent; /** @brief this pointer holds the algorithm selection listener */ QScopedPointer<berry::ISelectionListener> m_AlgorithmSelectionListener; ::map::deployment::DLLHandle::Pointer m_LoadedDLLHandle; ::map::algorithm::RegistrationAlgorithmBase::Pointer m_LoadedAlgorithm; ::map::deployment::DLLInfo::ConstPointer m_SelectedAlgorithmInfo; typedef map::algorithm::facet::IterativeAlgorithmInterface IIterativeAlgorithm; typedef map::algorithm::facet::MultiResRegistrationAlgorithmInterface IMultiResAlgorithm; typedef map::algorithm::facet::StoppableAlgorithmInterface IStoppableAlgorithm; mitk::DataNode::Pointer m_spSelectedTargetNode; mitk::DataNode::Pointer m_spSelectedMovingNode; /*Data of the selected target node that should be used for registration. Can be the direct return of node->GetData(), but can also be a sub set (like a special time frame).*/ mitk::BaseData::ConstPointer m_spSelectedTargetData; /*Data of the selected moving node that should be used for registration. Can be the direct return of node->GetData(), but can also be a sub set (like a special time frame).*/ mitk::BaseData::ConstPointer m_spSelectedMovingData; mitk::DataNode::Pointer m_spSelectedTargetMaskNode; mitk::DataNode::Pointer m_spSelectedMovingMaskNode; /*Data of the selected target mask node that should be used for registration. Can be the direct return of node->GetData(), but can also be a sub set (like a special time frame).*/ mitk::Image::ConstPointer m_spSelectedTargetMaskData; /*Data of the selected moving mask node that should be used for registration. Can be the direct return of node->GetData(), but can also be a sub set (like a special time frame).*/ mitk::Image::ConstPointer m_spSelectedMovingMaskData; // boolean variables to control visibility of GUI elements bool m_CanLoadAlgorithm; bool m_ValidInputs; bool m_Working; Ui::MatchPointAdvancedControls m_Controls; }; #endif diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox index 0f87905d06..6d6b5c88ec 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/documentation/UserManual/Manual.dox @@ -1,56 +1,56 @@ /** \page org_mitk_views_matchpoint_evaluator The MatchPoint Registration Evaluation View \imageMacro{map_evaluator_doc.svg, "Icon of the MatchPoint Registration Evaluator", 3} \tableofcontents \section MAP_REGEVAL_Introduction Introduction This view offers the possibility to evaluate the quality of the registration/mapping of two given images by visual inspection. This can either by used to assess the visual quality of a registration or to assess how well the image contents are already aligned by default. To achieve the latter, one may select no registration. Then the images will be displayed in evaluation mode assuming an identity transform (so no mapping). It is one of several MatchPoint registration plug-ins.\n \section MAP_REGEVAL_Usage Usage \imageMacro{map_view_evaluator_example.png, "Example screenshot showing the main elements of the view.", 14} (1) The currently selected registration that should be used to map the moving image for evaluation. Click to change. If no registration is selected, a direct evaluation will be performed.\n (2) Reset button will remove the currently selected registration.\n (3) Auto select option. If active the view will try to deduce and automatically select (if loaded in the application) the moving and target image when the registration changes. The view assumes that the moving and target images used to determine the registration should be used.\n (4) The currently selected moving data. Click to change.\n (5) The currently selected target data. Click to change.\n (6) Start/Stop button used to activate/deactivate the evaluation. This button become active when at least the moving and the target image are selected.\n (7) Selection of the visualization style. (only visible if evaluation is active)\n (8) Style specific settings. (only visible if evaluation is active)\n If the evaluation view is active you can choose between different modes of visualization. For more details see \ref MAP_REGEVAL_Styles .\n To stop the evaluation mode, you may use the "Stop evaluation" button or just close the evaluation view. \remark The evaluation view will use the level window settings of the used images. So to change the level windowing of the evaluation view, you must change the level windowing of the respective input images (moving image and target image). \section MAP_REGEVAL_Accuracy Evaluating accuracy Important note: Please be aware, that a visual inspection of registration quality is only a weak surrogate for a thorough accuracy analysis based on representative and suitable ground truth data. From a visually good mapping you can not deduce a correct registration. This is especially true if the degrees of freedom of the registration increases. For a rigid registration it might by feasible to discern correct and incorrect registration. But for none rigid registrations you definitely you should use this view only for first visual inspection (to check if it SEEMS to do the right thing and is worth further exploration) or illustrating the registration effect for registration you have assessed in a sound way. \section MAP_REGEVAL_Styles Visualization styles You can choose from the following visualization styles to evaluate the registration/mapping quality:\n \li "Blend": Blends the images with a user defined weight. Default is 50:50. \imageMacro{map_view_blend_settings.png, "Settings of the Blend style", 8} (1) Click to set the weights to 100% target image.\n (2) Click to set the weights to 50:50 (equal blend).\n (3) Slider to adjust the weights between target image and the mapped input image. The spin box shows the weight of the mapped input image.\n (4) Click to set the weights to 100% mapped input image.\n (5) Click to toggle the weight between both images.\n \imageMacro{map_style_blend.png, "Example for mode: Blend (50:50)", 5} \li "Checkerboard": Checkerboard style that composes both images by showing image 1 in all light squares and image 2 in all dark squares. You can define the resolution/number of squares of the checkerboard. \imageMacro{map_style_checkerboard.png, "Example for mode: Checkerboard", 5} \li "Color blend": Color blend of the images (blue: target image; yellow: moving). Areas where you see no color implies good intensity matchings. \imageMacro{map_style_color_blend.png, "Example for mode: Color blend", 5} \li "Contour": Blend mode that displays one image as blue "background" and the other image in yellow contours. You can choose the role of the images. \imageMacro{map_style_contour.png, "Example for mode: Contour", 5} \li "Difference": Displays the absolute difference of both images. -\li "Wipe": Blend mode that makes a rectilinear combination of the images. You can choose the mode how the images are splitted. The split is synchronized with the current selection. So you may interact with the split border to position it on interesting areas. +\li "Wipe": Blend mode that makes a rectilinear combination of the images. You can choose the mode how the images are split. The split is synchronized with the current selection. So you may interact with the split border to position it on interesting areas. \imageMacro{map_style_wipe_cross.png, "Example for mode: Wipe cross", 5} \imageMacro{map_style_wipe_horizontal.png, "Example for mode: Wipe horizontal", 5} */ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.h b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.h index e923a6fe7f..3cb3750594 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.h +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.h @@ -1,114 +1,114 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMatchPointRegistrationEvaluator_h #define QmitkMatchPointRegistrationEvaluator_h #include <QmitkAbstractView.h> #include <mitkIRenderWindowPartListener.h> #include <QmitkSliceNavigationListener.h> #include "ui_QmitkMatchPointRegistrationEvaluator.h" /*! \brief QmitkMatchPointRegistrationEvaluator \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \ingroup ${plugin_target}_internal */ class QmitkMatchPointRegistrationEvaluator : public QmitkAbstractView, public mitk::IRenderWindowPartListener { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; /** * Creates smartpointer typedefs */ berryObjectMacro(QmitkMatchPointRegistrationEvaluator); QmitkMatchPointRegistrationEvaluator(); ~QmitkMatchPointRegistrationEvaluator() override; void CreateQtPartControl(QWidget *parent) override; protected slots: /// \brief Called when the user clicks the GUI button void OnEvalBtnPushed(); void OnStopBtnPushed(); void OnSettingsChanged(mitk::DataNode*); void OnSliceChanged(); void OnNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes); protected: void NodeRemoved(const mitk::DataNode* node) override; void SetFocus() override; void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; Ui::MatchPointRegistrationEvaluatorControls m_Controls; private: QWidget *m_Parent; void Error(QString msg); /** * Checks if appropriated nodes are selected in the data manager. If nodes are selected, * they are stored m_spSelectedRegNode, m_spSelectedInputNode and m_spSelectedRefNode. * They are also checked for vadility and stored in m_ValidInput,... . - * It also sets the info lables accordingly.*/ + * It also sets the info labels accordingly.*/ void CheckInputs(); /** * Updates the state of controls regarding to selected eval object.*/ void ConfigureControls(); /** Configure the node selectors predicates according to the selected algorithm. */ void ConfigureNodePredicates(); mitk::DataNode::Pointer m_selectedEvalNode; QmitkSliceNavigationListener m_SliceChangeListener; itk::TimeStamp m_selectedNodeTime; itk::TimeStamp m_currentPositionTime; bool m_activeEvaluation; /** @brief currently valid selected position in the inspector*/ mitk::Point3D m_currentSelectedPosition; /** @brief currently selected timepoint*/ mitk::TimePointType m_currentSelectedTimePoint; mitk::DataNode::Pointer m_spSelectedRegNode; mitk::DataNode::Pointer m_spSelectedMovingNode; mitk::DataNode::Pointer m_spSelectedTargetNode; static const std::string HelperNodeName; }; #endif diff --git a/Plugins/org.mitk.gui.qt.matchpoint.framereg/src/internal/QmitkMatchPointFrameCorrection.cpp b/Plugins/org.mitk.gui.qt.matchpoint.framereg/src/internal/QmitkMatchPointFrameCorrection.cpp index e7c2cac264..c94f8f78ad 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.framereg/src/internal/QmitkMatchPointFrameCorrection.cpp +++ b/Plugins/org.mitk.gui.qt.matchpoint.framereg/src/internal/QmitkMatchPointFrameCorrection.cpp @@ -1,724 +1,724 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "org_mitk_gui_qt_matchpoint_framereg_Activator.h" // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> #include <berryISelectionProvider.h> #include <berryQModelIndexObject.h> // Mitk #include <mitkStatusBar.h> #include <mitkPointSet.h> #include <mitkImageTimeSelector.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateOr.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateDimension.h> #include <mitkNodePredicateGeometry.h> #include <mitkMAPAlgorithmInfoSelection.h> #include <mitkRegistrationHelper.h> #include <mitkResultNodeGenerationHelper.h> // Qmitk #include "QmitkMatchPointFrameCorrection.h" #include <QmitkRegistrationJob.h> #include <QmitkMappingJob.h> // Qt #include <QMessageBox> #include <QFileDialog> #include <QErrorMessage> #include <QThreadPool> #include <QDateTime> // MatchPoint #include <mapImageRegistrationAlgorithmInterface.h> #include <mapPointSetRegistrationAlgorithmInterface.h> #include <mapRegistrationAlgorithmInterface.h> #include <mapMaskedRegistrationAlgorithmInterface.h> #include <mapAlgorithmEvents.h> #include <mapAlgorithmWrapperEvent.h> #include <mapExceptionObjectMacros.h> #include <mapConvert.h> #include <mapDeploymentDLLAccess.h> const std::string QmitkMatchPointFrameCorrection::VIEW_ID = "org.mitk.views.matchpoint.algorithm.framereg"; QmitkMatchPointFrameCorrection::QmitkMatchPointFrameCorrection() : m_Parent(nullptr), m_LoadedDLLHandle(nullptr), m_LoadedAlgorithm(nullptr), m_CanLoadAlgorithm(false), m_Working(false) { m_spSelectedTargetData = nullptr; m_spSelectedTargetMaskData = nullptr; } QmitkMatchPointFrameCorrection::~QmitkMatchPointFrameCorrection() { // remove selection service berry::ISelectionService* s = this->GetSite()->GetWorkbenchWindow()->GetSelectionService(); if (s) { s->RemoveSelectionListener(m_AlgorithmSelectionListener.data()); } } void QmitkMatchPointFrameCorrection::SetFocus() { } void QmitkMatchPointFrameCorrection::CreateConnections() { connect(m_Controls.imageNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointFrameCorrection::OnNodeSelectionChanged); connect(m_Controls.maskNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointFrameCorrection::OnNodeSelectionChanged); // ------ // Tab 1 - Shared library loading interface // ------ connect(m_Controls.m_pbLoadSelected, SIGNAL(clicked()), this, SLOT(OnLoadAlgorithmButtonPushed())); // ----- // Tab 2 - Execution // ----- connect(m_Controls.m_pbStartReg, SIGNAL(clicked()), this, SLOT(OnStartRegBtnPushed())); connect(m_Controls.m_pbSaveLog, SIGNAL(clicked()), this, SLOT(OnSaveLogBtnPushed())); // ----- // Tab 4 - Frames // ----- connect(m_Controls.m_btnFrameSelAll, SIGNAL(clicked()), this, SLOT(OnFramesSelectAllPushed())); connect(m_Controls.m_btnFrameDeSelAll, SIGNAL(clicked()), this, SLOT(OnFramesDeSelectAllPushed())); connect(m_Controls.m_btnFrameInvert, SIGNAL(clicked()), this, SLOT(OnFramesInvertPushed())); } const map::deployment::DLLInfo* QmitkMatchPointFrameCorrection::GetSelectedAlgorithmDLL() const { return m_SelectedAlgorithmInfo; } void QmitkMatchPointFrameCorrection::OnSelectedAlgorithmChanged() { std::stringstream descriptionString; ::map::deployment::DLLInfo::ConstPointer currentItemInfo = GetSelectedAlgorithmDLL(); if (!currentItemInfo) { return; } m_Controls.m_teAlgorithmDetails->updateInfo(currentItemInfo); m_Controls.m_lbSelectedAlgorithm->setText(QString::fromStdString( currentItemInfo->getAlgorithmUID().getName())); // enable loading m_CanLoadAlgorithm = true; this->AdaptFolderGUIElements(); } void QmitkMatchPointFrameCorrection::OnLoadAlgorithmButtonPushed() { map::deployment::DLLInfo::ConstPointer dllInfo = GetSelectedAlgorithmDLL(); if (!dllInfo) { Error(QStringLiteral("No valid algorithm is selected. Cannot load algorithm. ABORTING.")); return; } ::map::deployment::DLLHandle::Pointer tempDLLHandle = ::map::deployment::openDeploymentDLL( dllInfo->getLibraryFilePath()); ::map::algorithm::RegistrationAlgorithmBase::Pointer tempAlgorithm = ::map::deployment::getRegistrationAlgorithm(tempDLLHandle); if (tempAlgorithm.IsNull()) { Error(QStringLiteral("Error. Cannot load selected algorithm.")); return; } this->m_LoadedAlgorithm = tempAlgorithm; this->m_LoadedDLLHandle = tempDLLHandle; this->m_Controls.m_AlgoConfigurator->setAlgorithm(m_LoadedAlgorithm); this->AdaptFolderGUIElements(); this->ConfigureNodeSelectorPredicates(); this->CheckInputs(); this->ConfigureRegistrationControls(); this->ConfigureProgressInfos(); this->m_Controls.m_tabs->setCurrentIndex(1); } void QmitkMatchPointFrameCorrection::Error(QString msg) { mitk::StatusBar::GetInstance()->DisplayErrorText(msg.toLatin1()); MITK_ERROR << msg.toStdString().c_str(); m_Controls.m_teLog->append(QString("") + msg + QString("")); } void QmitkMatchPointFrameCorrection::AdaptFolderGUIElements() { m_Controls.m_pbLoadSelected->setEnabled(m_CanLoadAlgorithm); } void QmitkMatchPointFrameCorrection::CreateQtPartControl(QWidget* parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Parent = parent; this->m_Controls.imageNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.imageNodeSelector->SetSelectionIsOptional(false); this->m_Controls.maskNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.maskNodeSelector->SetSelectionIsOptional(true); this->m_Controls.imageNodeSelector->SetInvalidInfo("Select dymamic image."); this->m_Controls.imageNodeSelector->SetPopUpTitel("Select dynamic image."); this->m_Controls.imageNodeSelector->SetPopUpHint("Select a dynamic image (time resolved) that should be frame corrected."); this->m_Controls.maskNodeSelector->SetInvalidInfo("Select target mask."); this->m_Controls.maskNodeSelector->SetPopUpTitel("Select target mask."); this->m_Controls.maskNodeSelector->SetPopUpHint("Select a target mask (mask of the target/first frame)."); m_Controls.m_tabs->setCurrentIndex(0); m_Controls.m_mapperSettings->AllowSampling(false); m_AlgorithmSelectionListener.reset(new berry::SelectionChangedAdapter<QmitkMatchPointFrameCorrection>(this, &QmitkMatchPointFrameCorrection::OnAlgorithmSelectionChanged)); // register selection listener GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddSelectionListener( m_AlgorithmSelectionListener.data()); this->ConfigureNodeSelectorPredicates(); this->CreateConnections(); this->AdaptFolderGUIElements(); this->CheckInputs(); this->ConfigureProgressInfos(); this->ConfigureRegistrationControls(); berry::ISelection::ConstPointer selection = GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.matchpoint.algorithm.browser"); this->UpdateAlgorithmSelection(selection); } void QmitkMatchPointFrameCorrection::ConfigureNodeSelectorPredicates() { auto isImage = mitk::MITKRegistrationHelper::ImageNodePredicate(); mitk::NodePredicateBase::Pointer maskDimensionPredicate = mitk::NodePredicateOr::New(mitk::NodePredicateDimension::New(3), mitk::NodePredicateDimension::New(4)).GetPointer(); mitk::NodePredicateDimension::Pointer imageDimensionPredicate = mitk::NodePredicateDimension::New(4); m_Controls.imageNodeSelector->setEnabled(m_LoadedAlgorithm.IsNotNull()); m_Controls.maskNodeSelector->setEnabled(m_LoadedAlgorithm.IsNotNull()); m_Controls.imageNodeSelector->SetNodePredicate(mitk::NodePredicateAnd::New(isImage, imageDimensionPredicate)); mitk::NodePredicateAnd::Pointer maskPredicate = mitk::NodePredicateAnd::New(mitk::MITKRegistrationHelper::MaskNodePredicate(), maskDimensionPredicate); if (m_spSelectedTargetData != nullptr) { auto hasSameGeometry = mitk::NodePredicateGeometry::New(m_spSelectedTargetData->GetGeometry()); hasSameGeometry->SetCheckPrecision(1e-10); maskPredicate = mitk::NodePredicateAnd::New(maskPredicate, hasSameGeometry); } m_Controls.maskNodeSelector->SetNodePredicate(maskPredicate); } void QmitkMatchPointFrameCorrection::CheckInputs() { mitk::DataNode::Pointer oldTargetNode = m_spSelectedTargetNode; m_spSelectedTargetNode = nullptr; m_spSelectedTargetData = nullptr; m_spSelectedTargetMaskNode = nullptr; m_spSelectedTargetMaskData = nullptr; if (m_LoadedAlgorithm.IsNull()) { m_Controls.m_lbLoadedAlgorithmName->setText( - QStringLiteral("No algorithm seleted!")); + QStringLiteral("No algorithm selected!")); } else { m_spSelectedTargetNode = m_Controls.imageNodeSelector->GetSelectedNode(); if (m_spSelectedTargetNode.IsNotNull()) { m_spSelectedTargetData = m_spSelectedTargetNode->GetData(); } m_spSelectedTargetMaskNode = m_Controls.maskNodeSelector->GetSelectedNode(); if (m_spSelectedTargetMaskNode.IsNotNull()) { m_spSelectedTargetMaskData = dynamic_cast<mitk::Image*>(m_spSelectedTargetMaskNode->GetData()); } } if (oldTargetNode != m_spSelectedTargetNode) { ConfigureFrameList(); } } mitk::DataStorage::SetOfObjects::Pointer QmitkMatchPointFrameCorrection::GetRegNodes() const { mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetAll(); mitk::DataStorage::SetOfObjects::Pointer result = mitk::DataStorage::SetOfObjects::New(); for (mitk::DataStorage::SetOfObjects::const_iterator pos = nodes->begin(); pos != nodes->end(); ++pos) { if (mitk::MITKRegistrationHelper::IsRegNode(*pos)) { result->push_back(*pos); } } return result; } std::string QmitkMatchPointFrameCorrection::GetDefaultJobName() const { mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetRegNodes().GetPointer(); mitk::DataStorage::SetOfObjects::ElementIdentifier newIndex = 0; bool isUnique = false; std::string baseName = "corrected #"; if (m_spSelectedTargetNode.IsNotNull()) { baseName = m_spSelectedTargetNode->GetName() + "corrected #"; } std::string result = baseName; while (!isUnique) { ++newIndex; result = baseName + ::map::core::convert::toStr(newIndex); isUnique = this->GetDataStorage()->GetNamedNode(result) == nullptr; } return result; } void QmitkMatchPointFrameCorrection::ConfigureRegistrationControls() { m_Controls.m_tabSelection->setEnabled(!m_Working); m_Controls.m_leRegJobName->setEnabled(!m_Working); m_Controls.m_pbStartReg->setEnabled(false); m_Controls.imageNodeSelector->setEnabled(!m_Working); m_Controls.maskNodeSelector->setEnabled(!m_Working); if (m_LoadedAlgorithm.IsNotNull()) { m_Controls.m_tabSettings->setEnabled(!m_Working); m_Controls.m_tabExclusion->setEnabled(!m_Working); m_Controls.m_tabExecution->setEnabled(true); m_Controls.m_pbStartReg->setEnabled(m_spSelectedTargetNode.IsNotNull() && !m_Working); m_Controls.m_leRegJobName->setEnabled(!m_Working); typedef ::map::algorithm::facet::MaskedRegistrationAlgorithmInterface<3, 3> MaskRegInterface; const MaskRegInterface* pMaskReg = dynamic_cast<const MaskRegInterface*> (m_LoadedAlgorithm.GetPointer()); m_Controls.maskNodeSelector->setVisible(pMaskReg != nullptr); m_Controls.label_TargetMask->setVisible(pMaskReg != nullptr); if (!pMaskReg) { m_Controls.maskNodeSelector->SetCurrentSelection(QmitkSingleNodeSelectionWidget::NodeList()); } this->m_Controls.m_lbLoadedAlgorithmName->setText( QString::fromStdString(m_LoadedAlgorithm->getUID()->toStr())); } else { m_Controls.m_tabSettings->setEnabled(false); m_Controls.m_tabExclusion->setEnabled(false); m_Controls.m_tabExecution->setEnabled(false); this->m_Controls.m_lbLoadedAlgorithmName->setText( QStringLiteral("no algorithm loaded!")); m_Controls.maskNodeSelector->setVisible(false); m_Controls.label_TargetMask->setVisible(false); } if (!m_Working) { this->m_Controls.m_leRegJobName->setText(QString::fromStdString(this->GetDefaultJobName())); } } void QmitkMatchPointFrameCorrection::ConfigureProgressInfos() { const IIterativeAlgorithm* pIterative = dynamic_cast<const IIterativeAlgorithm*> (m_LoadedAlgorithm.GetPointer()); const IMultiResAlgorithm* pMultiRes = dynamic_cast<const IMultiResAlgorithm*> (m_LoadedAlgorithm.GetPointer()); m_Controls.m_progBarIteration->setVisible(pIterative); m_Controls.m_lbProgBarIteration->setVisible(pIterative); if (pIterative) { QString format = "%p% (%v/%m)"; if (!pIterative->hasMaxIterationCount()) { format = "%v"; m_Controls.m_progBarIteration->setMaximum(0); } else { m_Controls.m_progBarIteration->setMaximum(pIterative->getMaxIterations()); } m_Controls.m_progBarIteration->setFormat(format); } if (pMultiRes) { m_Controls.m_progBarLevel->setMaximum(pMultiRes->getResolutionLevels()); } else { m_Controls.m_progBarLevel->setMaximum(1); } m_Controls.m_progBarIteration->reset(); m_Controls.m_progBarLevel->reset(); m_Controls.m_progBarFrame->reset(); } void QmitkMatchPointFrameCorrection::ConfigureFrameList() { m_Controls.m_listFrames->clear(); if (m_spSelectedTargetData.IsNotNull()) { mitk::TimeGeometry::ConstPointer tg = m_spSelectedTargetData->GetTimeGeometry(); for (unsigned int i = 1; i < tg->CountTimeSteps(); ++i) { QString lable = "Timepoint #" + QString::number(i) + QString(" (") + QString::number( tg->GetMinimumTimePoint(i)) + QString(" ms - " + QString::number(tg->GetMaximumTimePoint( i)) + QString(" ms)")); QListWidgetItem* item = new QListWidgetItem(lable, m_Controls.m_listFrames); item->setFlags(Qt::ItemIsUserCheckable | Qt::ItemIsEnabled); item->setCheckState(Qt::Checked); } } } void QmitkMatchPointFrameCorrection::OnFramesSelectAllPushed() { for (int row = 0; row < m_Controls.m_listFrames->count(); row++) { QListWidgetItem* item = m_Controls.m_listFrames->item(row); item->setCheckState(Qt::Checked); } }; void QmitkMatchPointFrameCorrection::OnFramesDeSelectAllPushed() { for (int row = 0; row < m_Controls.m_listFrames->count(); row++) { QListWidgetItem* item = m_Controls.m_listFrames->item(row); item->setCheckState(Qt::Unchecked); } }; void QmitkMatchPointFrameCorrection::OnFramesInvertPushed() { for (int row = 0; row < m_Controls.m_listFrames->count(); row++) { QListWidgetItem* item = m_Controls.m_listFrames->item(row); if (item->checkState() == Qt::Unchecked) { item->setCheckState(Qt::Checked); } else { item->setCheckState(Qt::Unchecked); } } }; mitk::TimeFramesRegistrationHelper::IgnoreListType QmitkMatchPointFrameCorrection::GenerateIgnoreList() const { mitk::TimeFramesRegistrationHelper::IgnoreListType result; for (int row = 0; row < m_Controls.m_listFrames->count(); row++) { QListWidgetItem* item = m_Controls.m_listFrames->item(row); if (item->checkState() == Qt::Unchecked) { result.push_back(row + 1); } } return result; } void QmitkMatchPointFrameCorrection::OnNodeSelectionChanged(QList<mitk::DataNode::Pointer> /*nodes*/) { if (!m_Working) { ConfigureNodeSelectorPredicates(); CheckInputs(); ConfigureRegistrationControls(); } } void QmitkMatchPointFrameCorrection::OnStartRegBtnPushed() { this->m_Working = true; //////////////////////////////// //configure GUI this->ConfigureProgressInfos(); m_Controls.m_progBarIteration->reset(); m_Controls.m_progBarLevel->reset(); this->ConfigureRegistrationControls(); if (m_Controls.m_checkClearLog->checkState() == Qt::Checked) { this->m_Controls.m_teLog->clear(); } ///////////////////////// //create job and put it into the thread pool QmitkFramesRegistrationJob* pJob = new QmitkFramesRegistrationJob(m_LoadedAlgorithm); pJob->setAutoDelete(true); pJob->m_spTargetData = m_spSelectedTargetData; pJob->m_TargetDataUID = mitk::EnsureUID(this->m_spSelectedTargetNode->GetData()); pJob->m_IgnoreList = this->GenerateIgnoreList(); if (m_spSelectedTargetMaskData.IsNotNull()) { pJob->m_spTargetMask = m_spSelectedTargetMaskData; pJob->m_TargetMaskDataUID = mitk::EnsureUID(this->m_spSelectedTargetMaskNode->GetData()); } pJob->m_MappedName = m_Controls.m_leRegJobName->text().toStdString(); m_Controls.m_mapperSettings->ConfigureJobSettings(pJob); connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnRegJobError(QString))); connect(pJob, SIGNAL(Finished()), this, SLOT(OnRegJobFinished())); connect(pJob, SIGNAL(ResultIsAvailable(mitk::Image::Pointer, const QmitkFramesRegistrationJob*)), this, SLOT(OnMapResultIsAvailable(mitk::Image::Pointer, const QmitkFramesRegistrationJob*)), Qt::BlockingQueuedConnection); connect(pJob, SIGNAL(AlgorithmInfo(QString)), this, SLOT(OnAlgorithmInfo(QString))); connect(pJob, SIGNAL(AlgorithmStatusChanged(QString)), this, SLOT(OnAlgorithmStatusChanged(QString))); connect(pJob, SIGNAL(AlgorithmIterated(QString, bool, unsigned long)), this, SLOT(OnAlgorithmIterated(QString, bool, unsigned long))); connect(pJob, SIGNAL(LevelChanged(QString, bool, unsigned long)), this, SLOT(OnLevelChanged(QString, bool, unsigned long))); connect(pJob, SIGNAL(FrameRegistered(double)), this, SLOT(OnFrameRegistered(double))); connect(pJob, SIGNAL(FrameMapped(double)), this, SLOT(OnFrameMapped(double))); connect(pJob, SIGNAL(FrameProcessed(double)), this, SLOT(OnFrameProcessed(double))); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); } void QmitkMatchPointFrameCorrection::OnSaveLogBtnPushed() { QDateTime currentTime = QDateTime::currentDateTime(); QString fileName = tr("registration_log_") + currentTime.toString(tr("yyyy-MM-dd_hh-mm-ss")) + tr(".txt"); fileName = QFileDialog::getSaveFileName(nullptr, tr("Save registration log"), fileName, tr("Text files (*.txt)")); if (fileName.isEmpty()) { QMessageBox::critical(nullptr, tr("No file selected!"), tr("Cannot save registration log file. Please selected a file.")); } else { std::ofstream file; std::ios_base::openmode iOpenFlag = std::ios_base::out | std::ios_base::trunc; file.open(fileName.toStdString().c_str(), iOpenFlag); if (!file.is_open()) { mitkThrow() << "Cannot open or create specified file to save. File path: " << fileName.toStdString(); } file << this->m_Controls.m_teLog->toPlainText().toStdString() << std::endl; file.close(); } } void QmitkMatchPointFrameCorrection::OnRegJobError(QString err) { Error(err); }; void QmitkMatchPointFrameCorrection::OnRegJobFinished() { this->m_Working = false; auto* renderWindowPart = this->GetRenderWindowPart(); if (nullptr != renderWindowPart) renderWindowPart->RequestUpdate(); this->CheckInputs(); this->ConfigureRegistrationControls(); this->ConfigureProgressInfos(); }; void QmitkMatchPointFrameCorrection::OnMapResultIsAvailable(mitk::Image::Pointer spMappedData, const QmitkFramesRegistrationJob* job) { m_Controls.m_teLog->append(QString("Corrected image stored. Name: ") + QString::fromStdString(job->m_MappedName) + QString("")); mitk::DataNode::Pointer spResultNode = mitk::generateMappedResultNode(job->m_MappedName, spMappedData.GetPointer(), "", job->m_TargetDataUID, false, job->m_InterpolatorLabel); this->GetDataStorage()->Add(spResultNode, this->m_spSelectedTargetNode); auto* renderWindowPart = this->GetRenderWindowPart(); if (nullptr != renderWindowPart) renderWindowPart->RequestUpdate(); }; void QmitkMatchPointFrameCorrection::OnMapJobError(QString err) { Error(err); }; void QmitkMatchPointFrameCorrection::OnAlgorithmIterated(QString info, bool hasIterationCount, unsigned long currentIteration) { if (hasIterationCount) { m_Controls.m_progBarIteration->setValue(currentIteration); } m_Controls.m_teLog->append(info); }; void QmitkMatchPointFrameCorrection::OnLevelChanged(QString info, bool hasLevelCount, unsigned long currentLevel) { if (hasLevelCount) { m_Controls.m_progBarLevel->setValue(currentLevel); } m_Controls.m_teLog->append(QString("") + info + QString("")); }; void QmitkMatchPointFrameCorrection::OnAlgorithmStatusChanged(QString info) { m_Controls.m_teLog->append(QString("") + info + QString(" ")); }; void QmitkMatchPointFrameCorrection::OnAlgorithmInfo(QString info) { m_Controls.m_teLog->append(QString("") + info + QString("")); }; void QmitkMatchPointFrameCorrection::OnFrameProcessed(double progress) { m_Controls.m_teLog->append(QStringLiteral("Frame processed...")); m_Controls.m_progBarFrame->setValue(100 * progress); }; void QmitkMatchPointFrameCorrection::OnFrameRegistered(double progress) { m_Controls.m_teLog->append(QStringLiteral("Frame registered...")); m_Controls.m_progBarFrame->setValue(100 * progress); }; void QmitkMatchPointFrameCorrection::OnFrameMapped(double progress) { m_Controls.m_teLog->append(QStringLiteral("Frame mapped...")); m_Controls.m_progBarFrame->setValue(100 * progress); }; void QmitkMatchPointFrameCorrection::OnAlgorithmSelectionChanged(const berry::IWorkbenchPart::Pointer& sourcepart, const berry::ISelection::ConstPointer& selection) { // check for null selection if (selection.IsNull()) { return; } if (sourcepart != this) { UpdateAlgorithmSelection(selection); } } void QmitkMatchPointFrameCorrection::UpdateAlgorithmSelection(berry::ISelection::ConstPointer selection) { mitk::MAPAlgorithmInfoSelection::ConstPointer currentSelection = selection.Cast<const mitk::MAPAlgorithmInfoSelection>(); if (currentSelection) { mitk::MAPAlgorithmInfoSelection::AlgorithmInfoVectorType infoVector = currentSelection->GetSelectedAlgorithmInfo(); if (!infoVector.empty()) { // only the first selection is of interest, the rest will be skipped. this->m_SelectedAlgorithmInfo = infoVector[0]; } } this->OnSelectedAlgorithmChanged(); }; diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.cpp b/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.cpp index 3026cd148c..fd78a425ed 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.cpp +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.cpp @@ -1,559 +1,559 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "org_mitk_gui_qt_matchpoint_mapper_Activator.h" // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Mitk #include <mitkImageAccessByItk.h> #include <mitkStatusBar.h> #include "mitkImageMappingHelper.h" #include "mitkMAPRegistrationWrapper.h" #include "mitkMatchPointPropertyTags.h" #include "mitkRegistrationHelper.h" #include <mitkResultNodeGenerationHelper.h> #include <mitkUIDHelper.h> #include <mitkMAPAlgorithmHelper.h> #include <mitkResultNodeGenerationHelper.h> #include <mitkNodePredicateFunction.h> #include <mitkNodePredicateOr.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateDataProperty.h> // Qmitk #include "QmitkMatchPointMapper.h" // Qt #include <QMessageBox> #include <QFileDialog> #include <QErrorMessage> #include <QThreadPool> const std::string QmitkMatchPointMapper::VIEW_ID = "org.mitk.views.matchpoint.mapper"; QmitkMatchPointMapper::QmitkMatchPointMapper() : m_Parent(nullptr), m_preparedForBinaryInput(false) { } void QmitkMatchPointMapper::SetFocus() { //m_Controls.buttonPerformImageProcessing->setFocus(); } void QmitkMatchPointMapper::CreateConnections() { connect(m_Controls.registrationNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointMapper::OnRegNodeSelectionChanged); connect(m_Controls.inputNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointMapper::OnInputNodeSelectionChanged); connect(m_Controls.referenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointMapper::OnReferenceNodeSelectionChanged); connect(m_Controls.m_cbManualRef, SIGNAL(clicked()), this, SLOT(OnManualRefChecked())); connect(m_Controls.m_cbLinkFactors, SIGNAL(clicked()), this, SLOT(OnLinkSampleFactorChecked())); connect(m_Controls.m_sbXFactor, SIGNAL(valueChanged(double)), this, SLOT(OnXFactorChanged(double))); connect(m_Controls.m_pbMap, SIGNAL(clicked()), this, SLOT(OnMapBtnPushed())); connect(m_Controls.m_pbRefine, SIGNAL(clicked()), this, SLOT(OnRefineBtnPushed())); } void QmitkMatchPointMapper::Error(QString msg) { mitk::StatusBar::GetInstance()->DisplayErrorText(msg.toLatin1()); MITK_ERROR << msg.toStdString().c_str(); m_Controls.m_teLog->append(QStringLiteral("") + msg + QStringLiteral("")); } void QmitkMatchPointMapper::CreateQtPartControl(QWidget* parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Parent = parent; this->m_Controls.registrationNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.registrationNodeSelector->SetSelectionIsOptional(true); this->m_Controls.inputNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.inputNodeSelector->SetSelectionIsOptional(false); this->m_Controls.referenceNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.referenceNodeSelector->SetSelectionIsOptional(false); this->m_Controls.registrationNodeSelector->SetInvalidInfo("Select valid registration."); this->m_Controls.registrationNodeSelector->SetEmptyInfo("Assuming identity mapping. Select registration to change."); this->m_Controls.registrationNodeSelector->SetPopUpTitel("Select registration."); this->m_Controls.registrationNodeSelector->SetPopUpHint("Select a registration object that should be used for the mapping of the input data. If no registration is selected, identity will be assumed for the mapping."); this->m_Controls.inputNodeSelector->SetInvalidInfo("Select input data."); this->m_Controls.inputNodeSelector->SetPopUpTitel("Select input data."); this->m_Controls.inputNodeSelector->SetPopUpHint("Select the input data for the mapping. (Images or point sets are supported so far)."); this->m_Controls.referenceNodeSelector->SetInvalidInfo("Select the reference image."); this->m_Controls.referenceNodeSelector->SetPopUpTitel("Select the reference image."); - this->m_Controls.referenceNodeSelector->SetPopUpHint("Select the reference image that specifies the target geometrie the input should be mapped into."); + this->m_Controls.referenceNodeSelector->SetPopUpHint("Select the reference image that specifies the target geometry the input should be mapped into."); this->ConfigureRegNodePredicate(); this->ConfigureNodePredicates(); // show first page m_Controls.m_tabs->setCurrentIndex(0); this->CreateConnections(); this->CheckInputs(); this->ConfigureProgressInfos(); this->ConfigureMappingControls(); } /** Method checks if the currently selected reg node has a direct kernel that * can be decomposed in a rotation matrix and a offset. If this is true, true * is returned. In all other cases false is returned.*/ bool QmitkMatchPointMapper::IsAbleToRefineGeometry() const { bool result = false; if (this->m_spSelectedRegNode.IsNotNull()) { const mitk::MAPRegistrationWrapper* wrapper = dynamic_cast<const mitk::MAPRegistrationWrapper*> (this->m_spSelectedRegNode->GetData()); //if the helper does not return null, we can refine the geometry. result = mitk::MITKRegistrationHelper::getAffineMatrix(wrapper, false).IsNotNull(); } return result; } bool QmitkMatchPointMapper::IsBinaryInput() const { auto maskPredicate = mitk::MITKRegistrationHelper::MaskNodePredicate(); bool result = false; if(this->m_spSelectedInputNode.IsNotNull()) { result = maskPredicate->CheckNode(this->m_spSelectedInputNode); } return result; } bool QmitkMatchPointMapper::IsPointSetInput() const { bool result = false; if (this->m_spSelectedInputNode.IsNotNull()) { result = dynamic_cast<const mitk::PointSet*>(this->m_spSelectedInputNode->GetData()) != nullptr; } return result; } mitk::DataNode::Pointer QmitkMatchPointMapper::GetAutoRefNodeByReg() { mitk::DataNode::Pointer spResult = nullptr; if (this->m_spSelectedRegNode.IsNotNull() && this->m_spSelectedRegNode->GetData()) { std::string nodeName; mitk::BaseProperty* uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgTargetData); if (uidProp) { //search for the target node mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID, uidProp); spResult = this->GetDataStorage()->GetNode(predicate); } } if (spResult.IsNull() && this->m_spSelectedInputNode.IsNotNull()) { //no really reference is available -> use the input as reference spResult = this->m_spSelectedInputNode; if (this->m_spSelectedRefNode != spResult) { m_Controls.m_teLog->append( QStringLiteral("Cannot determine reference automatically. Use input image as reference.")); } } return spResult; } void QmitkMatchPointMapper::ConfigureRegNodePredicate(const mitk::DataNode* input) { mitk::NodePredicateBase::ConstPointer nodePredicate = mitk::MITKRegistrationHelper::RegNodePredicate(); if (input != nullptr) { unsigned int dimension = 0; auto inputImage = dynamic_cast<mitk::Image*>(input->GetData()); auto pointset = dynamic_cast<const mitk::PointSet*>(input->GetData()); if (inputImage) { dimension = inputImage->GetDimension(); if (inputImage->GetTimeSteps() > 1) { //images has multiple time steps -> remove one dimension. dimension -= 1; } } else if (pointset) { dimension = 3; } auto dimCheck = [dimension](const mitk::DataNode * node) { const mitk::MAPRegistrationWrapper* wrapper = dynamic_cast < const mitk::MAPRegistrationWrapper* >(node->GetData()); return wrapper != nullptr && wrapper->GetMovingDimensions() == dimension; }; mitk::NodePredicateFunction::Pointer hasCorrectDim = mitk::NodePredicateFunction::New(dimCheck); nodePredicate = mitk::NodePredicateAnd::New(nodePredicate, hasCorrectDim).GetPointer(); } this->m_Controls.registrationNodeSelector->SetNodePredicate(nodePredicate); } std::function<bool(const mitk::DataNode *)> GenerateDimCheckLambda(unsigned int dim) { auto dimCheck = [dim](const mitk::DataNode * node) { auto inputImage = dynamic_cast<mitk::Image*>(node->GetData()); return inputImage != nullptr && (inputImage->GetDimension() == dim || (inputImage->GetDimension() == dim + 1 && inputImage->GetTimeSteps()>1)); }; return dimCheck; } void QmitkMatchPointMapper::ConfigureNodePredicates(const mitk::DataNode* reg) { auto isImage = mitk::MITKRegistrationHelper::ImageNodePredicate(); auto isPointSet = mitk::MITKRegistrationHelper::PointSetNodePredicate(); auto isData = mitk::NodePredicateOr::New(isImage, isPointSet); mitk::NodePredicateBase::ConstPointer inputPredicate = isData.GetPointer(); mitk::NodePredicateBase::ConstPointer refPredicate = isImage.GetPointer(); if (reg != nullptr) { const mitk::MAPRegistrationWrapper* wrapper = dynamic_cast <const mitk::MAPRegistrationWrapper*>(reg->GetData()); if (wrapper != nullptr) { auto movingDim = wrapper->GetMovingDimensions(); auto dimCheck = GenerateDimCheckLambda(movingDim); auto hasCorrectDim = mitk::NodePredicateFunction::New(dimCheck); if (movingDim == 3) { //Remark: Point sets are always 3D auto is3DInput = mitk::NodePredicateOr::New(isPointSet, mitk::NodePredicateAnd::New(isImage, hasCorrectDim)); inputPredicate = is3DInput.GetPointer(); } else { auto is2DInput = mitk::NodePredicateAnd::New(isImage, hasCorrectDim); inputPredicate = is2DInput.GetPointer(); } auto targetDim = wrapper->GetTargetDimensions(); auto targetDimCheck = GenerateDimCheckLambda(targetDim); auto hasCorrectTargetDim = mitk::NodePredicateFunction::New(targetDimCheck); auto isRef = mitk::NodePredicateAnd::New(isImage, hasCorrectTargetDim); refPredicate = isRef; } } this->m_Controls.inputNodeSelector->SetNodePredicate(inputPredicate); this->m_Controls.referenceNodeSelector->SetNodePredicate(refPredicate); } void QmitkMatchPointMapper::CheckInputs() { this->m_spSelectedRegNode = this->m_Controls.registrationNodeSelector->GetSelectedNode(); this->m_spSelectedInputNode = this->m_Controls.inputNodeSelector->GetSelectedNode(); this->m_spSelectedRefNode = this->m_Controls.referenceNodeSelector->GetSelectedNode(); if (!(m_Controls.m_cbManualRef->isChecked())) { auto autoRefNode = this->GetAutoRefNodeByReg(); if (this->m_spSelectedRefNode != autoRefNode) { this->m_spSelectedRefNode = autoRefNode; QmitkSingleNodeSelectionWidget::NodeList selection; if (this->m_spSelectedRefNode.IsNotNull()) { selection.append(this->m_spSelectedRefNode); } this->m_Controls.referenceNodeSelector->SetCurrentSelection(selection); } } if (this->m_spSelectedRefNode.IsNotNull() && this->m_spSelectedRefNode->GetData() && this->m_spSelectedRefNode->GetData()->GetTimeSteps() > 1) { m_Controls.m_teLog->append( QStringLiteral("Selected reference image has multiple time steps. Only geometry of time step 1 is used as reference.")); } } void QmitkMatchPointMapper::ConfigureMappingControls() { bool validInput = m_spSelectedInputNode.IsNotNull(); bool validRef = m_spSelectedRefNode.IsNotNull(); this->m_Controls.referenceNodeSelector->setEnabled(this->m_Controls.m_cbManualRef->isChecked()); this->m_Controls.m_pbMap->setEnabled(validInput && validRef); this->m_Controls.m_pbRefine->setEnabled(validInput && this->IsAbleToRefineGeometry() && !this->IsPointSetInput()); if (validInput) { if (m_spSelectedRegNode.IsNotNull()) { this->m_Controls.m_leMappedName->setText(tr("mapped_") + QString::fromStdString(m_spSelectedInputNode->GetName()) + tr("_by_") + QString::fromStdString(m_spSelectedRegNode->GetName())); } else { this->m_Controls.m_leMappedName->setText(tr("resampled_") + QString::fromStdString(m_spSelectedInputNode->GetName())); } } else { this->m_Controls.m_leMappedName->setText(tr("mappedData")); } if (this->IsBinaryInput() != this->m_preparedForBinaryInput) { if (this->IsBinaryInput()) { m_Controls.m_teLog->append( - QStringLiteral("Binary input (mask) detected. Preparing for mask mapping (default interpolation: nearest neigbour; padding value: 0)")); + QStringLiteral("Binary input (mask) detected. Preparing for mask mapping (default interpolation: nearest neighbour; padding value: 0)")); this->m_Controls.m_comboInterpolator->setCurrentIndex(0); this->m_Controls.m_sbErrorValue->setValue(0); this->m_Controls.m_sbPaddingValue->setValue(0); } else { this->m_Controls.m_comboInterpolator->setCurrentIndex(1); } this->m_preparedForBinaryInput = this->IsBinaryInput(); } OnLinkSampleFactorChecked(); } void QmitkMatchPointMapper::ConfigureProgressInfos() { } void QmitkMatchPointMapper::OnRegNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes) { mitk::DataNode::Pointer regNode; if (!nodes.isEmpty()) { regNode = nodes.front(); } this->ConfigureNodePredicates(regNode); this->CheckInputs(); this->ConfigureMappingControls(); } void QmitkMatchPointMapper::OnInputNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes) { mitk::DataNode::Pointer inputNode; if (!nodes.isEmpty()) { inputNode = nodes.front(); } this->ConfigureRegNodePredicate(inputNode); this->CheckInputs(); this->ConfigureMappingControls(); } void QmitkMatchPointMapper::OnReferenceNodeSelectionChanged(QList<mitk::DataNode::Pointer> /*nodes*/) { this->CheckInputs(); this->ConfigureMappingControls(); } void QmitkMatchPointMapper::OnManualRefChecked() { this->CheckInputs(); this->ConfigureMappingControls(); } void QmitkMatchPointMapper::OnLinkSampleFactorChecked() { this->m_Controls.m_sbYFactor->setEnabled(!(this->m_Controls.m_cbLinkFactors->isChecked())); this->m_Controls.m_sbZFactor->setEnabled(!(this->m_Controls.m_cbLinkFactors->isChecked())); if (m_Controls.m_cbLinkFactors->isChecked()) { this->m_Controls.m_sbYFactor->setValue(this->m_Controls.m_sbXFactor->value()); this->m_Controls.m_sbZFactor->setValue(this->m_Controls.m_sbXFactor->value()); } } void QmitkMatchPointMapper::OnMapBtnPushed() { SpawnMappingJob(); } void QmitkMatchPointMapper::OnRefineBtnPushed() { SpawnMappingJob(true); } void QmitkMatchPointMapper::SpawnMappingJob(bool doGeometryRefinement) { if (m_Controls.m_checkClearLog->checkState() == Qt::Checked) { this->m_Controls.m_teLog->clear(); } ///////////////////////// //create job and put it into the thread pool QmitkMappingJob* pJob = new QmitkMappingJob(); pJob->setAutoDelete(true); pJob->m_spInputData = this->m_spSelectedInputNode->GetData(); pJob->m_InputDataUID = mitk::EnsureUID(this->m_spSelectedInputNode->GetData()); pJob->m_doGeometryRefinement = doGeometryRefinement; pJob->m_spRegNode = m_spSelectedRegNode; if (m_spSelectedRegNode.IsNull()) { pJob->m_spRegNode = mitk::DataNode::New(); pJob->m_spRegNode->SetData(mitk::GenerateIdentityRegistration3D().GetPointer()); pJob->m_spRegNode->SetName("Auto_Generated_Identity_Transform"); m_Controls.m_teLog->append( QStringLiteral("No registration selected. Preforming mapping with identity transform")); } if (!doGeometryRefinement) { pJob->m_spRefGeometry = m_spSelectedRefNode->GetData()->GetGeometry()->Clone().GetPointer(); //check for super/sub sampling if (m_Controls.m_groupActivateSampling->isChecked()) { pJob->m_spRefGeometry = mitk::ImageMappingHelper::GenerateSuperSampledGeometry(pJob->m_spRefGeometry, m_Controls.m_sbXFactor->value(), m_Controls.m_sbYFactor->value(), m_Controls.m_sbZFactor->value()); } } pJob->m_MappedName = m_Controls.m_leMappedName->text().toStdString(); pJob->m_allowUndefPixels = m_Controls.m_groupAllowUndefPixels->isChecked(); pJob->m_paddingValue = m_Controls.m_sbPaddingValue->value(); pJob->m_allowUnregPixels = m_Controls.m_groupAllowUnregPixels->isChecked(); pJob->m_errorValue = m_Controls.m_sbErrorValue->value(); pJob->m_InterpolatorLabel = m_Controls.m_comboInterpolator->currentText().toStdString(); switch (m_Controls.m_comboInterpolator->currentIndex()) { case 0: pJob->m_InterpolatorType = mitk::ImageMappingInterpolator::NearestNeighbor; break; case 1: pJob->m_InterpolatorType = mitk::ImageMappingInterpolator::Linear; break; case 2: pJob->m_InterpolatorType = mitk::ImageMappingInterpolator::BSpline_3; break; case 3: pJob->m_InterpolatorType = mitk::ImageMappingInterpolator::WSinc_Hamming; break; case 4: pJob->m_InterpolatorType = mitk::ImageMappingInterpolator::WSinc_Welch; break; } connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnMapJobError(QString))); connect(pJob, SIGNAL(MapResultIsAvailable(mitk::BaseData::Pointer, const QmitkMappingJob*)), this, SLOT(OnMapResultIsAvailable(mitk::BaseData::Pointer, const QmitkMappingJob*)), Qt::BlockingQueuedConnection); connect(pJob, SIGNAL(AlgorithmInfo(QString)), this, SLOT(OnMappingInfo(QString))); m_Controls.m_teLog->append(QStringLiteral("Started mapping job. Name: ") + m_Controls.m_leMappedName->text() + QStringLiteral("")); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); } void QmitkMatchPointMapper::OnMapJobError(QString err) { Error(err); } void QmitkMatchPointMapper::OnMapResultIsAvailable(mitk::BaseData::Pointer spMappedData, const QmitkMappingJob* job) { m_Controls.m_teLog->append(QStringLiteral("Mapped entity stored. Name: ") + QString::fromStdString(job->m_MappedName) + QStringLiteral("")); mitk::DataNode::Pointer spMappedNode = mitk::generateMappedResultNode(job->m_MappedName, spMappedData, job->GetRegistration()->getRegistrationUID(), job->m_InputDataUID, job->m_doGeometryRefinement, job->m_InterpolatorLabel); this->GetDataStorage()->Add(spMappedNode); auto* renderWindowPart = this->GetRenderWindowPart(); if (nullptr != renderWindowPart) renderWindowPart->RequestUpdate(); this->CheckInputs(); this->ConfigureMappingControls(); } void QmitkMatchPointMapper::OnMappingInfo(QString info) { m_Controls.m_teLog->append(QStringLiteral("") + info + QStringLiteral("")); } void QmitkMatchPointMapper::OnXFactorChanged(double d) { if (m_Controls.m_cbLinkFactors->isChecked()) { this->m_Controls.m_sbYFactor->setValue(d); this->m_Controls.m_sbZFactor->setValue(d); } } diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.h b/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.h index 2b39adbb9f..5e2e880d13 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.h +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.h @@ -1,157 +1,157 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMatchPointMapper_h #define QmitkMatchPointMapper_h #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include <QSortFilterProxyModel> #include "ui_QmitkMatchPointMapper.h" #include "QmitkMappingJob.h" /*! \brief QmitkMatchPointMapper View class that implements the logic/functionality to map point sets or images based on MatchPoint registration objects. \ingroup ${plugin_target}_internal */ class QmitkMatchPointMapper : public QmitkAbstractView { Q_OBJECT public: static const std::string VIEW_ID; /** * Creates smartpointer typedefs */ berryObjectMacro(QmitkMatchPointMapper); QmitkMatchPointMapper(); void CreateQtPartControl(QWidget *parent) override; protected slots: /** * @brief Connect all GUI elements to its corresponding slots */ virtual void CreateConnections(); void OnManualRefChecked(); void OnLinkSampleFactorChecked(); void OnXFactorChanged(double d); void OnMapBtnPushed(); void OnRefineBtnPushed(); void OnMapJobError(QString err); void OnMapResultIsAvailable(mitk::BaseData::Pointer spMappedData, const QmitkMappingJob* job); void OnMappingInfo(QString info); void OnRegNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes); void OnInputNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes); void OnReferenceNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes); protected: void SetFocus() override; Ui::MatchPointMapperControls m_Controls; private: QWidget *m_Parent; void Error(QString msg); /** Method checks if the currently selected reg node has a direct kernel that * can be decomposed in a rotation matrix and a offset. If this is true, true * is returned. In all other cases false is returned.*/ bool IsAbleToRefineGeometry() const; /** Method checks if the currently selected input is a binary image (property binary == true). * If this is true, true is returned. In all other cases false is returned.*/ bool IsBinaryInput() const; /** Method checks if the currently selected input is a point set. * If this is true, true is returned. In all other cases false is returned.*/ bool IsPointSetInput() const; /** If a registration node is set, this function determines the auto reference node. * The auto reference node is the node of the target data used to determine the * registration object or, if the first cannot be determined, the currently selected input * node. * @return Pointer to the reference node (target data of the registration algorithm run). * Function may return nullptr if the referenced node cannot be found or is not defined * by the registration.*/ mitk::DataNode::Pointer GetAutoRefNodeByReg(); /** * Checks if appropriated nodes are selected in the data manager. If nodes are selected, * they are stored m_spSelectedRegNode, m_spSelectedInputNode and m_spSelectedRefNode. * They are also checked for vadility and stored in m_ValidInput,... . - * It also sets the info lables accordingly.*/ + * It also sets the info labels accordingly.*/ void CheckInputs(); /** Methods checks the validity of the currently stored * m_spSelectedRegNode, m_spSelectedInputNode and m_spSelectedRefNode. * Results are returned via the parameters. Details of the evaluation are * printed to the log widget.*/ void CheckNodesValidity(bool& validReg, bool& validInput, bool& validRef); /** * Updates the state of mapping control button regarding to selected * input, registration and reference.*/ void ConfigureMappingControls(); /** - * Configures the progress bars accoarding to the choosen algorithm. + * Configures the progress bars accoarding to the chosen algorithm. */ void ConfigureProgressInfos(); /** Configure the reg node selector predicates. If a input pointer is passed, the predicate will be configured according to the input. */ void ConfigureRegNodePredicate(const mitk::DataNode* input = nullptr); /** Configure the input and ref node selector predicates. If a reg pointer is passed, the predicate will be configured according to the input. */ void ConfigureNodePredicates(const mitk::DataNode* reg = nullptr); /** * Used to generate, configure and execute a mapping job regarding the * current settings. * @param doGeometryRefinement Set true if only a geometry refinement should be done. * Set to false if a mapping/resampling of the input should be done.*/ void SpawnMappingJob(bool doGeometryRefinement = false); mitk::DataNode::Pointer m_spSelectedRegNode; mitk::DataNode::Pointer m_spSelectedInputNode; mitk::DataNode::Pointer m_spSelectedRefNode; /** used for the internal logic to indicate of the current settings are set for mapping binary images (used by ConfigureMappingControls()).*/ bool m_preparedForBinaryInput; }; #endif diff --git a/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.ui b/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.ui index a1da741298..380289d0e9 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.ui +++ b/Plugins/org.mitk.gui.qt.matchpoint.mapper/src/internal/QmitkMatchPointMapper.ui @@ -1,565 +1,565 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>MatchPointMapperControls</class> <widget class="QWidget" name="MatchPointMapperControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>392</width> <height>816</height> </rect> </property> <layout class="QVBoxLayout" name="verticalLayout"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_4"> <property name="text"> <string>Selected registration:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <property name="spacing"> <number>3</number> </property> <item> <widget class="QmitkSingleNodeSelectionWidget" name="registrationNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="label_5"> <property name="text"> <string>Input data (images or point sets):</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <property name="spacing"> <number>3</number> </property> <item> <widget class="QmitkSingleNodeSelectionWidget" name="inputNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="m_cbManualRef"> <property name="toolTip"> <string>Select reference manually instat of determined by registration...</string> </property> <property name="text"> <string>Select reference image manually:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <property name="spacing"> <number>3</number> </property> <item> <widget class="QmitkSingleNodeSelectionWidget" name="referenceNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <widget class="QTabWidget" name="m_tabs"> <property name="enabled"> <bool>true</bool> </property> <property name="currentIndex"> <number>0</number> </property> <property name="documentMode"> <bool>false</bool> </property> <property name="tabsClosable"> <bool>false</bool> </property> <property name="movable"> <bool>false</bool> </property> <widget class="QWidget" name="m_tabExecution"> <attribute name="title"> <string>Execution</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_2"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_9"> <property name="text"> <string>Mapped data name:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="m_leMappedName"> <property name="toolTip"> <string>Name of the resulting mapped image</string> </property> <property name="text"> <string>mappedImage</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <item> <widget class="QPushButton" name="m_pbMap"> <property name="toolTip"> <string><html><head/><body>Starts the mapping of the input image with the current settings.</body></html></string> </property> <property name="text"> <string>Map</string> </property> </widget> </item> <item> <widget class="QPushButton" name="m_pbRefine"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> - <string><html><head/><body>Applys the registration by refining the geometry of the data and not by resampling it. This option can only be selected if the chosen registration is 3D and can be decomposed in a rotation matrix and offset.</body></html></string> + <string><html><head/><body>Applies the registration by refining the geometry of the data and not by resampling it. This option can only be selected if the chosen registration is 3D and can be decomposed in a rotation matrix and offset.</body></html></string> </property> <property name="text"> <string>Refine geometry</string> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="label_log"> <property name="text"> <string>Log:</string> </property> </widget> </item> <item> <widget class="QTextEdit" name="m_teLog"> <property name="font"> <pointsize>9</pointsize> </property> <property name="tabChangesFocus"> <bool>true</bool> </property> <property name="lineWrapMode"> <enum>QTextEdit::NoWrap</enum> </property> <property name="readOnly"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QCheckBox" name="m_checkClearLog"> <property name="text"> <string>Clear log on mapping start</string> </property> </widget> </item> </layout> </widget> <widget class="QWidget" name="m_tabSettings"> <attribute name="title"> <string>Settings</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_3"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QGroupBox" name="m_groupAllowUndefPixels"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>50</weight> <bold>false</bold> </property> <property name="toolTip"> <string><html><head/><body>Allows that pixels may not be defined in the mapped image because they are outside of the field of view of the used input image.The pixels will be marked with the given padding value.If unchecked the mapping will be aborted in a case of undefined pixels.</body></html></string> </property> <property name="title"> <string>Allow undefined pixels</string> </property> <property name="flat"> <bool>false</bool> </property> <property name="checkable"> <bool>true</bool> </property> <layout class="QHBoxLayout" name="horizontalLayout_6"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>9</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>9</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_7"> <property name="text"> <string>Padding value:</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_sbPaddingValue"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="toolTip"> <string>Pixel value that indicates pixels that are outside of the input image</string> </property> <property name="minimum"> <number>-5000</number> </property> <property name="maximum"> <number>5000</number> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="m_groupAllowUnregPixels"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>50</weight> <bold>false</bold> </property> <property name="toolTip"> - <string><html><head/><body>Allows that pixels may not be registred because they are outside of the field of view of the used registration. The location in the correlated input image pixel(s) are therefore unkown. The pixels will be marked witrh the given error value.If unchecked the mapping will be aborted in a case of unregistered pixels.</body></html></string> + <string><html><head/><body>Allows that pixels may not be registered because they are outside of the field of view of the used registration. The location in the correlated input image pixel(s) are therefore unknown. The pixels will be marked with the given error value.If unchecked the mapping will be aborted in a case of unregistered pixels.</body></html></string> </property> <property name="title"> <string>Allow unregistered pixels</string> </property> <property name="flat"> <bool>false</bool> </property> <property name="checkable"> <bool>true</bool> </property> <layout class="QHBoxLayout" name="horizontalLayout_7"> <property name="spacing"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_6"> <property name="text"> <string>Error value:</string> </property> </widget> </item> <item> <widget class="QSpinBox" name="m_sbErrorValue"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="toolTip"> - <string><html><head/><body>Value of pixels that cannot be registered because of an unsufficient field of view of the selected registration instance.</body></html></string> + <string><html><head/><body>Value of pixels that cannot be registered because of an insufficient field of view of the selected registration instance.</body></html></string> </property> <property name="minimum"> <number>-5000</number> </property> <property name="maximum"> <number>5000</number> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QLabel" name="label_8"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Interpolator:</string> </property> </widget> </item> <item> <widget class="QComboBox" name="m_comboInterpolator"> <property name="enabled"> <bool>true</bool> </property> <property name="toolTip"> <string><html><head/><body>Interpolation function that should be used to map the pixel values from the input image into the result image.</body></html></string> </property> <property name="currentIndex"> <number>1</number> </property> <item> <property name="text"> <string>Nearest Neighbor</string> </property> </item> <item> <property name="text"> <string>Linear</string> </property> </item> <item> <property name="text"> <string>BSpline (3rd order)</string> </property> </item> <item> <property name="text"> <string>Windowed Sinc (Hamming)</string> </property> </item> <item> <property name="text"> <string>Windowed Sinc (Welch)</string> </property> </item> </widget> </item> <item> <widget class="QGroupBox" name="m_groupActivateSampling"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="title"> <string>Activate super/sub sampling</string> </property> <property name="checkable"> <bool>true</bool> </property> <property name="checked"> <bool>false</bool> </property> <layout class="QVBoxLayout" name="verticalLayout_4"> <property name="spacing"> <number>5</number> </property> <item> <widget class="QCheckBox" name="m_cbLinkFactors"> <property name="toolTip"> <string><html><head/><body>Check to ensure that x, y and z dimension use the same sampling factor.</body></html></string> </property> <property name="text"> <string>linked factors</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_8"> <item> <widget class="QLabel" name="label_10"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>x:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbXFactor"> <property name="toolTip"> <string><html><head/><body>Indicate the sampling factor to change the resolution.2.0: doubled resolution; e.g. 100 pixels -> 200 pixels and spacing 1 -> spacing 0.50.5: half resolution; e.g. 100 pixels -> 50 pixels and spacing 1 -> spacing 2</body></html></string> </property> </widget> </item> <item> <widget class="QLabel" name="label_12"> <property name="text"> <string>y:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbYFactor"/> </item> <item> <widget class="QLabel" name="label_11"> <property name="text"> <string>z:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbZFactor"/> </item> </layout> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Preferred</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>700</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> <container>1</container> </customwidget> </customwidgets> <resources/> <connections/> <designerdata> <property name="gridDeltaX"> <number>5</number> </property> <property name="gridDeltaY"> <number>5</number> </property> <property name="gridSnapX"> <bool>true</bool> </property> <property name="gridSnapY"> <bool>true</bool> </property> <property name="gridVisible"> <bool>true</bool> </property> </designerdata> </ui> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg index 22ad383050..9711f6cfdf 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_grid_settings.svg @@ -1,379 +1,379 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?>  <svg xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" version="1.1" id="svg4485" width="804.48956" height="124" viewBox="0 0 804.48956 124" sodipodi:docname="map_view_visualizer_grid_settings.svg" inkscape:version="0.92.3 (2405546, 2018-03-11)" inkscape:export-filename="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_vis_settings.png" inkscape:export-xdpi="96" inkscape:export-ydpi="96"> <metadata id="metadata4491"> <rdf:RDF> <cc:Work rdf:about=""> <dc:format>image/svg+xml</dc:format> <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage" /> <dc:title /> </cc:Work> </rdf:RDF> </metadata> <defs id="defs4489"> <marker inkscape:isstock="true" style="overflow:visible" id="marker5562" refX="0" refY="0" orient="auto" inkscape:stockid="DotS"> <path transform="matrix(0.2,0,0,0.2,1.48,0.2)" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" id="path5560" inkscape:connector-curvature="0" /> </marker> <marker inkscape:isstock="true" style="overflow:visible" id="marker5474" refX="0" refY="0" orient="auto" inkscape:stockid="DotS"> <path transform="matrix(0.2,0,0,0.2,1.48,0.2)" style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" id="path5472" inkscape:connector-curvature="0" /> </marker> <marker inkscape:stockid="DotM" orient="auto" refY="0" refX="0" id="marker4945" style="overflow:visible" inkscape:isstock="true"> <path id="path4943" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.4,0,0,0.4,2.96,0.4)" inkscape:connector-curvature="0" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="DotS" style="overflow:visible" inkscape:isstock="true"> <path id="path4564" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" inkscape:connector-curvature="0" /> </marker> <marker inkscape:stockid="DotM" orient="auto" refY="0" refX="0" id="DotM" style="overflow:visible" inkscape:isstock="true"> <path id="path4561" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.4,0,0,0.4,2.96,0.4)" inkscape:connector-curvature="0" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-6" style="overflow:visible" inkscape:isstock="true" inkscape:collect="always"> <path inkscape:connector-curvature="0" id="path5279-4" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-5" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-0" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-0" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-3" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-01" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-7" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-9" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-1" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:isstock="true" style="overflow:visible" id="marker5562-8" refX="0" refY="0" orient="auto" inkscape:stockid="DotS"> <path transform="matrix(0.2,0,0,0.2,1.48,0.2)" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" id="path5560-3" inkscape:connector-curvature="0" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-9-8" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-1-6" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-3" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-31" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> <marker inkscape:stockid="DotS" orient="auto" refY="0" refX="0" id="marker5281-0-4" style="overflow:visible" inkscape:isstock="true"> <path inkscape:connector-curvature="0" id="path5279-5-16" d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z" style="fill:#ff0000;fill-opacity:1;fill-rule:evenodd;stroke:#ff0000;stroke-width:1.00000003pt;stroke-opacity:1" transform="matrix(0.2,0,0,0.2,1.48,0.2)" /> </marker> </defs> <sodipodi:namedview pagecolor="#ffffff" bordercolor="#666666" borderopacity="1" objecttolerance="10" gridtolerance="10" guidetolerance="10" inkscape:pageopacity="0" inkscape:pageshadow="2" inkscape:window-width="1680" inkscape:window-height="987" id="namedview4487" showgrid="false" inkscape:zoom="1" inkscape:cx="226.92706" inkscape:cy="7.1012534" inkscape:window-x="-8" inkscape:window-y="-8" inkscape:window-maximized="1" inkscape:current-layer="svg4485" /> <image sodipodi:absref="D:\Dev\MITK\sMaster\Plugins\org.mitk.gui.qt.matchpoint.visualizer\documentation\UserManual\map_view_visualizer_grid_settings_raw.png" xlink:href="map_view_visualizer_grid_settings_raw.png" y="0" x="0" id="image4493" preserveAspectRatio="none" height="124" width="329" mask="none" /> <path style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-6)" d="M 224.61004,71.1402 H 335.6722 331.70571" id="path4495-3" inkscape:connector-curvature="0" /> <path style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-9)" d="M 147.02514,44.4793 H 335.6722 328.93484" id="path4495-7-6" inkscape:connector-curvature="0" /> <text xml:space="preserve" style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none" x="338.88538" y="50.520752" id="text9677-5"><tspan sodipodi:role="line" id="tspan9675-8" x="338.88538" y="50.520752" - style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(9) Set freqency of visible gride frames</tspan></text> + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(9) Set frequency of visible grid frames</tspan></text> <text xml:space="preserve" style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none" x="338.88538" y="77.520752" id="text9677-1"><tspan sodipodi:role="line" id="tspan9675-1" x="338.88538" y="77.520752" style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(10) Visibility of start grid of the mapping direction</tspan></text> <flowRoot xml:space="preserve" id="flowRoot4717" style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1" transform="translate(0,-393)"><flowRegion id="flowRegion4719"><rect id="rect4721" width="337" height="48" x="353" y="188" /></flowRegion><flowPara id="flowPara4723" /></flowRoot> <path style="fill:#ff0000;stroke:#ff0000;stroke-width:5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-start:url(#marker5281-0-4)" d="M 105.40533,98.0047 H 335.6722 327.44843" id="path4495-7-5" inkscape:connector-curvature="0" /> <text xml:space="preserve" style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#ff0000;fill-opacity:1;stroke:none" x="338.88538" y="103.521" id="text9677-09-9"><tspan sodipodi:role="line" id="tspan9675-0-2" x="338.88538" y="103.521" style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000">(11) Color of the start grid</tspan><tspan sodipodi:role="line" x="338.88538" y="153.521" style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:21.33333397px;font-family:Arial;-inkscape-font-specification:Arial;fill:#ff0000" id="tspan4725-7" /></text> <flowRoot xml:space="preserve" id="flowRoot6290" style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1" transform="translate(0,-392)"><flowRegion id="flowRegion6292"><rect id="rect6294" width="839" height="562" x="-158" y="273" /></flowRegion><flowPara id="flowPara6296" /></flowRoot> <flowRoot xml:space="preserve" id="flowRoot6719" style="font-style:normal;font-weight:normal;font-size:40px;line-height:1.25;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"><flowRegion id="flowRegion6721"><rect id="rect6723" width="620" height="252" x="-129" y="-103" /></flowRegion><flowPara id="flowPara6725" /></flowRoot></svg> diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp index 9f9ea6f8ac..3ef952d07d 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.cpp @@ -1,798 +1,798 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "org_mitk_gui_qt_matchpoint_visualizer_Activator.h" // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Mitk #include <mitkStatusBar.h> #include <mitkProperties.h> #include <mitkColorProperty.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateDataProperty.h> #include <mitkNodePredicateFunction.h> #include "mitkRegVisDirectionProperty.h" #include "mitkRegVisStyleProperty.h" #include "mitkRegVisColorStyleProperty.h" #include "mitkRegVisPropertyTags.h" #include "mitkRegVisHelper.h" #include "mitkMatchPointPropertyTags.h" #include "mitkRegistrationHelper.h" // Qmitk #include "QmitkMatchPointRegistrationVisualizer.h" // Qt #include <QMessageBox> #include <QErrorMessage> const std::string QmitkMatchPointRegistrationVisualizer::VIEW_ID = "org.mitk.views.matchpoint.visualizer"; QmitkMatchPointRegistrationVisualizer::QmitkMatchPointRegistrationVisualizer() : m_Parent(nullptr), m_internalUpdateGuard(false), m_spSelectedFOVRefNode(nullptr), m_spSelectedRegNode(nullptr) { } void QmitkMatchPointRegistrationVisualizer::SetFocus() { } void QmitkMatchPointRegistrationVisualizer::CreateConnections() { connect(m_Controls->registrationNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationVisualizer::OnNodeSelectionChanged); connect(m_Controls->fovReferenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationVisualizer::OnNodeSelectionChanged); connect(m_Controls->m_pbStyleGrid, SIGNAL(clicked()), this, SLOT(OnStyleButtonPushed())); connect(m_Controls->m_pbStyleGlyph, SIGNAL(clicked()), this, SLOT(OnStyleButtonPushed())); connect(m_Controls->m_pbStylePoints, SIGNAL(clicked()), this, SLOT(OnStyleButtonPushed())); connect(m_Controls->m_comboDirection, SIGNAL(currentIndexChanged(int)), this, SLOT(OnDirectionChanged(int))); connect(m_Controls->m_pbUpdateViz, SIGNAL(clicked()), this, SLOT(OnUpdateBtnPushed())); connect(m_Controls->radioColorUni, SIGNAL(toggled(bool)), m_Controls->btnUniColor, SLOT(setEnabled(bool))); connect(m_Controls->radioColorVecMag, SIGNAL(toggled(bool)), m_Controls->groupColorCoding, SLOT(setEnabled(bool))); connect(m_Controls->m_pbStyleGrid, SIGNAL(toggled(bool)), m_Controls->tabGrid, SLOT(setEnabled(bool))); connect(m_Controls->cbVevMagInterlolate, SIGNAL(toggled(bool)), this, SLOT(OnColorInterpolationChecked(bool))); connect(m_Controls->m_checkUseRefSize, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry())); connect(m_Controls->m_checkUseRefSpacing, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry())); connect(m_Controls->m_checkUseRefOrigin, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry())); connect(m_Controls->m_checkUseRefOrientation, SIGNAL(clicked()), this, SLOT(TransferFOVRefGeometry())); } void QmitkMatchPointRegistrationVisualizer::Error(QString msg) { mitk::StatusBar::GetInstance()->DisplayErrorText(msg.toLatin1()); MITK_ERROR << msg.toStdString().c_str(); } void QmitkMatchPointRegistrationVisualizer::CreateQtPartControl(QWidget* parent) { m_Controls = new Ui::MatchPointRegVisControls; // create GUI widgets from the Qt Designer's .ui file m_Controls->setupUi(parent); m_Parent = parent; this->m_Controls->registrationNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls->registrationNodeSelector->SetSelectionIsOptional(false); this->m_Controls->fovReferenceNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls->fovReferenceNodeSelector->SetSelectionIsOptional(false); m_Controls->registrationNodeSelector->SetInvalidInfo("Select registration."); m_Controls->registrationNodeSelector->SetPopUpTitel("Select registration."); m_Controls->registrationNodeSelector->SetPopUpHint("Select the registration object whose registration visualization should be edited."); m_Controls->fovReferenceNodeSelector->SetInvalidInfo("Select a FOV reference image."); m_Controls->fovReferenceNodeSelector->SetPopUpTitel("Select a FOV reference image."); m_Controls->fovReferenceNodeSelector->SetPopUpHint("Select the the image that should be used to define the field of view (FOV) for the registration visualization. The visualization will use the image geometry (size, orientation, spacing...)."); this->ConfigureNodePredicates(); this->m_Controls->btnVecMagColorSmall->setDisplayColorName(false); this->m_Controls->btnVecMagColorMedium->setDisplayColorName(false); this->m_Controls->btnVecMagColorLarge->setDisplayColorName(false); this->m_Controls->btnVecMagColorNeg->setDisplayColorName(false); this->m_Controls->btnUniColor->setDisplayColorName(false); this->m_Controls->btnStartGridColor->setDisplayColorName(false); this->CreateConnections(); this->m_Controls->radioColorUni->setChecked(false); this->m_Controls->radioColorVecMag->setChecked(true); this->CheckInputs(); this->LoadStateFromNode(); this->ConfigureVisualizationControls(); //deactivate because currently not an implemented style this->m_Controls->m_pbStylePoints->setVisible(false); } void QmitkMatchPointRegistrationVisualizer::ConfigureNodePredicates() { m_Controls->registrationNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::RegNodePredicate()); auto geometryCheck = [](const mitk::DataNode * node) { return node->GetData() && node->GetData()->GetGeometry(); }; mitk::NodePredicateFunction::Pointer hasGeometry = mitk::NodePredicateFunction::New(geometryCheck); auto nodePredicate = mitk::NodePredicateAnd::New(mitk::MITKRegistrationHelper::ImageNodePredicate().GetPointer(), hasGeometry.GetPointer()); m_Controls->fovReferenceNodeSelector->SetNodePredicate(nodePredicate.GetPointer()); } mitk::MAPRegistrationWrapper* QmitkMatchPointRegistrationVisualizer::GetCurrentRegistration() { mitk::MAPRegistrationWrapper* result = nullptr; if (this->m_spSelectedRegNode.IsNotNull()) { result = dynamic_cast<mitk::MAPRegistrationWrapper*>(this->m_spSelectedRegNode->GetData()); assert(result); } return result; } mitk::DataNode::Pointer QmitkMatchPointRegistrationVisualizer::GetSelectedRegNode() const { return m_Controls->registrationNodeSelector->GetSelectedNode(); } mitk::DataNode::Pointer QmitkMatchPointRegistrationVisualizer::GetRefNodeOfReg(bool target) const { mitk::DataNode::Pointer spResult = nullptr; if (this->m_spSelectedRegNode.IsNotNull() && m_spSelectedRegNode->GetData()) { std::string nodeName; mitk::BaseProperty* uidProp; if (target) { uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgTargetData); } else { uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgMovingData); } if (uidProp) { //search for the target node mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID, uidProp); spResult = this->GetDataStorage()->GetNode(predicate); } } return spResult; } mitk::DataNode::Pointer QmitkMatchPointRegistrationVisualizer::GetSelectedDataNode() { return m_Controls->fovReferenceNodeSelector->GetSelectedNode(); } void QmitkMatchPointRegistrationVisualizer::CheckInputs() { this->m_spSelectedRegNode = this->GetSelectedRegNode(); this->InitRegNode(); this->m_spSelectedFOVRefNode = this->GetSelectedDataNode(); } void QmitkMatchPointRegistrationVisualizer::ConfigureVisualizationControls() { if (!m_internalUpdateGuard) { m_internalUpdateGuard = true; m_Controls->groupViz->setVisible(this->m_spSelectedRegNode.IsNotNull()); m_Controls->m_pbUpdateViz->setEnabled(this->m_spSelectedRegNode.IsNotNull()); m_Controls->m_boxSettings->setEnabled(this->m_spSelectedRegNode.IsNotNull()); m_Controls->m_boxStyles->setEnabled(this->m_spSelectedRegNode.IsNotNull()); this->ActualizeRegInfo(this->GetCurrentRegistration()); this->m_Controls->m_checkUseRefSize->setEnabled(this->m_spSelectedRegNode.IsNotNull() && this->m_spSelectedFOVRefNode.IsNotNull()); this->m_Controls->m_checkUseRefOrigin->setEnabled(this->m_spSelectedRegNode.IsNotNull() && this->m_spSelectedFOVRefNode.IsNotNull()); this->m_Controls->m_checkUseRefSpacing->setEnabled(this->m_spSelectedRegNode.IsNotNull() && this->m_spSelectedFOVRefNode.IsNotNull()); m_internalUpdateGuard = false; } } void QmitkMatchPointRegistrationVisualizer::StoreStateInNode() { if (this->m_spSelectedRegNode.IsNotNull()) { //general this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisDirection, mitk::RegVisDirectionProperty::New(this->m_Controls->m_comboDirection->currentIndex())); this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisGrid, this->m_Controls->m_pbStyleGrid->isChecked()); this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisGlyph, this->m_Controls->m_pbStyleGlyph->isChecked()); this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisPoints, this->m_Controls->m_pbStylePoints->isChecked()); //Visualization if (this->m_Controls->radioColorUni->isChecked()) { this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisColorStyle, mitk::RegVisColorStyleProperty::New(0)); } else { this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisColorStyle, mitk::RegVisColorStyleProperty::New(1)); } float tmpColor[3]; tmpColor[0] = this->m_Controls->btnUniColor->color().redF(); tmpColor[1] = this->m_Controls->btnUniColor->color().greenF(); tmpColor[2] = this->m_Controls->btnUniColor->color().blueF(); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorUni, mitk::ColorProperty::New(tmpColor), nullptr, true); tmpColor[0] = this->m_Controls->btnVecMagColorNeg->color().redF(); tmpColor[1] = this->m_Controls->btnVecMagColorNeg->color().greenF(); tmpColor[2] = this->m_Controls->btnVecMagColorNeg->color().blueF(); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor1Value, mitk::ColorProperty::New(tmpColor), nullptr, true); tmpColor[0] = this->m_Controls->btnVecMagColorSmall->color().redF(); tmpColor[1] = this->m_Controls->btnVecMagColorSmall->color().greenF(); tmpColor[2] = this->m_Controls->btnVecMagColorSmall->color().blueF(); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Value, mitk::ColorProperty::New(tmpColor), nullptr, true); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Magnitude, mitk::DoubleProperty::New(this->m_Controls->sbVecMagSmall->value()), nullptr, true); tmpColor[0] = this->m_Controls->btnVecMagColorMedium->color().redF(); tmpColor[1] = this->m_Controls->btnVecMagColorMedium->color().greenF(); tmpColor[2] = this->m_Controls->btnVecMagColorMedium->color().blueF(); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Value, mitk::ColorProperty::New(tmpColor), nullptr, true); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Magnitude, mitk::DoubleProperty::New(this->m_Controls->sbVecMagMedium->value()), nullptr, true); tmpColor[0] = this->m_Controls->btnVecMagColorLarge->color().redF(); tmpColor[1] = this->m_Controls->btnVecMagColorLarge->color().greenF(); tmpColor[2] = this->m_Controls->btnVecMagColorLarge->color().blueF(); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Value, mitk::ColorProperty::New(tmpColor), nullptr, true); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Magnitude, mitk::DoubleProperty::New(this->m_Controls->sbVecMagLarge->value()), nullptr, true); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorInterpolate, mitk::BoolProperty::New(this->m_Controls->cbVevMagInterlolate->isChecked()), nullptr, true); //Grid Settings this->m_spSelectedRegNode->SetIntProperty(mitk::nodeProp_RegVisGridFrequence, this->m_Controls->m_sbGridFrequency->value()); this->m_spSelectedRegNode->SetBoolProperty(mitk::nodeProp_RegVisGridShowStart, this->m_Controls->m_groupShowStartGrid->isChecked()); tmpColor[0] = this->m_Controls->btnStartGridColor->color().redF(); tmpColor[1] = this->m_Controls->btnStartGridColor->color().greenF(); tmpColor[2] = this->m_Controls->btnStartGridColor->color().blueF(); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridStartColor, mitk::ColorProperty::New(tmpColor), nullptr, true); //FOV mitk::Vector3D value; value[0] = this->m_Controls->m_sbFOVSizeX->value(); value[1] = this->m_Controls->m_sbFOVSizeY->value(); value[2] = this->m_Controls->m_sbFOVSizeZ->value(); this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVSize, mitk::Vector3DProperty::New(value)); value[0] = this->m_Controls->m_sbGridSpX->value(); value[1] = this->m_Controls->m_sbGridSpY->value(); value[2] = this->m_Controls->m_sbGridSpZ->value(); this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVSpacing, mitk::Vector3DProperty::New(value)); mitk::Point3D origin; origin[0] = this->m_Controls->m_sbFOVOriginX->value(); origin[1] = this->m_Controls->m_sbFOVOriginY->value(); origin[2] = this->m_Controls->m_sbFOVOriginZ->value(); this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrigin, mitk::Point3dProperty::New(origin)); mitk::Vector3D orientationRow1; mitk::Vector3D orientationRow2; mitk::Vector3D orientationRow3; orientationRow1.SetVnlVector(m_FOVRefOrientation.GetVnlMatrix().get_row(0).as_ref()); orientationRow2.SetVnlVector(m_FOVRefOrientation.GetVnlMatrix().get_row(1).as_ref()); orientationRow3.SetVnlVector(m_FOVRefOrientation.GetVnlMatrix().get_row(2).as_ref()); this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrientation1, mitk::Vector3DProperty::New(orientationRow1)); this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrientation2, mitk::Vector3DProperty::New(orientationRow2)); this->m_spSelectedRegNode->SetProperty(mitk::nodeProp_RegVisFOVOrientation3, mitk::Vector3DProperty::New(orientationRow3)); } } void QmitkMatchPointRegistrationVisualizer::LoadStateFromNode() { if (this->m_spSelectedRegNode.IsNotNull()) { mitk::RegVisDirectionProperty* directionProp = nullptr; if (this->m_spSelectedRegNode->GetProperty(directionProp, mitk::nodeProp_RegVisDirection)) { this->m_Controls->m_comboDirection->setCurrentIndex(directionProp->GetValueAsId()); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisDirection) + QStringLiteral(" has not the assumed type.")); } bool styleActive = false; if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisGrid, styleActive)) { this->m_Controls->m_pbStyleGrid->setChecked(styleActive); this->m_Controls->tabGrid->setEnabled(styleActive); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisGrid) + QStringLiteral(" has not the assumed type.")); } if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisGlyph, styleActive)) { this->m_Controls->m_pbStyleGlyph->setChecked(styleActive); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisGlyph) + QStringLiteral(" has not the assumed type.")); } if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisPoints, styleActive)) { this->m_Controls->m_pbStylePoints->setChecked(styleActive); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisPoints) + QStringLiteral(" has not the assumed type.")); } /////////////////////////////////////////////////////// //visualization mitk::RegVisColorStyleProperty* colorStyleProp = nullptr; if (this->m_spSelectedRegNode->GetProperty(colorStyleProp, mitk::nodeProp_RegVisColorStyle)) { this->m_Controls->radioColorUni->setChecked(colorStyleProp->GetValueAsId() == 0); this->m_Controls->radioColorVecMag->setChecked(colorStyleProp->GetValueAsId() == 1); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisColorStyle) + QStringLiteral(" has not the assumed type.")); } QColor tmpColor; float colorUni[3] = { 0.0, 0.0, 0.0 }; this->m_spSelectedRegNode->GetColor(colorUni, nullptr, mitk::nodeProp_RegVisColorUni); tmpColor.setRgbF(colorUni[0], colorUni[1], colorUni[2]); this->m_Controls->btnUniColor->setColor(tmpColor); float color1[3] = { 0.0, 0.0, 0.0 }; this->m_spSelectedRegNode->GetColor(color1, nullptr, mitk::nodeProp_RegVisColor1Value); tmpColor.setRgbF(color1[0], color1[1], color1[2]); this->m_Controls->btnVecMagColorNeg->setColor(tmpColor); float color2[3] = { 0.25, 0.25, 0.25 }; this->m_spSelectedRegNode->GetColor(color2, nullptr, mitk::nodeProp_RegVisColor2Value); tmpColor.setRgbF(color2[0], color2[1], color2[2]); this->m_Controls->btnVecMagColorSmall->setColor(tmpColor); float color3[3] = { 0.5, 0.5, 0.5 }; this->m_spSelectedRegNode->GetColor(color3, nullptr, mitk::nodeProp_RegVisColor3Value); tmpColor.setRgbF(color3[0], color3[1], color3[2]); this->m_Controls->btnVecMagColorMedium->setColor(tmpColor); float color4[3] = { 1.0, 1.0, 1.0 }; this->m_spSelectedRegNode->GetColor(color4, nullptr, mitk::nodeProp_RegVisColor4Value); tmpColor.setRgbF(color4[0], color4[1], color4[2]); this->m_Controls->btnVecMagColorLarge->setColor(tmpColor); double mag2 = 0; this->m_spSelectedRegNode->GetPropertyValue(mitk::nodeProp_RegVisColor2Magnitude, mag2); double mag3 = 0; this->m_spSelectedRegNode->GetPropertyValue(mitk::nodeProp_RegVisColor3Magnitude, mag3); double mag4 = 0; this->m_spSelectedRegNode->GetPropertyValue(mitk::nodeProp_RegVisColor4Magnitude, mag4); bool interpolate = true; this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisColorInterpolate, interpolate); this->m_Controls->sbVecMagSmall->setValue(mag2); this->m_Controls->sbVecMagMedium->setValue(mag3); this->m_Controls->sbVecMagLarge->setValue(mag4); this->m_Controls->cbVevMagInterlolate->setChecked(interpolate); /////////////////////////////////////////////////////// //Grid general bool showStart = false; if (this->m_spSelectedRegNode->GetBoolProperty(mitk::nodeProp_RegVisGridShowStart, showStart)) { this->m_Controls->m_groupShowStartGrid->setChecked(showStart); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisGridShowStart) + QStringLiteral(" is not correctly defined.")); } int gridFrequ = 5; if (this->m_spSelectedRegNode->GetIntProperty(mitk::nodeProp_RegVisGridFrequence, gridFrequ)) { this->m_Controls->m_sbGridFrequency->setValue(gridFrequ); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisGridFrequence) + QStringLiteral(" is not correctly defined.")); } float colorStart[3] = { 0.0, 0.0, 0.0 }; this->m_spSelectedRegNode->GetColor(colorStart, nullptr, mitk::nodeProp_RegVisGridStartColor); tmpColor.setRgbF(colorStart[0], colorStart[1], colorStart[2]); this->m_Controls->btnStartGridColor->setColor(tmpColor); /////////////////////////////////////////////////////// //FOV mitk::Vector3DProperty* valueProp = nullptr; if (this->m_spSelectedRegNode->GetProperty(valueProp, mitk::nodeProp_RegVisFOVSize)) { this->m_Controls->m_sbFOVSizeX->setValue(valueProp->GetValue()[0]); this->m_Controls->m_sbFOVSizeY->setValue(valueProp->GetValue()[1]); this->m_Controls->m_sbFOVSizeZ->setValue(valueProp->GetValue()[2]); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisFOVSize) + QStringLiteral(" is not correctly defined.")); } if (this->m_spSelectedRegNode->GetProperty(valueProp, mitk::nodeProp_RegVisFOVSpacing)) { this->m_Controls->m_sbGridSpX->setValue(valueProp->GetValue()[0]); this->m_Controls->m_sbGridSpY->setValue(valueProp->GetValue()[1]); this->m_Controls->m_sbGridSpZ->setValue(valueProp->GetValue()[2]); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisFOVSpacing) + QStringLiteral(" is not correctly defined.")); } mitk::Point3dProperty* originProp = nullptr; if (this->m_spSelectedRegNode->GetProperty(originProp, mitk::nodeProp_RegVisFOVOrigin)) { this->m_Controls->m_sbFOVOriginX->setValue(originProp->GetValue()[0]); this->m_Controls->m_sbFOVOriginY->setValue(originProp->GetValue()[1]); this->m_Controls->m_sbFOVOriginZ->setValue(originProp->GetValue()[2]); } else { - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. Node property ") + QString( + this->Error(QStringLiteral("Cannot configure plugin controls correctly. Node property ") + QString( mitk::nodeProp_RegVisFOVOrigin) + QStringLiteral(" is not correctly defined.")); } mitk::Vector3DProperty* orientationProp1; mitk::Vector3DProperty* orientationProp2; mitk::Vector3DProperty* orientationProp3; if (this->m_spSelectedRegNode->GetProperty(orientationProp1, mitk::nodeProp_RegVisFOVOrientation1) && this->m_spSelectedRegNode->GetProperty(orientationProp2, mitk::nodeProp_RegVisFOVOrientation2) && this->m_spSelectedRegNode->GetProperty(orientationProp3, mitk::nodeProp_RegVisFOVOrientation3)) { this->m_Controls->m_sbFOVOriginX->setValue(originProp->GetValue()[0]); this->m_Controls->m_sbFOVOriginY->setValue(originProp->GetValue()[1]); this->m_Controls->m_sbFOVOriginZ->setValue(originProp->GetValue()[2]); m_FOVRefOrientation.GetVnlMatrix().set_row(0, orientationProp1->GetValue().GetVnlVector()); m_FOVRefOrientation.GetVnlMatrix().set_row(1, orientationProp2->GetValue().GetVnlVector()); m_FOVRefOrientation.GetVnlMatrix().set_row(2, orientationProp3->GetValue().GetVnlVector()); } else { m_FOVRefOrientation.SetIdentity(); - this->Error(QStringLiteral("Cannot configure plugin controlls correctly. One of the node propertiesy ") + + this->Error(QStringLiteral("Cannot configure plugin controls correctly. One of the node propertiesy ") + QString(mitk::nodeProp_RegVisFOVOrientation1) + QString(mitk::nodeProp_RegVisFOVOrientation2) + QString(mitk::nodeProp_RegVisFOVOrientation3) + QStringLiteral(" is not correctly defined.")); } this->UpdateOrientationMatrixWidget(); } } void QmitkMatchPointRegistrationVisualizer::CheckAndSetDefaultFOVRef() { //check if node has a default reference node. mitk::DataNode::Pointer defaultRef = this->GetRefNodeOfReg( this->m_Controls->m_comboDirection->currentIndex() == 1); //direction value 1 = show inverse mapping -> we need the target image used for the registration. //if there is a default node and no m_spSelectedFOVRefNode is set -> set default node and transfer values if (defaultRef.IsNotNull() && this->m_spSelectedFOVRefNode.IsNull()) { //there is a default ref and no ref lock -> select default ref and transfer its values this->m_spSelectedFOVRefNode = defaultRef; QmitkSingleNodeSelectionWidget::NodeList selection({ defaultRef }); this->m_Controls->fovReferenceNodeSelector->SetCurrentSelection(selection); this->m_Controls->m_checkUseRefSize->setChecked(true); this->m_Controls->m_checkUseRefOrigin->setChecked(true); this->m_Controls->m_checkUseRefSpacing->setChecked(true); this->m_Controls->m_checkUseRefOrientation->setChecked(true); } if (this->m_spSelectedFOVRefNode.IsNotNull()) { - //auto transfere values + //auto transfer values this->TransferFOVRefGeometry(); } } void QmitkMatchPointRegistrationVisualizer::OnNodeSelectionChanged(QList<mitk::DataNode::Pointer> /*nodes*/) { this->CheckInputs(); this->LoadStateFromNode(); this->CheckAndSetDefaultFOVRef(); this->ConfigureVisualizationControls(); } void QmitkMatchPointRegistrationVisualizer::ActualizeRegInfo(mitk::MAPRegistrationWrapper* currentReg) { std::stringstream descriptionString; m_Controls->m_teRegInfo->clear(); if (currentReg) { descriptionString << "Moving dimension: " << currentReg->GetMovingDimensions() << " "; descriptionString << "Target dimension: " << currentReg->GetTargetDimensions() << " "; descriptionString << "Limited moving representation: " << currentReg->HasLimitedMovingRepresentation() << " "; descriptionString << "Limited target representation: " << currentReg->HasLimitedTargetRepresentation() << " "; mitk::MAPRegistrationWrapper::TagMapType tagMap = currentReg->GetTags(); descriptionString << " Tags: "; for (mitk::MAPRegistrationWrapper::TagMapType::const_iterator pos = tagMap.begin(); pos != tagMap.end(); ++pos) { descriptionString << pos->first << " : " << pos->second << " "; } } else { descriptionString << "no registration selected!"; } m_Controls->m_teRegInfo->insertHtml(QString::fromStdString(descriptionString.str())); } void QmitkMatchPointRegistrationVisualizer::OnDirectionChanged(int) { this->CheckAndSetDefaultFOVRef(); this->ConfigureVisualizationControls(); } void QmitkMatchPointRegistrationVisualizer::OnUpdateBtnPushed() { this->StoreStateInNode(); mitk::Geometry3D::Pointer gridDesc; unsigned int gridFrequ = 5; mitk::GetGridGeometryFromNode(this->m_spSelectedRegNode, gridDesc, gridFrequ); this->GetCurrentRegistration()->SetGeometry(gridDesc); mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); } void QmitkMatchPointRegistrationVisualizer::OnStyleButtonPushed() { } void QmitkMatchPointRegistrationVisualizer::OnColorInterpolationChecked(bool checked) { if (checked) { this->m_Controls->labelVecMagSmall->setText(QStringLiteral("=")); this->m_Controls->labelVecMagMedium->setText(QStringLiteral("=")); this->m_Controls->labelVecMagLarge->setText(QStringLiteral("=")); } else { this->m_Controls->labelVecMagSmall->setText(QStringLiteral(">")); this->m_Controls->labelVecMagMedium->setText(QStringLiteral(">")); this->m_Controls->labelVecMagLarge->setText(QStringLiteral(">")); } } mitk::ScalarType QmitkMatchPointRegistrationVisualizer::GetSaveSpacing(mitk::ScalarType gridRes, mitk::ScalarType spacing, unsigned int maxGridRes) const { mitk::ScalarType newSpacing = spacing; mitk::ScalarType scaling = gridRes / maxGridRes; if (scaling > 1.0) { newSpacing = spacing * scaling; } return newSpacing; } void QmitkMatchPointRegistrationVisualizer::TransferFOVRefGeometry() { if (this->m_spSelectedFOVRefNode.IsNotNull()) { assert(this->m_spSelectedFOVRefNode->GetData()); assert(this->m_spSelectedFOVRefNode->GetData()->GetGeometry()); mitk::BaseGeometry* gridRef = this->m_spSelectedFOVRefNode->GetData()->GetGeometry(); mitk::Vector3D spacing = gridRef->GetSpacing(); mitk::Point3D origin = gridRef->GetOrigin(); mitk::Geometry3D::BoundsArrayType bounds = gridRef->GetBounds(); mitk::AffineTransform3D::ConstPointer fovTransform = gridRef->GetIndexToWorldTransform(); if (this->m_Controls->m_checkUseRefSize->isChecked()) { this->m_Controls->m_sbFOVSizeX->setValue((bounds[1] - bounds[0])*spacing[0]); this->m_Controls->m_sbFOVSizeY->setValue((bounds[3] - bounds[2])*spacing[1]); this->m_Controls->m_sbFOVSizeZ->setValue((bounds[5] - bounds[4])*spacing[2]); } if (this->m_Controls->m_checkUseRefSpacing->isChecked()) { this->m_Controls->m_sbGridSpX->setValue(GetSaveSpacing((bounds[1] - bounds[0]), spacing[0], 20)); this->m_Controls->m_sbGridSpY->setValue(GetSaveSpacing((bounds[3] - bounds[2]), spacing[1], 20)); this->m_Controls->m_sbGridSpZ->setValue(GetSaveSpacing((bounds[5] - bounds[4]), spacing[2], 20)); } if (this->m_Controls->m_checkUseRefOrigin->isChecked()) { this->m_Controls->m_sbFOVOriginX->setValue(origin[0]); this->m_Controls->m_sbFOVOriginY->setValue(origin[1]); this->m_Controls->m_sbFOVOriginZ->setValue(origin[2]); } if (this->m_Controls->m_checkUseRefOrientation->isChecked()) { this->m_FOVRefOrientation = fovTransform->GetMatrix(); this->UpdateOrientationMatrixWidget(); } } } void QmitkMatchPointRegistrationVisualizer::UpdateOrientationMatrixWidget() { for (unsigned int r = 0; r < 3; ++r) { for (unsigned int c = 0; c < 3; ++c) { this->m_Controls->m_tableOrientation->item(r, c)->setText(QString::number(this->m_FOVRefOrientation.GetVnlMatrix().get(r, c))); } } } void QmitkMatchPointRegistrationVisualizer::InitRegNode() { if (this->m_spSelectedRegNode.IsNotNull()) { this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGrid, mitk::BoolProperty::New(true)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGlyph, mitk::BoolProperty::New(false)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisPoints, mitk::BoolProperty::New(false)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisDirection, mitk::RegVisDirectionProperty::New()); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorStyle, mitk::RegVisColorStyleProperty::New(1)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorUni, mitk::ColorProperty::New(0, 0.5, 0)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridFrequence, mitk::IntProperty::New(3)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridShowStart, mitk::BoolProperty::New(false)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisGridStartColor, mitk::ColorProperty::New(0.5, 0, 0)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVSize, mitk::Vector3DProperty::New(mitk::Vector3D(100.0))); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVSpacing, mitk::Vector3DProperty::New(mitk::Vector3D(5.0))); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor1Value, mitk::ColorProperty::New(0, 0, 0.5)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Value, mitk::ColorProperty::New(0, 0.7, 0)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor2Magnitude, mitk::DoubleProperty::New(1)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Value, mitk::ColorProperty::New(1, 1, 0)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor3Magnitude, mitk::DoubleProperty::New(5)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Value, mitk::ColorProperty::New(1, 0, 0)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColor4Magnitude, mitk::DoubleProperty::New(15)); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisColorInterpolate, mitk::BoolProperty::New(true)); mitk::Point3D origin; origin.Fill(0.0); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrigin, mitk::Point3dProperty::New(mitk::Point3D(origin))); mitk::Vector3D vec(0.0); vec.SetElement(0, 1.0); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrientation1, mitk::Vector3DProperty::New(vec)); vec.Fill(0.0); vec.SetElement(1, 1.0); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrientation2, mitk::Vector3DProperty::New(vec)); vec.Fill(0.0); vec.SetElement(2, 1.0); this->m_spSelectedRegNode->AddProperty(mitk::nodeProp_RegVisFOVOrientation3, mitk::Vector3DProperty::New(vec)); } } diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.h b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.h index 53ce98087c..966fd637ea 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.h +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.h @@ -1,158 +1,158 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMatchPointRegistrationVisualizer_h #define QmitkMatchPointRegistrationVisualizer_h #include <vtkPolyData.h> #include <vtkSmartPointer.h> #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include <QSortFilterProxyModel> #include "mitkMAPRegistrationWrapper.h" #include "ui_QmitkMatchPointRegistrationVisualizer.h" /*! \brief QmitkMatchPointRegistrationVisualizer \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \ingroup ${plugin_target}_internal */ class QmitkMatchPointRegistrationVisualizer : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; /** * Creates smartpointer typedefs */ berryObjectMacro(QmitkMatchPointRegistrationVisualizer); QmitkMatchPointRegistrationVisualizer(); void CreateQtPartControl(QWidget* parent) override; /** Returns the registration currently handled by the plugin. * May return nullptr, if no registration is selected/handled by * the plugin*/ mitk::MAPRegistrationWrapper* GetCurrentRegistration(); protected slots: /** * @brief Connect all GUI elements to its corresponding slots */ virtual void CreateConnections(); void OnStyleButtonPushed(); void OnDirectionChanged(int index); void OnUpdateBtnPushed(); void OnColorInterpolationChecked(bool); void OnNodeSelectionChanged(QList<mitk::DataNode::Pointer> nodes); void TransferFOVRefGeometry(); protected: void SetFocus() override; void ActualizeRegInfo(mitk::MAPRegistrationWrapper* currentReg); Ui::MatchPointRegVisControls* m_Controls; private: QWidget* m_Parent; void Error(QString msg); void CheckInputs(); /** Function returns the first data node containing a registration wrapper * in the current selection of the data manager. If nothing is selected or * no registration wrapper is selected it return nullptr.*/ mitk::DataNode::Pointer GetSelectedRegNode() const; /** If a registration node is set, this function determines the relevant referenced node. * The reference node is the node of the target or moving data (depending on the selected directions) * used to determine the* registration object. * @return Pointer to the reference node (moving or target data of the registration algorithm run). * Function may return nullptr if the referenced node cannot be found or is not defined * by the registration.*/ mitk::DataNode::Pointer GetRefNodeOfReg(bool target) const; /** Methods returns the first node selected in the data manager that does * NOT contain a registration wrapper and has a data pointer with a geometry. * Returned pointer may be nullptr if nothing is selected or no appropriate data * node is selected.*/ mitk::DataNode::Pointer GetSelectedDataNode(); /** Methods checks if the given gridRes is larger than maxGridRes and scales down the spacing if necessary. * @param gridRes the resolution of the "grid". * @param spacing the spacing that would be used on the grid. * @param maxGridRes the maximum resolution of the "grid".*/ mitk::ScalarType GetSaveSpacing(mitk::ScalarType gridRes, mitk::ScalarType spacing, unsigned int maxGridRes) const; /** * Checks for mandatory node properties and defines them with default values if they are missing.*/ void InitRegNode(); /** * Updates the gui controls regarding the current state of the instance.*/ void ConfigureVisualizationControls(); /** Configure the node selectors predicates according to the selected algorithm. */ void ConfigureNodePredicates(); /** * Updates the properties of the selected node according to the states of the gui controls.*/ void StoreStateInNode(); /** * Updates the state of the gui controls according to the properties of the selected node.*/ void LoadStateFromNode(); /** * Checks accordung to the current direction if there is a default FOV ref and sets it, * if the current FOV ref is not locked.*/ void CheckAndSetDefaultFOVRef(); void UpdateOrientationMatrixWidget(); /**indicates if the gui updates is triggered internally or by user. Needed to - * avoid update loops by ConfigureVisualizationControlls();*/ + * avoid update loops by ConfigureVisualizationControls();*/ bool m_internalUpdateGuard; mitk::DataNode::Pointer m_spSelectedFOVRefNode; mitk::DataNode::Pointer m_spSelectedRegNode; - /**Used to store informations about the FOV reference orientation. Default is identity matrix.*/ + /**Used to store information about the FOV reference orientation. Default is identity matrix.*/ mitk::AffineTransform3D::MatrixType m_FOVRefOrientation; }; #endif diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui index 899b10bbc1..4dc8b4a05e 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui @@ -1,1570 +1,1570 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>MatchPointRegVisControls</class> <widget class="QWidget" name="MatchPointRegVisControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>332</width> <height>738</height> </rect> </property> <layout class="QVBoxLayout" name="verticalLayout"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label"> <property name="palette"> <palette> <active> <colorrole role="WindowText"> <brush brushstyle="SolidPattern"> <color alpha="255"> <red>255</red> <green>0</green> <blue>0</blue> </color> </brush> </colorrole> </active> <inactive> <colorrole role="WindowText"> <brush brushstyle="SolidPattern"> <color alpha="255"> <red>255</red> <green>0</green> <blue>0</blue> </color> </brush> </colorrole> </inactive> <disabled> <colorrole role="WindowText"> <brush brushstyle="SolidPattern"> <color alpha="255"> <red>120</red> <green>120</green> <blue>120</blue> </color> </brush> </colorrole> </disabled> </palette> </property> <property name="text"> <string>Warning: This plugin is in an experimental state!</string> </property> </widget> </item> <item> <widget class="QLabel" name="label_4"> <property name="text"> <string>Registration:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <property name="spacing"> <number>3</number> </property> <item> <widget class="QmitkSingleNodeSelectionWidget" name="registrationNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="label_5"> <property name="text"> <string>Info:</string> </property> </widget> </item> <item> <widget class="QTextEdit" name="m_teRegInfo"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>75</height> </size> </property> <property name="maximumSize"> <size> <width>16777215</width> <height>130</height> </size> </property> <property name="readOnly"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QGroupBox" name="groupViz"> <property name="sizePolicy"> <sizepolicy hsizetype="MinimumExpanding" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="title"> <string/> </property> <property name="flat"> <bool>false</bool> </property> <layout class="QVBoxLayout" name="verticalLayout_2"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QPushButton" name="m_pbUpdateViz"> <property name="toolTip"> <string><html><head/><body>Updates the visualization with the current settings.</body></html></string> </property> <property name="text"> <string>Update visualization</string> </property> <property name="checkable"> <bool>false</bool> </property> </widget> </item> <item> <widget class="QLabel" name="label_13"> <property name="text"> <string>Show mapping direction:</string> </property> </widget> </item> <item> <widget class="QComboBox" name="m_comboDirection"> <property name="toolTip"> <string><html><head/><body>Select the direction/kernel of the registration you want to visualize:- "direct": select to show the direct mapping kernel (used for continuous spaced data like point sets).- "inverse": select to show the inverse mapping kernel (used for discrete spaced data like voxel images). If the selected registration does not support a direction, you cannot select it.</body></html></string> </property> <item> <property name="text"> <string>Direct</string> </property> </item> <item> <property name="text"> <string>Inverse</string> </property> </item> </widget> </item> <item> <widget class="QWidget" name="m_boxStyles" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>30</height> </size> </property> <layout class="QHBoxLayout" name="horizontalLayout_2"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>0</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>0</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QPushButton" name="m_pbStyleGrid"> <property name="toolTip"> - <string><html><head/><body>Select to vizualize registration via grid(s).</body></html></string> + <string><html><head/><body>Select to visualize registration via grid(s).</body></html></string> </property> <property name="text"> <string>Grid</string> </property> <property name="checkable"> <bool>true</bool> </property> <property name="checked"> <bool>true</bool> </property> <property name="autoExclusive"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QPushButton" name="m_pbStyleGlyph"> <property name="enabled"> <bool>true</bool> </property> <property name="toolTip"> - <string>Select to vizualize registration via glyphs.</string> + <string>Select to visualize registration via glyphs.</string> </property> <property name="text"> <string>Glyph</string> </property> <property name="checkable"> <bool>true</bool> </property> <property name="autoExclusive"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QPushButton" name="m_pbStylePoints"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> - <string>Select to vizualize registration via a pointset selected from the data manager...</string> + <string>Select to visualize registration via a pointset selected from the data manager...</string> </property> <property name="text"> <string>Points</string> </property> <property name="checkable"> <bool>true</bool> </property> <property name="autoExclusive"> <bool>true</bool> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QTabWidget" name="m_boxSettings"> <property name="currentIndex"> <number>2</number> </property> <widget class="QWidget" name="tabViz"> <attribute name="title"> <string>Visualization</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_5"> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <item> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <widget class="QLabel" name="label_15"> <property name="text"> <string>Color style:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_8"> <item> <widget class="QRadioButton" name="radioColorUni"> <property name="text"> <string>uni color:</string> </property> </widget> </item> <item> <widget class="ctkColorPickerButton" name="btnUniColor"> <property name="enabled"> <bool>false</bool> </property> <property name="minimumSize"> <size> <width>60</width> <height>0</height> </size> </property> <property name="autoFillBackground"> <bool>false</bool> </property> <property name="text"> <string/> </property> </widget> </item> <item> <spacer name="horizontalSpacer_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <widget class="QRadioButton" name="radioColorVecMag"> <property name="text"> <string>vector magnitude:</string> </property> </widget> </item> <item> <widget class="QGroupBox" name="groupColorCoding"> <property name="title"> <string>Color coding:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_8"> <item> <layout class="QGridLayout" name="gridLayout_3"> <property name="leftMargin"> <number>0</number> </property> <property name="rightMargin"> <number>0</number> </property> <property name="horizontalSpacing"> <number>7</number> </property> <property name="verticalSpacing"> <number>3</number> </property> <item row="3" column="7"> <spacer name="horizontalSpacer_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="2" column="7"> <spacer name="horizontalSpacer_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="1" column="7"> <spacer name="horizontalSpacer_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="0" column="7"> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="1" column="5"> <widget class="QLabel" name="label_29"> <property name="text"> <string>mm</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QLabel" name="label_3"> <property name="text"> <string>small:</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QLabel" name="label_2"> <property name="text"> <string>medium:</string> </property> </widget> </item> <item row="2" column="3"> <widget class="QLabel" name="labelVecMagMedium"> <property name="maximumSize"> <size> <width>30</width> <height>16777215</height> </size> </property> <property name="text"> <string>></string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item row="1" column="4"> <widget class="QDoubleSpinBox" name="sbVecMagSmall"> <property name="maximum"> <double>999.000000000000000</double> </property> <property name="singleStep"> <double>0.100000000000000</double> </property> </widget> </item> <item row="3" column="4"> <widget class="QDoubleSpinBox" name="sbVecMagLarge"> <property name="maximum"> <double>999.000000000000000</double> </property> </widget> </item> <item row="3" column="1"> <widget class="QLabel" name="label_9"> <property name="text"> <string>large:</string> </property> </widget> </item> <item row="3" column="3"> <widget class="QLabel" name="labelVecMagLarge"> <property name="maximumSize"> <size> <width>30</width> <height>16777215</height> </size> </property> <property name="text"> <string>></string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item row="3" column="5"> <widget class="QLabel" name="label_30"> <property name="text"> <string>mm</string> </property> </widget> </item> <item row="2" column="4"> <widget class="QDoubleSpinBox" name="sbVecMagMedium"> <property name="maximum"> <double>999.000000000000000</double> </property> </widget> </item> <item row="2" column="5"> <widget class="QLabel" name="label_31"> <property name="text"> <string>mm</string> </property> </widget> </item> <item row="1" column="3"> <widget class="QLabel" name="labelVecMagSmall"> <property name="maximumSize"> <size> <width>30</width> <height>16777215</height> </size> </property> <property name="text"> <string>></string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="label_6"> <property name="text"> <string>negligible:</string> </property> </widget> </item> <item row="3" column="2"> <widget class="ctkColorPickerButton" name="btnVecMagColorLarge"> <property name="minimumSize"> <size> <width>50</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string/> </property> </widget> </item> <item row="2" column="2"> <widget class="ctkColorPickerButton" name="btnVecMagColorMedium"> <property name="minimumSize"> <size> <width>50</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string/> </property> </widget> </item> <item row="1" column="2"> <widget class="ctkColorPickerButton" name="btnVecMagColorSmall"> <property name="minimumSize"> <size> <width>50</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string/> </property> </widget> </item> <item row="0" column="2"> <widget class="ctkColorPickerButton" name="btnVecMagColorNeg"> <property name="minimumSize"> <size> <width>50</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>40</width> <height>16777215</height> </size> </property> <property name="text"> <string/> </property> </widget> </item> </layout> </item> <item> <widget class="QCheckBox" name="cbVevMagInterlolate"> <property name="text"> <string>interpolate colors</string> </property> </widget> </item> </layout> </widget> </item> </layout> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tabGrid"> <property name="enabled"> <bool>true</bool> </property> <attribute name="title"> <string>Grid</string> </attribute> <attribute name="toolTip"> <string><html><head/><body>General grid visualization settings.</body></html></string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_3"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <layout class="QFormLayout" name="formLayout"> <property name="fieldGrowthPolicy"> <enum>QFormLayout::AllNonFixedFieldsGrow</enum> </property> <property name="horizontalSpacing"> <number>5</number> </property> <property name="verticalSpacing"> <number>5</number> </property> <item row="0" column="0"> <widget class="QLabel" name="label_16"> <property name="text"> <string>Grid frequency:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QSpinBox" name="m_sbGridFrequency"> <property name="toolTip"> <string><html><head/><body>Indicate the frequency of visible gridlines used for visualization.e.g. 1: every line of the grid is visible; 2: only every second line is visible ...</body></html></string> </property> <property name="maximum"> <number>200</number> </property> </widget> </item> </layout> </item> <item> <widget class="QGroupBox" name="m_groupShowStartGrid"> <property name="font"> <weight>50</weight> <bold>false</bold> </property> <property name="toolTip"> <string><html><head/><body>Allows that pixels may not be defined in the mapped image because they are outside of the field of view of the used input image.The pixels will be marked with the given padding value.If unchecked the mapping will be aborted in a case of undefined pixels.</body></html></string> </property> <property name="title"> <string>Show start grid</string> </property> <property name="flat"> <bool>false</bool> </property> <property name="checkable"> <bool>true</bool> </property> <property name="checked"> <bool>false</bool> </property> <layout class="QHBoxLayout" name="horizontalLayout_3"> <property name="leftMargin"> <number>11</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>11</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_14"> <property name="text"> <string>Color</string> </property> </widget> </item> <item> <widget class="ctkColorPickerButton" name="btnStartGridColor"> <property name="minimumSize"> <size> <width>60</width> <height>0</height> </size> </property> <property name="autoFillBackground"> <bool>false</bool> </property> <property name="text"> <string/> </property> </widget> </item> <item> <spacer name="horizontalSpacer_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Expanding</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>300</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="tabFOV"> <attribute name="title"> <string>FOV</string> </attribute> <attribute name="toolTip"> <string><html><head/><body>Field of view settings (FOV) for vizualizing the grid correctly (its origin, size and orientation).</body></html></string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_4"> <property name="spacing"> <number>5</number> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_18"> <property name="text"> <string>Size (in mm):</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <property name="spacing"> <number>0</number> </property> <item> <widget class="QLabel" name="label_20"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>x:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbFOVSizeX"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the size (in mm) of the grid in the x direction.</body></html></string> </property> <property name="decimals"> <number>2</number> </property> <property name="minimum"> <double>0.010000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> <item> <widget class="QLabel" name="label_21"> <property name="text"> <string>y:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbFOVSizeY"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the size (in mm) of the grid in the y direction.</body></html></string> </property> <property name="decimals"> <number>2</number> </property> <property name="minimum"> <double>0.010000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> <item> <widget class="QLabel" name="label_19"> <property name="text"> <string>z:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbFOVSizeZ"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the size (in mm) of the grid in the z direction.</body></html></string> </property> <property name="decimals"> <number>2</number> </property> <property name="minimum"> <double>0.010000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="label_24"> <property name="text"> <string>Origin (in mm):</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <property name="spacing"> <number>0</number> </property> <item> <widget class="QLabel" name="label_25"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>x:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbFOVOriginX"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the origin (in mm) of the grid in the x direction.</body></html></string> </property> <property name="minimum"> <double>-99999.000000000000000</double> </property> <property name="maximum"> <double>99999.000000000000000</double> </property> </widget> </item> <item> <widget class="QLabel" name="label_22"> <property name="text"> <string>y:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbFOVOriginY"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the origin (in mm) of the grid in the y direction.</body></html></string> </property> <property name="minimum"> <double>-99999.000000000000000</double> </property> <property name="maximum"> <double>99999.000000000000000</double> </property> </widget> </item> <item> <widget class="QLabel" name="label_23"> <property name="text"> <string>z:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbFOVOriginZ"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the origin (in mm) of the grid in the z direction.</body></html></string> </property> <property name="minimum"> <double>-99999.000000000000000</double> </property> <property name="maximum"> <double>99999.000000000000000</double> </property> <property name="value"> <double>0.000000000000000</double> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="label_17"> <property name="text"> <string>Spacing (in mm):</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_6"> <property name="spacing"> <number>0</number> </property> <item> <widget class="QLabel" name="label_10"> <property name="sizePolicy"> <sizepolicy hsizetype="Maximum" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>x:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbGridSpX"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the spacing/resolution of the grid in the x direction.</body></html></string> </property> <property name="minimum"> <double>0.010000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> <property name="value"> <double>0.010000000000000</double> </property> </widget> </item> <item> <widget class="QLabel" name="label_12"> <property name="text"> <string>y:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbGridSpY"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the spacing/resolution of the grid in the y direction.</body></html></string> </property> <property name="minimum"> <double>0.010000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> <property name="value"> <double>0.010000000000000</double> </property> </widget> </item> <item> <widget class="QLabel" name="label_11"> <property name="text"> <string>z:</string> </property> <property name="alignment"> <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="m_sbGridSpZ"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>10</width> <height>0</height> </size> </property> <property name="maximumSize"> <size> <width>50</width> <height>16777215</height> </size> </property> <property name="toolTip"> <string><html><head/><body>Indicate the spacing/resolution of the grid in the z direction.</body></html></string> </property> <property name="minimum"> <double>0.010000000000000</double> </property> <property name="maximum"> <double>9999.000000000000000</double> </property> <property name="value"> <double>0.010000000000000</double> </property> </widget> </item> </layout> </item> <item> <widget class="QLabel" name="label_27"> <property name="text"> <string>Orientation:</string> </property> </widget> </item> <item> <widget class="QTableWidget" name="m_tableOrientation"> <property name="enabled"> <bool>true</bool> </property> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="maximumSize"> <size> <width>160</width> <height>50</height> </size> </property> <property name="font"> <pointsize>7</pointsize> </property> <property name="showDropIndicator" stdset="0"> <bool>false</bool> </property> <property name="dragDropOverwriteMode"> <bool>false</bool> </property> <property name="wordWrap"> <bool>false</bool> </property> <property name="cornerButtonEnabled"> <bool>false</bool> </property> <attribute name="horizontalHeaderVisible"> <bool>false</bool> </attribute> <attribute name="horizontalHeaderMinimumSectionSize"> <number>20</number> </attribute> <attribute name="horizontalHeaderDefaultSectionSize"> <number>50</number> </attribute> <attribute name="verticalHeaderVisible"> <bool>false</bool> </attribute> <attribute name="verticalHeaderDefaultSectionSize"> <number>20</number> </attribute> <row> <property name="text"> <string>R1</string> </property> </row> <row> <property name="text"> <string>R2</string> </property> </row> <row> <property name="text"> <string>R3</string> </property> </row> <column> <property name="text"> <string>C1</string> </property> </column> <column> <property name="text"> <string>C2</string> </property> </column> <column> <property name="text"> <string>C3</string> </property> </column> <item row="0" column="0"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="0" column="1"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="0" column="2"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="1" column="0"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="1" column="1"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="1" column="2"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="2" column="0"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="2" column="1"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> <item row="2" column="2"> <property name="text"> <string>0</string> </property> <property name="flags"> <set>ItemIsEnabled</set> </property> </item> </widget> </item> <item> <widget class="QLabel" name="label_26"> <property name="text"> <string>FOV Reference:</string> </property> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_7"> <property name="spacing"> <number>3</number> </property> <item> <widget class="QmitkSingleNodeSelectionWidget" name="fovReferenceNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <layout class="QGridLayout" name="gridLayout"> <item row="0" column="0"> <widget class="QCheckBox" name="m_checkUseRefSize"> <property name="text"> <string>size</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="0" column="1"> <widget class="QCheckBox" name="m_checkUseRefOrigin"> <property name="text"> <string>origin</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="1" column="0"> <widget class="QCheckBox" name="m_checkUseRefSpacing"> <property name="text"> <string>spacing</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="1" column="1"> <widget class="QCheckBox" name="m_checkUseRefOrientation"> <property name="text"> <string>orientation</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </item> <item> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> </layout> </widget> </item> <item> <spacer name="verticalSpacer_5"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>ctkColorPickerButton</class> <extends>QPushButton</extends> <header>ctkColorPickerButton.h</header> </customwidget> </customwidgets> <resources/> <connections/> <designerdata> <property name="gridDeltaX"> <number>5</number> </property> <property name="gridDeltaY"> <number>5</number> </property> <property name="gridSnapX"> <bool>true</bool> </property> <property name="gridSnapY"> <bool>true</bool> </property> <property name="gridVisible"> <bool>true</bool> </property> </designerdata> </ui> diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox index d37a5712c8..1c52d57af5 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox @@ -1,90 +1,90 @@ /** \page org_mitk_views_measurement The Measurement View \imageMacro{measurement-dox.svg,"Icon of the Measurement View",2.00} <h1>Overview</h1> -The Measurement view allows you to measure distances, angles, paths and several geometric figures on 2D images or image slices of 3D and 4D images. The measurement view is repeatedly useable with the same or different measurement figures that are related to the chosen image and can be saved together with it for future use. +The Measurement view allows you to measure distances, angles, paths and several geometric figures on 2D images or image slices of 3D and 4D images. The measurement view is repeatedly usable with the same or different measurement figures that are related to the chosen image and can be saved together with it for future use. \imageMacro{QmitkMeasurementToolbox_BasicScreenEdited.jpg,"Image with measurements",16.00} <h1>Usage</h1> The first step to perform measurements is to select a reference image on top of the view. All resulting measurements will be assigned as child nodes of the image in the data manager. The standard working plane is 'Axial' but the other standard view planes ('Sagittal' and 'Coronal') are also valid for measurements. \imageMacro{QmitkMeasurementToolbox_MeasurementView.jpg,"Measurement View",7.60} After selecting an image, you can click on any of the geometrical symbols. The respective measurement will appear as soon as you click on the image location you want to measure. The view offers a variety of measurement options that are introduced in the following: <ul> <li> Line: Draws a line between two set points and returns the distance between these points. <li> Path: Draws a line between several set points (two and more) and calculates the overall length, which is all lines length summed up. Add the final point by double left-click. <li> Angle: Draws two lines from three set points connected in the second set point and return the inner angle at the second point. <li> Four Point / Double Angle: Draws two lines that may but do not have to intersect from four set points. The returned angle is the one depicted in the icon. <li> Circle: Draws a circle by setting two points, whereas the first set point is the center and the second the radius of the circle. The measured values are the radius and the included area. <li> Ellipse: Draws an ellipse that can be modified by three points. The middle point can be used to move the whole measurement. The lower point modifies the ellipse axes. The right point can be used to modify the radius of the ellipse. The measured values are the major and minor axes and the area. <li> Double Ellipse: Draws two ellipses by adjusting four points. The middle point can be used to move the whole measurement. The left point is used to adjust the distance between the two ellipses. The lower point modifies the ellipse axes. The right point can be used to modify the radius of the ellipse. Can be used for measuring e.g. the wall thickness of a vessel. The measured values are the major and minor axes and the thickness. <li> Rectangle: Draws a rectangle by setting two points at the opposing edges of the rectangle starting with the upper left corner. The measured values are the circumference and the included area. <li> Polygon: Draws a closed polygon that can have an arbitrary number of points. New points are added by left mouse-click. To finish the drawing the user can double click on the last control point. The measured values are circumference and area. <li> Bezier curve: Draws a bezier curve by adding some control points with left mouse-click. To finish the drawing the user can double-click on the last control point. The measured value is the length of the bezier curve. <li> Subdivision Polygon: Draws a closed subdivision polygon by adding some control points with left mouse-click. To finish the drawing the user can double-click on the last control point. The measured value is the circumference of the polygon. </ul> <h2>Fixed sizes of measurement figures</h2> The measurement view offers a fixed size for circle and double ellipses to preset a radius and a thickness. This is useful e.g. for diagnostic studies where you want to derive gray value statistics from a well defined region. <h2>Modify measurements</h2> All measurements can be modified later on by moving the respective control points. Note that they can only be modified if the view is open. <h2>Multiple measurement figures</h2> When applying more than one measurement figure to the image the actual measurement figure is depicted in red and the displayed values belong to this measurement figure. All other measurement figures appear white. They can be selected by a left-mouse click on the respective node. <h2>Save the measurement information</h2> The entire scene containing the image and the measurement figures can be saved for future use. Scenes are saved with a '.mitk' extension by pressing 'Save Project' and contain all nodes and relevant information. Alternatively, you can just save the measurement solely (with file extension '.pf') by right-click on the node in the data manager. The content of the measurement widget can be copied to the clipboard with the corresponding button for further use in a table calculation program (e.g. Open Office Calc etc.). <h2>Remove measurement figures or image</h2> If the single measurement figures or the image is not needed any longer, it can be removed solely or as an entire group. The image can't be removed without simultaneously removing all the dependent measurement figures that belong to the image tree in the data manager. To remove, just select the wanted items in the data manager list by right-clicking on the respective node or, if several items wanted to be removed, right-click on all wanted by simultaneously holding the ctrl-button pressed. */ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp index ada96a36f3..5fa5a9da06 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,469 +1,469 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkImageStatisticsView.h" #include <utility> // berry includes #include <berryIQtStyleManager.h> #include <berryWorkbenchPlugin.h> #include <QmitkChartWidget.h> #include <mitkImageStatisticsContainerNodeHelper.h> #include <mitkImageStatisticsPredicateHelper.h> #include <mitkImageTimeSelector.h> #include <mitkIntensityProfile.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateGeometry.h> #include <mitkNodePredicateSubGeometry.h> #include <mitkNodePredicateOr.h> #include <mitkNodePredicateFunction.h> #include <mitkSliceNavigationController.h> #include <mitkStatusBar.h> #include <mitkPlanarFigure.h> #include "mitkPlanarFigureMaskGenerator.h" #include "QmitkImageStatisticsDataGenerator.h" #include "mitkImageStatisticsContainerManager.h" #include <mitkPlanarFigureInteractor.h> const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; QmitkImageStatisticsView::~QmitkImageStatisticsView() { } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { m_Controls.setupUi(parent); m_Controls.widget_intensityProfile->SetTheme(GetColorTheme()); m_Controls.groupBox_histogram->setVisible(true); m_Controls.groupBox_intensityProfile->setVisible(false); m_Controls.label_currentlyComputingStatistics->setVisible(false); m_Controls.sliderWidget_histogram->setPrefix("Time: "); m_Controls.sliderWidget_histogram->setDecimals(0); m_Controls.sliderWidget_histogram->setVisible(false); m_Controls.sliderWidget_intensityProfile->setPrefix("Time: "); m_Controls.sliderWidget_intensityProfile->setDecimals(0); m_Controls.sliderWidget_intensityProfile->setVisible(false); ResetGUI(); m_DataGenerator = new QmitkImageStatisticsDataGenerator(parent); m_DataGenerator->SetDataStorage(this->GetDataStorage()); m_DataGenerator->SetAutoUpdate(true); m_Controls.widget_statistics->SetDataStorage(this->GetDataStorage()); m_Controls.imageNodesSelector->SetDataStorage(this->GetDataStorage()); m_Controls.imageNodesSelector->SetNodePredicate(mitk::GetImageStatisticsImagePredicate()); m_Controls.imageNodesSelector->SetSelectionCheckFunction(this->CheckForSameGeometry()); m_Controls.imageNodesSelector->SetSelectionIsOptional(false); m_Controls.imageNodesSelector->SetInvalidInfo(QStringLiteral("Please select images for statistics")); m_Controls.imageNodesSelector->SetPopUpTitel(QStringLiteral("Select input images")); m_Controls.roiNodesSelector->SetPopUpHint(QStringLiteral("You may select multiple images for the statistics computation. But all selected images must have the same geometry.")); m_Controls.roiNodesSelector->SetDataStorage(this->GetDataStorage()); m_Controls.roiNodesSelector->SetNodePredicate(this->GenerateROIPredicate()); m_Controls.roiNodesSelector->SetSelectionIsOptional(true); m_Controls.roiNodesSelector->SetEmptyInfo(QStringLiteral("Please select ROIs")); m_Controls.roiNodesSelector->SetPopUpTitel(QStringLiteral("Select ROIs for statistics computation")); m_Controls.roiNodesSelector->SetPopUpHint(QStringLiteral("You may select ROIs (e.g. planar figures, segmentations) that should be used for the statistics computation. The statistics will only computed for the image parts defined by the ROIs.")); CreateConnections(); this->m_TimePointChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_TimePointChangeListener, &QmitkSliceNavigationListener::SelectedTimePointChanged, this, & QmitkImageStatisticsView::OnSelectedTimePointChanged); } void QmitkImageStatisticsView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_TimePointChangeListener.RenderWindowPartActivated(renderWindowPart); } void QmitkImageStatisticsView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_TimePointChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void QmitkImageStatisticsView::CreateConnections() { connect(m_Controls.widget_statistics, &QmitkImageStatisticsWidget::IgnoreZeroValuedVoxelStateChanged, this, &QmitkImageStatisticsView::OnIgnoreZeroValuedVoxelStateChanged); connect(m_Controls.buttonSelection, &QAbstractButton::clicked, this, &QmitkImageStatisticsView::OnButtonSelectionPressed); connect(m_Controls.widget_histogram, &QmitkHistogramVisualizationWidget::RequestHistogramUpdate, this, &QmitkImageStatisticsView::OnRequestHistogramUpdate); connect(m_DataGenerator, &QmitkImageStatisticsDataGenerator::DataGenerationStarted, this, &QmitkImageStatisticsView::OnGenerationStarted); connect(m_DataGenerator, &QmitkImageStatisticsDataGenerator::GenerationFinished, this, &QmitkImageStatisticsView::OnGenerationFinished); connect(m_DataGenerator, &QmitkImageStatisticsDataGenerator::JobError, this, &QmitkImageStatisticsView::OnJobError); connect(m_Controls.imageNodesSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageStatisticsView::OnImageSelectionChanged); connect(m_Controls.roiNodesSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageStatisticsView::OnROISelectionChanged); connect(m_Controls.sliderWidget_intensityProfile, &ctkSliderWidget::valueChanged, this, &QmitkImageStatisticsView::UpdateIntensityProfile); } void QmitkImageStatisticsView::UpdateIntensityProfile() { m_Controls.groupBox_intensityProfile->setVisible(false); const auto selectedImageNodes = m_Controls.imageNodesSelector->GetSelectedNodes(); const auto selectedROINodes = m_Controls.roiNodesSelector->GetSelectedNodes(); if (selectedImageNodes.size()==1 && selectedROINodes.size()==1) { //only supported for one image and roi currently auto image = dynamic_cast<mitk::Image*>(selectedImageNodes.front()->GetData()); auto maskPlanarFigure = dynamic_cast<mitk::PlanarFigure*>(selectedROINodes.front()->GetData()); if (maskPlanarFigure != nullptr) { if (!maskPlanarFigure->IsClosed()) { mitk::Image::Pointer inputImage; if (image->GetDimension() == 4) { m_Controls.sliderWidget_intensityProfile->setVisible(true); unsigned int maxTimestep = image->GetTimeSteps(); m_Controls.sliderWidget_intensityProfile->setMaximum(maxTimestep - 1); // Intensity profile can only be calculated on 3D, so extract if 4D mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); int currentTimestep = static_cast<int>(m_Controls.sliderWidget_intensityProfile->value()); timeSelector->SetInput(image); timeSelector->SetTimeNr(currentTimestep); timeSelector->Update(); inputImage = timeSelector->GetOutput(); } else { m_Controls.sliderWidget_intensityProfile->setVisible(false); inputImage = image; } auto intensityProfile = mitk::ComputeIntensityProfile(inputImage, maskPlanarFigure); m_Controls.groupBox_intensityProfile->setVisible(true); m_Controls.widget_intensityProfile->Reset(); m_Controls.widget_intensityProfile->SetIntensityProfile(intensityProfile.GetPointer(), "Intensity Profile of " + selectedImageNodes.front()->GetName()); } } } } void QmitkImageStatisticsView::UpdateHistogramWidget() { m_Controls.groupBox_histogram->setVisible(false); const auto selectedImageNodes = m_Controls.imageNodesSelector->GetSelectedNodes(); const auto selectedMaskNodes = m_Controls.roiNodesSelector->GetSelectedNodes(); if (selectedImageNodes.size() == 1 && selectedMaskNodes.size()<=1) { //currently only supported for one image and roi due to histogram widget limitations. auto imageNode = selectedImageNodes.front(); const mitk::DataNode* roiNode = nullptr; const mitk::PlanarFigure* planarFigure = nullptr; if (!selectedMaskNodes.empty()) { roiNode = selectedMaskNodes.front(); planarFigure = dynamic_cast<const mitk::PlanarFigure*>(roiNode->GetData()); } if ((planarFigure == nullptr || planarFigure->IsClosed()) && imageNode->GetData()->GetTimeGeometry()->IsValidTimePoint(m_TimePointChangeListener.GetCurrentSelectedTimePoint())) { //if a planar figure is not closed, we show the intensity profile instead of the histogram. auto statisticsNode = m_DataGenerator->GetLatestResult(imageNode, roiNode, true); if (statisticsNode.IsNotNull()) { auto statistics = dynamic_cast<const mitk::ImageStatisticsContainer*>(statisticsNode->GetData()); if (statistics) { const auto timeStep = imageNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(m_TimePointChangeListener.GetCurrentSelectedTimePoint()); if (statistics->TimeStepExists(timeStep)) { std::stringstream label; label << imageNode->GetName(); if (imageNode->GetData()->GetTimeSteps() > 1) { label << "[" << timeStep << "]"; } if (roiNode) { label << " with " << roiNode->GetName(); } //Hardcoded labels are currently needed because the current histogram widget (and ChartWidget) - //do not allow correct removal or sound update/insertion of serveral charts. + //do not allow correct removal or sound update/insertion of several charts. //only thing that works for now is always to update/overwrite the same data label //This is a quick fix for T28223 and T28221 m_Controls.widget_histogram->SetHistogram(statistics->GetHistogramForTimeStep(timeStep), "histogram"); m_Controls.groupBox_histogram->setVisible(true); } } } } } } QmitkChartWidget::ColorTheme QmitkImageStatisticsView::GetColorTheme() const { ctkPluginContext *context = berry::WorkbenchPlugin::GetDefault()->GetPluginContext(); ctkServiceReference styleManagerRef = context->getServiceReference<berry::IQtStyleManager>(); if (styleManagerRef) { auto styleManager = context->getService<berry::IQtStyleManager>(styleManagerRef); if (styleManager->GetStyle().name == "Dark") { return QmitkChartWidget::ColorTheme::darkstyle; } else { return QmitkChartWidget::ColorTheme::lightstyle; } } return QmitkChartWidget::ColorTheme::darkstyle; } void QmitkImageStatisticsView::ResetGUI() { m_Controls.widget_statistics->Reset(); m_Controls.widget_statistics->setEnabled(false); m_Controls.widget_histogram->Reset(); m_Controls.widget_histogram->setEnabled(false); m_Controls.widget_histogram->SetTheme(GetColorTheme()); } void QmitkImageStatisticsView::OnGenerationStarted(const mitk::DataNode* /*imageNode*/, const mitk::DataNode* /*roiNode*/, const QmitkDataGenerationJobBase* /*job*/) { m_Controls.label_currentlyComputingStatistics->setVisible(true); } void QmitkImageStatisticsView::OnGenerationFinished() { m_Controls.label_currentlyComputingStatistics->setVisible(false); mitk::StatusBar::GetInstance()->Clear(); this->UpdateIntensityProfile(); this->UpdateHistogramWidget(); } void QmitkImageStatisticsView::OnSelectedTimePointChanged(const mitk::TimePointType& /*newTimePoint*/) { this->UpdateHistogramWidget(); } void QmitkImageStatisticsView::OnJobError(QString error, const QmitkDataGenerationJobBase* /*failedJob*/) { mitk::StatusBar::GetInstance()->DisplayErrorText(error.toStdString().c_str()); MITK_WARN << "Error when calculating statistics: " << error; } void QmitkImageStatisticsView::OnRequestHistogramUpdate(unsigned int nbins) { m_Controls.widget_statistics->SetHistogramNBins(nbins); m_DataGenerator->SetHistogramNBins(nbins); this->UpdateIntensityProfile(); this->UpdateHistogramWidget(); } void QmitkImageStatisticsView::OnIgnoreZeroValuedVoxelStateChanged(int state) { auto ignoreZeroValueVoxel = (state == Qt::Unchecked) ? false : true; m_Controls.widget_statistics->SetIgnoreZeroValueVoxel(ignoreZeroValueVoxel); m_DataGenerator->SetIgnoreZeroValueVoxel(ignoreZeroValueVoxel); this->UpdateIntensityProfile(); this->UpdateHistogramWidget(); } void QmitkImageStatisticsView::OnImageSelectionChanged(QmitkAbstractNodeSelectionWidget::NodeList /*nodes*/) { auto images = m_Controls.imageNodesSelector->GetSelectedNodesStdVector(); m_Controls.widget_statistics->SetImageNodes(images); m_Controls.widget_statistics->setEnabled(!images.empty()); m_Controls.roiNodesSelector->SetNodePredicate(this->GenerateROIPredicate()); m_DataGenerator->SetAutoUpdate(false); m_DataGenerator->SetImageNodes(images); m_DataGenerator->Generate(); m_DataGenerator->SetAutoUpdate(true); this->UpdateHistogramWidget(); this->UpdateIntensityProfile(); } void QmitkImageStatisticsView::OnROISelectionChanged(QmitkAbstractNodeSelectionWidget::NodeList /*nodes*/) { auto rois = m_Controls.roiNodesSelector->GetSelectedNodesStdVector(); m_Controls.widget_statistics->SetMaskNodes(rois); m_DataGenerator->SetAutoUpdate(false); m_DataGenerator->SetROINodes(rois); m_DataGenerator->Generate(); m_DataGenerator->SetAutoUpdate(true); this->UpdateHistogramWidget(); this->UpdateIntensityProfile(); } void QmitkImageStatisticsView::OnButtonSelectionPressed() { QmitkNodeSelectionDialog* dialog = new QmitkNodeSelectionDialog(nullptr, "Select input for the statistic","You may select images and ROIs to compute their statistic. ROIs may be segmentations or planar figures."); dialog->SetDataStorage(GetDataStorage()); dialog->SetSelectionCheckFunction(CheckForSameGeometry()); // set predicates auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto isImagePredicate = mitk::GetImageStatisticsImagePredicate(); auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); auto isImageOrMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isMaskOrPlanarFigurePredicate, isImagePredicate); dialog->SetNodePredicate(isImageOrMaskOrPlanarFigurePredicate); dialog->SetSelectionMode(QAbstractItemView::MultiSelection); dialog->SetCurrentSelection(m_Controls.imageNodesSelector->GetSelectedNodes()+m_Controls.roiNodesSelector->GetSelectedNodes()); if (dialog->exec()) { auto selectedNodeList = dialog->GetSelectedNodes(); m_Controls.imageNodesSelector->SetCurrentSelection(selectedNodeList); m_Controls.roiNodesSelector->SetCurrentSelection(selectedNodeList); } delete dialog; } QmitkNodeSelectionDialog::SelectionCheckFunctionType QmitkImageStatisticsView::CheckForSameGeometry() const { auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto lambda = [isMaskPredicate](const QmitkNodeSelectionDialog::NodeList& nodes) { if (nodes.empty()) { return std::string(); } const mitk::Image* imageNodeData = nullptr; for (auto& node : nodes) { auto castedData = dynamic_cast<const mitk::Image*>(node->GetData()); if (castedData != nullptr && !isMaskPredicate->CheckNode(node)) { imageNodeData = castedData; break; } } if (imageNodeData == nullptr) { std::stringstream ss; ss << "Select at least one image."; return ss.str(); } auto imageGeoPredicate = mitk::NodePredicateGeometry::New(imageNodeData->GetGeometry()); auto maskGeoPredicate = mitk::NodePredicateSubGeometry::New(imageNodeData->GetGeometry()); for (auto& rightNode : nodes) { if (imageNodeData != rightNode->GetData()) { bool validGeometry = true; if (isMaskPredicate->CheckNode(rightNode)) { validGeometry = maskGeoPredicate->CheckNode(rightNode); } else if (dynamic_cast<const mitk::Image*>(rightNode->GetData())) { validGeometry = imageGeoPredicate->CheckNode(rightNode); } else { const mitk::PlanarFigure* planar2 = dynamic_cast<const mitk::PlanarFigure*>(rightNode->GetData()); if (planar2) { validGeometry = mitk::PlanarFigureMaskGenerator::CheckPlanarFigureIsNotTilted(planar2->GetPlaneGeometry(), imageNodeData->GetGeometry()); } } if (!validGeometry) { std::stringstream ss; ss << "Invalid selection: All selected nodes must have the same geometry.Differing node i.a.: \""; ss << rightNode->GetName() <<"\""; return ss.str(); } } } return std::string(); }; return lambda; } mitk::NodePredicateBase::Pointer QmitkImageStatisticsView::GenerateROIPredicate() const { auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); mitk::NodePredicateBase::Pointer result = isMaskOrPlanarFigurePredicate.GetPointer(); if(!m_Controls.imageNodesSelector->GetSelectedNodes().empty()) { auto image = m_Controls.imageNodesSelector->GetSelectedNodes().front()->GetData(); auto imageGeoPredicate = mitk::NodePredicateSubGeometry::New(image->GetGeometry()); auto lambda = [image, imageGeoPredicate](const mitk::DataNode* node) { bool sameGeometry = true; if (dynamic_cast<const mitk::Image*>(node->GetData()) != nullptr) { sameGeometry = imageGeoPredicate->CheckNode(node); } else { const auto planar2 = dynamic_cast<const mitk::PlanarFigure*>(node->GetData()); if (planar2) { sameGeometry = mitk::PlanarFigureMaskGenerator::CheckPlanarFigureIsNotTilted(planar2->GetPlaneGeometry(), image->GetGeometry()); } } return sameGeometry; }; result = mitk::NodePredicateAnd::New(isMaskOrPlanarFigurePredicate, mitk::NodePredicateFunction::New(lambda)).GetPointer(); } return result; } diff --git a/Plugins/org.mitk.gui.qt.mitkworkbench.intro/src/internal/QmitkMitkWorkbenchIntroPart.h b/Plugins/org.mitk.gui.qt.mitkworkbench.intro/src/internal/QmitkMitkWorkbenchIntroPart.h index 8ae94926fa..83a0bbea8b 100644 --- a/Plugins/org.mitk.gui.qt.mitkworkbench.intro/src/internal/QmitkMitkWorkbenchIntroPart.h +++ b/Plugins/org.mitk.gui.qt.mitkworkbench.intro/src/internal/QmitkMitkWorkbenchIntroPart.h @@ -1,75 +1,75 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMitkWorkbenchIntroPart_h #define QmitkMitkWorkbenchIntroPart_h #include <QtCore/qconfig.h> #include <berryQtIntroPart.h> #include <ui_QmitkWelcomeScreenViewControls.h> /** * \ingroup org_mitk_gui_qt_welcomescreen_internal * \brief QmitkMitkWorkbenchIntroPart * The WelcomeView Module is an helpful feature to people new to MITK. The main idea is to provide first * information about the MITK Workbench. * The WelcomeView is realized by making use of the QTWebKit Module. The Qt WebKit module * provides an HTML browser engine that makes it easy to embed web content into native applications, and to enhance * web content with native controls. * For the welcome view of the application the QWebView, QWebPage classes have been used. The shown WelcomeView * html start page is styled by an external css stylesheet. The required resources as well as the html pages are integrated * into the QtResource system. The QT resource system allows the storage of files like html pages, css pages, jpgs etc. * as binaries within the executable. - * This minimizes the risk of loosing resource files as well as the risk of getting files deleted. In order to use the Qt + * This minimizes the risk of losing resource files as well as the risk of getting files deleted. In order to use the Qt * resource system the resource files have to be added to the associated qrt resource file list. * * The foundation is set to design more complex html pages. The Q::WebPage gives options to set a * LinkDelegationPolicy. The used policy defines how links to external or internal resources are handled. To fit our needs * the delegate all links policy is used. This requires all external as well as internal links of the html pages to be handle * explicitly. In order to change mitk working modes (perspectives) a mitk url scheme has been designed. The url scheme * is set to mitk. The url host provides information about what's next to do. In our case, the case of switching to a * particular working mode the host is set to perspectives. The followed path provides information about the perspective id. * (e.g. mitk//::mitk.perspectives/org.mitk.qt.defaultperspective) The the generic design of the mitk url scheme allows to * execute other task depending on the mitk url host. * \sa QmitkWelcomePage Editor */ class QmitkMitkWorkbenchIntroPart : public berry::QtIntroPart { // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: QmitkMitkWorkbenchIntroPart(); ~QmitkMitkWorkbenchIntroPart() override; void CreateQtPartControl(QWidget *parent) override; void StandbyStateChanged(bool) override; void SetFocus() override; void ReloadPage(); private: void CreateConnections(); void OnLoadFinished(bool ok); Ui::QmitkWelcomeScreenViewControls* m_Controls; class Impl; Impl* m_Impl; }; #endif diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox index e36ba450a7..06ca9f1d18 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox +++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox @@ -1,67 +1,67 @@ /** \page org_mitk_views_moviemaker The Movie Maker View \imageMacro{moviemakericon_black.svg,"Icon of the Movie Maker Plugin.",2.00} \tableofcontents \section org_mitk_views_moviemakerOverview Overview The Movie Maker View allows you to create basic animations of your scene and to record them to video files. Individual animations are arranged in a timeline and can be played back sequentially or in parallel. The Movie Maker View uses the external FFmpeg command-line application to write compressed video files. You must install FFmpeg and set its corresponding path in the "Movie Maker" preferences (Ctrl+P) to be able to record your movies to video files. \imageMacro{QmitkMovieMaker_Preferences.png,"The Movie Maker preferences page.",12.00} \section org_mitk_views_moviemakerUsage Usage \imageMacro{QmitkMovieMaker_MovieMakerView.png,"The Movie Maker View.",16.00} To create a movie, add an animation to the timeline by clicking the "Add animation" button. You can choose between the available types of animations, e.g., Orbit or Slice. -The bottons sourroundng the timeline allow you to arrange, remove, or add further animations to your movie. +The buttons surroundng the timeline allow you to arrange, remove, or add further animations to your movie. Each animation can be set to either begin with the previous animation, i.e., run in parallel, or to start after the previous animation, i.e., run sequentially. In combination with delays, rather complex animation arrangements are possible. To set animation specific parameters, select the corresponding animation in the timeline first. You can play back, pause and stop your movie with the controls at the bottom of the Movie Maker View. Click the "Record" button to finally record your movie to a video file with the specified frame rate resp. number of frames per second. Choose the render window that you want to record. By default, movies are recorded into *.webm files using the open and royalty-free VP9 video codec. You can switch to the widespread *.mp4 file format using the non-free H.264 video codec in the Movie Maker preferences. \subsection org_mitk_views_moviemakerOrbitUsage Orbit Animation The Orbit animation rotates the camera in the 3D window around the scene. -Align the camera directly in the 3D window and enter the number of degrees for the orbitting. +Align the camera directly in the 3D window and enter the number of degrees for the orbiting. If you are planning to have a specific view in the middle of your movie you can play the movie and pause it at the specific frame of interest. Adjust the camera in the 3D window and restart the animation. \imageMacro{QmitkMovieMaker_Orbit.png,"The Orbit animation.",12.00} \subsection org_mitk_views_moviemakerSliceUsage Slice Animation The Slice animation slices through an image. You can choose the image plane (axial, sagittal, or coronal), as well as the start and end points of the slicing. Look at the Image Navigator View to get an idea of the desired values. Toggle "Reverse" to slice from the higher slice number to the lower slice number. \imageMacro{QmitkMovieMaker_Slice.png,"The Slice animation.",12.00} \subsection org_mitk_views_moviemakerTimeUsage Time Animation The Time animation steps through the individual time steps of the current scene. You can specify the range of the animated time steps. Look at the Image Navigator View to get an idea of the desired values. Toggle "Reverse" to step from later time steps to previous time steps. \imageMacro{QmitkMovieMaker_Time.gif,"The Time animation.",12.00} */ diff --git a/Plugins/org.mitk.gui.qt.moviemaker/src/internal/QmitkScreenshotMaker.cpp b/Plugins/org.mitk.gui.qt.moviemaker/src/internal/QmitkScreenshotMaker.cpp index 22adac61e4..81fdc308ee 100644 --- a/Plugins/org.mitk.gui.qt.moviemaker/src/internal/QmitkScreenshotMaker.cpp +++ b/Plugins/org.mitk.gui.qt.moviemaker/src/internal/QmitkScreenshotMaker.cpp @@ -1,512 +1,512 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkScreenshotMaker.h" //#include "QmitkMovieMakerControls.h" #include "QmitkStepperAdapter.h" #include "mitkVtkPropRenderer.h" #include <QmitkRenderWindow.h> #include <QmitkRenderWindowWidget.h> #include <iostream> #include <vtkRenderer.h> #include <vtkCamera.h> #include <QAction> #include <QFileDialog> #include <QTimer> #include <QDateTime> #include <QSpinBox> #include <QComboBox> #include <QColor> #include <QColorDialog> #include <QApplication> #include "vtkImageWriter.h" #include "vtkJPEGWriter.h" #include "vtkPNGWriter.h" #include "vtkRenderLargeImage.h" #include "vtkRenderWindowInteractor.h" #include "vtkRenderer.h" #include "vtkTestUtilities.h" #include <vtkActor.h> #include "vtkMitkRenderProp.h" #include <vtkRenderer.h> #include <vtkRenderWindow.h> #include "vtkRenderWindowInteractor.h" #include <qradiobutton.h> #include "mitkSliceNavigationController.h" #include "mitkPlanarFigure.h" #include <mitkWorkbenchUtil.h> #include <mitkImage.h> #include <itksys/SystemTools.hxx> QmitkScreenshotMaker::QmitkScreenshotMaker(QObject *parent, const char * /*name*/) : QmitkAbstractView(), m_Controls(nullptr), m_BackgroundColor(QColor(0,0,0)), m_SelectedNode(nullptr) { parentWidget = parent; } QmitkScreenshotMaker::~QmitkScreenshotMaker() { } void QmitkScreenshotMaker::CreateConnections() { if (m_Controls) { connect((QObject*) m_Controls->m_AllViews, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateMultiplanar3DHighresScreenshot())); connect((QObject*) m_Controls->m_Shot, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateMultiplanarScreenshots())); connect((QObject*) m_Controls->m_BackgroundColor, SIGNAL(clicked()), (QObject*) this, SLOT(SelectBackgroundColor())); connect((QObject*) m_Controls->btnScreenshot, SIGNAL(clicked()), this, SLOT(GenerateScreenshot())); connect((QObject*) m_Controls->m_HRScreenshot, SIGNAL(clicked()), this, SLOT(Generate3DHighresScreenshot())); QString styleSheet = "background-color:rgb(0,0,0)"; m_Controls->m_BackgroundColor->setStyleSheet(styleSheet); } } mitk::DataNode::Pointer QmitkScreenshotMaker::GetTopLayerNode() { mitk::DataNode::Pointer out = nullptr; int layer = -1; auto nodes = GetDataStorage()->GetAll(); for (auto node = nodes->begin(); node!=nodes->end(); ++node) { if (!(*node)->IsVisible(nullptr)) continue; int current_layer; (*node)->GetIntProperty("layer", current_layer); if (current_layer>layer) { out = (*node); layer = current_layer; } } return out; } void QmitkScreenshotMaker::MultichannelScreenshot(mitk::VtkPropRenderer* renderer, QString fileName, QString filter) { auto node = GetTopLayerNode(); if (node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData())) { auto image = dynamic_cast<mitk::Image*>(node->GetData()); std::string fname = itksys::SystemTools::GetFilenamePath(fileName.toStdString()) + "/" + itksys::SystemTools::GetFilenameWithoutExtension(fileName.toStdString()); std::string ext = itksys::SystemTools::GetFilenameExtension(fileName.toStdString()); mitk::PixelType chPixelType = image->GetImageDescriptor()->GetChannelTypeById(0); if (image->GetDimension() == 4) { - MITK_INFO << "LOOPING THROUGH FOURTH DIMESNION IS NOT IMPLEMENTED"; + MITK_INFO << "LOOPING THROUGH FOURTH DIMENSION IS NOT IMPLEMENTED"; } else if (chPixelType.GetNumberOfComponents()>1) { for(int unsigned c=0; c<chPixelType.GetNumberOfComponents(); ++c) { node->SetProperty("Image.Displayed Component", mitk::IntProperty::New(c)); this->TakeScreenshot(renderer->GetVtkRenderer(), 1, QString(fname.c_str()) + "_" + QString::number(c) + QString(ext.c_str()), filter); } } else this->TakeScreenshot(renderer->GetVtkRenderer(), 1, fileName, filter); } else this->TakeScreenshot(renderer->GetVtkRenderer(), 1, fileName, filter); } void QmitkScreenshotMaker::GenerateScreenshot() { if (m_LastFile.size()==0) m_LastFile = QDir::currentPath()+"/screenshot.png"; QString filter; QString fileName = QFileDialog::getSaveFileName(nullptr, "Save screenshot to...", m_LastFile, m_PNGExtension + ";;" + m_JPGExtension, &filter); if (fileName.size()>0) m_LastFile = fileName; auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* renderer = renderWindowPart->GetQmitkRenderWindow(m_Controls->m_DirectionBox->currentText())->GetRenderer(); if (renderer == nullptr) return; if (m_Controls->m_AllChannelsBox->isChecked()) MultichannelScreenshot(renderer, fileName, filter); else this->TakeScreenshot(renderer->GetVtkRenderer(), 1, fileName, filter); } void QmitkScreenshotMaker::GenerateMultiplanarScreenshots() { if (m_LastPath.size()==0) m_LastPath = QDir::currentPath(); QString filePath = QFileDialog::getExistingDirectory(nullptr, "Save screenshots to...", m_LastPath); if (filePath.size()>0) m_LastPath = filePath; if( filePath.isEmpty() ) { return; } //emit StartBlockControls(); auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); renderWindowPart->EnableDecorations(false, QStringList{mitk::IRenderWindowPart::DECORATION_CORNER_ANNOTATION}); auto windowCount = m_Controls->m_DirectionBox->count(); for (int i = 0; i < windowCount; ++i) { auto windowName = m_Controls->m_DirectionBox->itemText(i); QString fileName = QDir::separator() + windowName + QString::fromStdString(".png"); int c = 1; while (QFile::exists(filePath + fileName)) { fileName = QDir::separator() + windowName + QString::fromStdString("_"); fileName += QString::number(c); fileName += ".png"; c++; } vtkRenderer* renderer = renderWindowPart->GetQmitkRenderWindow(windowName)->GetRenderer()->GetVtkRenderer(); if (renderer != nullptr) { if (m_Controls->m_AllChannelsBox->isChecked()) MultichannelScreenshot(renderWindowPart->GetQmitkRenderWindow(windowName)->GetRenderer(), filePath + fileName, m_PNGExtension); else this->TakeScreenshot(renderer, 1, filePath + fileName); } } /// TODO I do not find a simple way of doing this through the render window part API, /// however, I am also not convinced that this code is needed at all. The colour /// of the crosshair planes is never set to any colour other than these. /// I suggest a new 'mitk::DataNode* mitk::ILinkedRendererPart::GetSlicingPlane(const std::string& name) const' /// function to introduce that could return the individual ("axial", "sagittal" or /// "coronal" crosshair planes. // mitk::DataNode* n = renderWindowPart->GetSlicingPlane("axial"); // if (n) // { // n->SetProperty( "color", mitk::ColorProperty::New( 1,0,0 ) ); // } // // n = renderWindowPart->GetSlicingPlane("sagittal"); // if (n) // { // n->SetProperty( "color", mitk::ColorProperty::New( 0,1,0 ) ); // } // // n = renderWindowPart->GetSlicingPlane("coronal"); // if (n) // { // n->SetProperty( "color", mitk::ColorProperty::New( 0,0,1 ) ); // } renderWindowPart->EnableDecorations(true, QStringList{mitk::IRenderWindowPart::DECORATION_CORNER_ANNOTATION}); } void QmitkScreenshotMaker::Generate3DHighresScreenshot() { if (m_LastFile.size()==0) m_LastFile = QDir::currentPath()+"/3D_screenshot.png"; QString filter; QString fileName = QFileDialog::getSaveFileName(nullptr, "Save screenshot to...", m_LastFile, m_PNGExtension + ";;" + m_JPGExtension, &filter); if (fileName.size()>0) m_LastFile = fileName; GenerateHR3DAtlasScreenshots(fileName, filter); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkScreenshotMaker::GenerateMultiplanar3DHighresScreenshot() { if (m_LastPath.size()==0) m_LastPath = QDir::currentPath(); QString filePath = QFileDialog::getExistingDirectory( nullptr, "Save screenshots to...", m_LastPath); if (filePath.size()>0) m_LastPath = filePath; if( filePath.isEmpty() ) { return; } QString fileName = "/3D_View1.png"; int c = 1; while (QFile::exists(filePath+fileName)) { fileName = QString("/3D_View1_"); fileName += QString::number(c); fileName += ".png"; c++; } GetCam()->Azimuth( -7.5 ); GetCam()->Roll(-4); GenerateHR3DAtlasScreenshots(filePath+fileName); GetCam()->Roll(4); fileName = "/3D_View2.png"; c = 1; while (QFile::exists(filePath+fileName)) { fileName = QString("/3D_View2_"); fileName += QString::number(c); fileName += ".png"; c++; } GetCam()->Azimuth( 90 ); GetCam()->Elevation( 4 ); GenerateHR3DAtlasScreenshots(filePath+fileName); fileName = "/3D_View3.png"; c = 1; while (QFile::exists(filePath+fileName)) { fileName = QString("/3D_View3_"); fileName += QString::number(c); fileName += ".png"; c++; } GetCam()->Elevation( 90 ); GetCam()->Roll( -2.5 ); GenerateHR3DAtlasScreenshots(filePath+fileName); GetCam()->Roll( 2.5 ); // not negative because direction of elevation has flipped GetCam()->Elevation( 94 ); GetCam()->Azimuth( -82.5 ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkScreenshotMaker::GenerateHR3DAtlasScreenshots(QString fileName, QString filter) { // only works correctly for 3D RenderWindow auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* renderer = renderWindowPart->GetQmitkRenderWindow("3d")->GetRenderer()->GetVtkRenderer(); if (nullptr != renderer) { renderWindowPart->EnableDecorations(false); this->TakeScreenshot(renderer, this->m_Controls->m_MagFactor->text().toFloat(), fileName, filter); renderWindowPart->EnableDecorations(true); } } vtkCamera* QmitkScreenshotMaker::GetCam() { auto* renderer = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("3d")->GetRenderer(); vtkCamera* cam = nullptr; const mitk::VtkPropRenderer *propRenderer = dynamic_cast<const mitk::VtkPropRenderer * >( renderer ); if (propRenderer) { // get vtk renderer vtkRenderer* vtkrenderer = propRenderer->GetVtkRenderer(); if (vtkrenderer) { // get vtk camera vtkCamera* vtkcam = vtkrenderer->GetActiveCamera(); if (vtkcam) { // vtk smart pointer handling cam = vtkcam; cam->Register( nullptr ); } } } return cam; } void QmitkScreenshotMaker::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes) { if(nodes.size()) m_SelectedNode = nodes[0]; } void QmitkScreenshotMaker::UpdateDirectionBox(mitk::IRenderWindowPart* renderWindowPart) { m_Controls->m_DirectionBox->clear(); auto renderWindows = renderWindowPart->GetQmitkRenderWindows(); bool has3DWindow = false; for (auto name : renderWindows.keys()) { auto window = renderWindows[name]; if (window->GetRenderer()->GetMapperID() == mitk::BaseRenderer::Standard3D) { has3DWindow = true; } else { auto windowName = name; auto renderWindowWidget = dynamic_cast<QmitkRenderWindowWidget*>(window->parentWidget()); if (renderWindowWidget) { windowName = QString::fromStdString(renderWindowWidget->GetCornerAnnotationText()); } m_Controls->m_DirectionBox->insertItem(m_Controls->m_DirectionBox->count() + 1, windowName); } } renderWindows = renderWindowPart->GetQmitkRenderWindows(); m_Controls->groupBox->setEnabled(has3DWindow); } void QmitkScreenshotMaker::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { m_Parent = parent; m_Controls = new Ui::QmitkScreenshotMakerControls; m_Controls->setupUi(parent); auto renderWindowPart = this->GetRenderWindowPart(); if (renderWindowPart) { this->UpdateDirectionBox(renderWindowPart); } // Initialize "Selected Window" combo box const mitk::RenderingManager::RenderWindowVector rwv = mitk::RenderingManager::GetInstance()->GetAllRegisteredRenderWindows(); } this->CreateConnections(); } void QmitkScreenshotMaker::SetFocus() { m_Controls->btnScreenshot->setFocus(); } void QmitkScreenshotMaker::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { m_Parent->setEnabled(true); this->UpdateDirectionBox(renderWindowPart); } void QmitkScreenshotMaker::RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderWindowPart) { this->UpdateDirectionBox(renderWindowPart); } void QmitkScreenshotMaker::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_Parent->setEnabled(false); m_Controls->m_DirectionBox->clear(); } void QmitkScreenshotMaker::TakeScreenshot(vtkRenderer* renderer, unsigned int magnificationFactor, QString fileName, QString filter) { if ((renderer == nullptr) ||(magnificationFactor < 1) || fileName.isEmpty()) return; bool doubleBuffering( renderer->GetRenderWindow()->GetDoubleBuffer() ); renderer->GetRenderWindow()->DoubleBufferOff(); vtkImageWriter* fileWriter = nullptr; QFileInfo fi(fileName); QString suffix = fi.suffix().toLower(); if (suffix.isEmpty() || (suffix != "png" && suffix != "jpg" && suffix != "jpeg")) { if (filter == m_PNGExtension) { suffix = "png"; } else if (filter == m_JPGExtension) { suffix = "jpg"; } fileName += "." + suffix; } if (suffix.compare("jpg", Qt::CaseInsensitive) == 0 || suffix.compare("jpeg", Qt::CaseInsensitive) == 0) { vtkJPEGWriter* w = vtkJPEGWriter::New(); w->SetQuality(100); w->ProgressiveOff(); fileWriter = w; } else //default is png { fileWriter = vtkPNGWriter::New(); } vtkRenderLargeImage* magnifier = vtkRenderLargeImage::New(); magnifier->SetInput(renderer); magnifier->SetMagnification(magnificationFactor); //magnifier->Update(); fileWriter->SetInputConnection(magnifier->GetOutputPort()); fileWriter->SetFileName(fileName.toLatin1()); // vtkRenderLargeImage has problems with different layers, therefore we have to // temporarily deactivate all other layers. // we set the background to white, because it is nicer than black... double oldBackground[3]; renderer->GetBackground(oldBackground); // QColor color = QColorDialog::getColor(); double bgcolor[] = {m_BackgroundColor.red()/255.0, m_BackgroundColor.green()/255.0, m_BackgroundColor.blue()/255.0}; renderer->SetBackground(bgcolor); mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); renderWindowPart->EnableDecorations(false); fileWriter->Write(); fileWriter->Delete(); renderWindowPart->EnableDecorations(true); renderer->SetBackground(oldBackground); renderer->GetRenderWindow()->SetDoubleBuffer(doubleBuffering); } void QmitkScreenshotMaker::SelectBackgroundColor() { m_BackgroundColor = QColorDialog::getColor(); m_Controls->m_BackgroundColor->setAutoFillBackground(true); QString styleSheet = "background-color:rgb("; styleSheet.append(QString::number(m_BackgroundColor.red())); styleSheet.append(","); styleSheet.append(QString::number(m_BackgroundColor.green())); styleSheet.append(","); styleSheet.append(QString::number(m_BackgroundColor.blue())); styleSheet.append(")"); m_Controls->m_BackgroundColor->setStyleSheet(styleSheet); } diff --git a/Plugins/org.mitk.gui.qt.overlaymanager/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.overlaymanager/documentation/doxygen/modules.dox index 82586ab590..1fdb12fbbf 100644 --- a/Plugins/org.mitk.gui.qt.overlaymanager/documentation/doxygen/modules.dox +++ b/Plugins/org.mitk.gui.qt.overlaymanager/documentation/doxygen/modules.dox @@ -1,16 +1,16 @@ /** \defgroup org_mitk_gui_qt_overlaymanager org.mitk.gui.qt.overlaymanager \ingroup MITKPlugins - \brief This is the overlaymanager plugin. Annotations that have been addded to the OverlayManager can be viewed and modified. The plugin also allows to add new annotations. + \brief This is the overlaymanager plugin. Annotations that have been added to the OverlayManager can be viewed and modified. The plugin also allows to add new annotations. */ /** \defgroup org_mitk_gui_qt_overlaymanager_internal Internal \ingroup org_mitk_gui_qt_overlaymanager \brief This subcategory includes the internal classes of the org.mitk.gui.qt.overlaymanager plugin. Other plugins must not rely on these classes. They contain implementation details and their interface may change at any time. We mean it. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox index 1ed993e8e2..dc7a2ebaa9 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/documentation/UserManual/Manual.dox @@ -1,105 +1,103 @@ /** \page org_mitk_views_pharmacokinetics_mri The DCE MR Perfusion DataFit View \imageMacro{pharmacokinetics_mri_doc.svg,"Icon of the DCE MR Perfusion View",3.0} \tableofcontents \section FIT_DCE_Introduction Introduction In dynamic contrast-enhanced (DCE) MRI, pharmacokinetic (PK) modeling can be used to quantify tissue physiology. Parameters describing the tissue microvasculature can be derived by fitting a pharmacokinetic model, e.g. a compartment model, to the dynamic data. This view offers a comprehensive set of tools to perform pharmacokinetic analysis. \section FIT_DCE_Contact Contact information If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \subsection FIT_DCE_Cite Citation information If you use the view for your research please cite our work as reference:\n\n Debus C and Floca R, Ingrisch M, Kompan I, Maier-Hein K, Abdollahi A, Nolden M, MITK-ModelFit: generic open-source framework for model fits and their exploration in medical imaging – design, implementation and application on the example of DCE-MRI. https://doi.org/10.1186/s12859-018-2588-1 (BMC Bioinformatics 2019 20:31) \section FIT_DCE_Data_and_ROI_Selection Time series and mask selection \imageMacro{dce_mri_maskAndFittingStrategy.png, "Time series and mask selection.", 10} In principle, every model can be fitted on the entire image. However, for model configuration reasons (e.g. AIF required) and computational time cost, this is often not advisable. Therefore, apart from the image to be fitted (Selected Time Series), a ROI segmentation can be defined (Selected Mask), within which model fitting is performed. The view currently offers Pixel based and/or ROI based averaged fits of time-varying curves. The ROI based fitting option becomes enabled, if a mask is selected. \section FIT_DCE_General_models Supported models Currently the following pharmacokinetic models for gadolinium-based contrast agent are available: - The Descriptive Brix model \ref FIT_DCE_lit_ref1 "[1]" -- A semi-quantitative two/three segment linear model (2SL/3SL) - The standard tofts model \ref FIT_DCE_lit_ref2 "[2]" - The extended Tofts model \ref FIT_DCE_lit_ref3 "[3]" - The two compartment exchange model (2CXM) \ref FIT_DCE_lit_ref4 "[4, 5]" \section FIT_DCE_Settings Model settings \imageMacro{dce_mri_modelSettings.png, "Model settings of the view for the standard Tofts model.", 10} \subsection FIT_DCE_Settings_model Model specific settings Selecting one of the \ref FIT_DCE_General_models "supported models" will open below tabs for further configuration of the model. - The descriptive Brix model requires only definition of the duration of the bolus, i.e. the overall time of the injection (Injection Time [min]). -- The 3SL is a semi-quantitative descriptive model that distinguishes three different segments of the signal: A constant baseline, the initial fast rise (wash-in) and the final slow rise / signal decrease (washout). Each of these segments is approximated by a linear curve, with change points in-between. It requires no further configuration. - The standard Tofts model, the extended Tofts model and the 2CXM are compartment models that require the input of the concentration time curve in the tissue feeding artery, the arterial input function (AIF). In the DCE MR Perfusion Datafit View, the arterial input function can be defined in several ways. For patient individual image derived AIFs, select the radio button Select AIF from Image. In that case, a segmentation ROI for the artery has to be selected. This can be done by clicking on the AIF Mask selection widget and selecting a suitable AIF segmentation from the data loaded in the Data Manager. In cases where the respective artery does not lie in the same image as the investigated tissue (e.g. in animal experiments, where a slice through the heart is used for AIF extraction), a dedicated AIF image can be selected using the corresponding Dedicated AIF image selection widget. An alternative option is to define the AIF via an external file by selecting Select AIF from File (e.g. for population derived AIFs or AIFs from blood sampling). By clicking the Browse button, one can select a csv file that holds the AIF values and corresponding timepoints (in tuple format (Time, Value)). Caution: the file must not contain a header line, but the first line must start with Time and Intensity values. Furthermore, the Hematocrit Level has to be set (from 0 to 1) for conversion from whole blood to plasma concentration. It is set as default to the literature value of 0.45. \subsection FIT_DCE_Settings_start Start parameter \imageMacro{dce_mri_start.png, "Example screenshot for start parameter settings.", 10} In cases of noisy data it can be useful to define the initial starting values of the parameter estimates, at which optimization starts, in order to prevent optimization results in local optima. Each model has default scalar values (applied to every voxel) for initial values of each parameter, however these can be adjusted. Moreover, initial values can also be defined locally for each individual voxel via starting value images. To load a starting value image, change the Type from scalar to image. This can be done by double-clicking on the type cell. In the Value column, selection of a starting value image will be available. \subsection FIT_DCE_Settings_constraint Constraints settings \imageMacro{dce_mri_constraints.png, "Example screenshot for constraints settings.", 10} To limit the fitting search space and to exclude unphysical/illogical results for model parameter estimates, constraints to individual parameters as well as combinations can be imposed. Each model has default constraints, however, new ones can be defined or removed by the + and – buttons in the table. The first column specifies the parameter(s) involved in the constraint (if multiple parameters are selected, their sum will be used) by selection in the drop down menu. The second column Type defines whether the constraint defines an upper or lower boundary. Value defines the actual constraint value, that should not be crossed, and Width allows for a certain tolerance width. \subsection FIT_DCE_Settings_concentration Signal to concentration conversion settings \imageMacro{dce_mri_concentration.png, "Example screenshot for concentration conversion settings.", 10} Most models require contrast agent concentration values as input rather than raw signal intensities (i.e. all compartment models). The DCE MR Perfusion DataFit View offers a variety of tools for the conversion from signal to concentration: by means of relative and absolute signal enhancement, via a T1-map calculated by the variable flip angle method, as well as a special conversion for turbo flash sequences. A more detailed description of these conversion methods, for example the exact formulas used for the absolute and relative signal enhancement calculations, can be found here: \ref org_mitk_views_pharmacokinetics_concentration_mri. For the conversion methods, a baseline image prior to contrast agent arrival is required. In many data sets, multiple baseline images are available. The Baseline Range Selection allows for selection of a range of time frames, from which the average image (along the time dimension) is calculated and set as baseline input image. Remark: The number of the first time frame is 0. \section FIT_DCE_Fitting Executing a fit In order to distinguish results from different model fits to the data, a Fitting name can be defined. As default, the name of the model and the fitting strategy (pixel/ROI) are given. This name will then be appended by the respective parameter name.\n\n For development purposes and evaluation of the fits, the option Generate debug parameter images is available. Enabling this option will result in additional parameter maps displaying the status of the optimizer at fit termination. In the following definitions, an evaluation describes the process of cost function calculation and evaluation by the optimizer for a given parameter set. - Stop condition: Reasons for the fit termination, i.e. criterion reached, maximum number of iterations,... - Optimization time: The overall time from fitting start to termination. - Number of iterations: The number of iterations from fitting start to termination. - Constraint penalty ratio: Ratio between evaluations that were penalized and all evaluations. 0.0 means no evaluation was penalized; 1.0 all evaluations were. Evaluations that hit the failure threshold count as penalized, too. - Constraint last failed parameter: Ratio between evaluations that were beyond the failure threshold. 0.0 means no evaluation was a failure (but some may be penalized). - Constraint failure ratio: Index of the first (in terms of index position) parameter, which failed the constraints in the last evaluation. After all necessary configurations are set, the button Start Modelling is enabled, which starts the fitting routine. Progress can be seen in the message box on the bottom. Resulting parameter maps will afterwards be added to the Data Manager as sub-nodes of the analyzed 4D image. \section FIT_DCE_lit References/Literature - \anchor FIT_DCE_lit_ref1 [1] Brix G, Semmler W, Port R, Schad LR, Layer G, Lorenz WJ. Pharmacokinetic parameters in CNS Gd-DTPA enhanced MR imaging. J Comput Assist Tomogr. 1991;15:621–8. - \anchor FIT_DCE_lit_ref2 [2] Tofts PS, Kermode AG. Measurement of the blood-brain barrier permeability and leakage space using dynamic MR imaging. 1. Fundamental concepts. Magn Reson Med. 1991;17:357–67. - \anchor FIT_DCE_lit_ref3 [3] Sourbron SP, Buckley DL. On the scope and interpretation of the Tofts models for DCE-MRI. Magn Reson Med. 2011;66:735–45. - \anchor FIT_DCE_lit_ref4 [4] Brix G, Kiessling F, Lucht R, Darai S, Wasser K, Delorme S, et al. Microcirculation and microvasculature in breast tumors: Pharmacokinetic analysis of dynamic MR image series. Magn Reson Med. 2004;52:420–9. - \anchor FIT_DCE_lit_ref5 [5] Sourbron, Buckley. Tracer kinetic modelling in MRI: estimating perfusion and capillary permeability - pdf. Phys Med Biol. 2012. https://iopscience.iop.org/article/10.1088/0031-9155/57/2/R1/pdf. Accessed 1 May 2016. */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp index 5158170817..95b4584c78 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp @@ -1,1485 +1,1362 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "MRPerfusionView.h" #include "boost/tokenizer.hpp" #include "boost/math/constants/constants.hpp" #include <iostream> #include "mitkWorkbenchUtil.h" #include "mitkAterialInputFunctionGenerator.h" #include "mitkConcentrationCurveGenerator.h" #include <mitkDescriptivePharmacokineticBrixModelFactory.h> #include <mitkDescriptivePharmacokineticBrixModelParameterizer.h> #include <mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.h> -#include "mitkThreeStepLinearModelFactory.h" -#include "mitkThreeStepLinearModelParameterizer.h" -#include "mitkTwoStepLinearModelFactory.h" -#include "mitkTwoStepLinearModelParameterizer.h" #include <mitkExtendedToftsModelFactory.h> #include <mitkExtendedToftsModelParameterizer.h> #include <mitkStandardToftsModelFactory.h> #include <mitkStandardToftsModelParameterizer.h> #include "mitkTwoCompartmentExchangeModelFactory.h" #include "mitkTwoCompartmentExchangeModelParameterizer.h" -#include "mitkNumericTwoCompartmentExchangeModelFactory.h" -#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" #include <mitkInitialParameterizationDelegateBase.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateOr.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateDimension.h> #include "mitkNodePredicateFunction.h" #include <mitkPixelBasedParameterFitImageGenerator.h> #include <mitkROIBasedParameterFitImageGenerator.h> #include <mitkLevenbergMarquardtModelFitFunctor.h> #include <mitkSumOfSquaredDifferencesFitCostFunction.h> #include <mitkNormalizedSumOfSquaredDifferencesFitCostFunction.h> #include <mitkSimpleBarrierConstraintChecker.h> #include <mitkModelFitResultHelper.h> #include <mitkImageTimeSelector.h> #include <mitkMaskedDynamicImageStatisticsGenerator.h> #include <mitkExtractTimeGrid.h> #include <mitkModelFitResultRelationRule.h> #include <QMessageBox> #include <QThreadPool> #include <QFileDialog> // Includes for image casting between ITK and MITK #include <mitkImage.h> #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include <itkImage.h> #include <itkImageRegionIterator.h> const std::string MRPerfusionView::VIEW_ID = "org.mitk.views.pharmacokinetics.mri"; inline double convertToDouble(const std::string& data) { std::istringstream stepStream(data); stepStream.imbue(std::locale("C")); double value = 0.0; if (!(stepStream >> value) || !(stepStream.eof())) { mitkThrow() << "Cannot convert string to double. String: " << data; } return value; } void MRPerfusionView::SetFocus() { m_Controls.btnModelling->setFocus(); } void MRPerfusionView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_Controls.btnModelling->setEnabled(false); this->InitModelComboBox(); m_Controls.timeSeriesNodeSelector->SetNodePredicate(this->m_isValidTimeSeriesImagePredicate); m_Controls.timeSeriesNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.timeSeriesNodeSelector->SetSelectionIsOptional(false); m_Controls.timeSeriesNodeSelector->SetInvalidInfo("Please select time series."); m_Controls.timeSeriesNodeSelector->SetAutoSelectNewNodes(true); m_Controls.maskNodeSelector->SetNodePredicate(this->m_IsMaskPredicate); m_Controls.maskNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.maskNodeSelector->SetSelectionIsOptional(true); m_Controls.maskNodeSelector->SetEmptyInfo("Please select (optional) mask."); connect(m_Controls.btnModelling, SIGNAL(clicked()), this, SLOT(OnModellingButtonClicked())); connect(m_Controls.comboModel, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int))); connect(m_Controls.radioPixelBased, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.timeSeriesNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &MRPerfusionView::OnNodeSelectionChanged); connect(m_Controls.maskNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &MRPerfusionView::OnNodeSelectionChanged); connect(m_Controls.AIFMaskNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &MRPerfusionView::UpdateGUIControls); connect(m_Controls.AIFImageNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &MRPerfusionView::UpdateGUIControls); //AIF setting m_Controls.groupAIF->hide(); m_Controls.btnAIFFile->setEnabled(false); m_Controls.btnAIFFile->setEnabled(false); m_Controls.radioAIFImage->setChecked(true); m_Controls.AIFMaskNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.AIFMaskNodeSelector->SetNodePredicate(m_IsMaskPredicate); m_Controls.AIFMaskNodeSelector->setVisible(true); m_Controls.AIFMaskNodeSelector->setEnabled(true); m_Controls.AIFMaskNodeSelector->SetAutoSelectNewNodes(true); m_Controls.AIFImageNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.AIFImageNodeSelector->SetNodePredicate(this->m_isValidTimeSeriesImagePredicate); m_Controls.AIFImageNodeSelector->setEnabled(false); m_Controls.checkDedicatedAIFImage->setEnabled(true); m_Controls.HCLSpinBox->setValue(mitk::AterialInputFunctionGenerator::DEFAULT_HEMATOCRIT_LEVEL); m_Controls.spinBox_baselineEndTimeStep->setMinimum(0); m_Controls.spinBox_baselineStartTimeStep->setMinimum(0); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFMaskNodeSelector, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.labelAIFMask, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFMaskNodeSelector, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFImageNodeSelector, SLOT(setVisible(bool))); connect(m_Controls.checkDedicatedAIFImage, SIGNAL(toggled(bool)), m_Controls.AIFImageNodeSelector, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.btnAIFFile, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.aifFilePath, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.btnAIFFile, SIGNAL(clicked()), this, SLOT(LoadAIFfromFile())); //Brix setting m_Controls.groupDescBrix->hide(); connect(m_Controls.injectiontime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); //Num2CX setting m_Controls.groupNum2CXM->hide(); connect(m_Controls.odeStepSize, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); //Model fit configuration m_Controls.groupBox_FitConfiguration->hide(); m_Controls.checkBox_Constraints->setEnabled(false); m_Controls.constraintManager->setEnabled(false); m_Controls.initialValuesManager->setEnabled(false); m_Controls.initialValuesManager->setDataStorage(this->GetDataStorage()); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.initialValuesManager, SIGNAL(initialValuesChanged(void)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), m_Controls.initialValuesManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setVisible(bool))); //Concentration m_Controls.groupConcentration->hide(); m_Controls.groupBoxEnhancement->hide(); m_Controls.groupBoxTurboFlash->hide(); m_Controls.radioButtonNoConversion->setChecked(true); m_Controls.groupBox_T1MapviaVFA->hide(); m_Controls.spinBox_baselineStartTimeStep->setValue(0); m_Controls.spinBox_baselineEndTimeStep->setValue(0); connect(m_Controls.radioButtonTurboFlash, SIGNAL(toggled(bool)), m_Controls.groupBoxTurboFlash, SLOT(setVisible(bool))); connect(m_Controls.radioButtonTurboFlash, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.relaxationtime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.recoverytime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.relaxivity, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), m_Controls.groupBoxEnhancement, SLOT(setVisible(bool))); connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), m_Controls.groupBoxEnhancement, SLOT(setVisible(bool))); connect(m_Controls.factorSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.spinBox_baselineStartTimeStep, SIGNAL(valueChanged(int)), this, SLOT(UpdateGUIControls())); connect(m_Controls.spinBox_baselineEndTimeStep, SIGNAL(valueChanged(int)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButtonUsingT1viaVFA, SIGNAL(toggled(bool)), m_Controls.groupBox_T1MapviaVFA, SLOT(setVisible(bool))); connect(m_Controls.radioButtonUsingT1viaVFA, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.FlipangleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.RelaxivitySpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.TRSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); m_Controls.PDWImageNodeSelector->SetNodePredicate(m_isValidPDWImagePredicate); m_Controls.PDWImageNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.PDWImageNodeSelector->SetInvalidInfo("Please select PDW Image."); m_Controls.PDWImageNodeSelector->setEnabled(false); connect(m_Controls.radioButtonUsingT1viaVFA, SIGNAL(toggled(bool)), m_Controls.PDWImageNodeSelector, SLOT(setEnabled(bool))); UpdateGUIControls(); } bool MRPerfusionView::IsTurboFlashSequenceFlag() const { return this->m_Controls.radioButtonTurboFlash->isChecked(); }; void MRPerfusionView::UpdateGUIControls() { m_Controls.lineFitName->setPlaceholderText(QString::fromStdString(this->GetDefaultFitName())); m_Controls.lineFitName->setEnabled(!m_FittingInProgress); m_Controls.checkBox_Constraints->setEnabled(m_modelConstraints.IsNotNull()); bool isDescBrixFactory = dynamic_cast<mitk::DescriptivePharmacokineticBrixModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isToftsFactory = dynamic_cast<mitk::StandardToftsModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast<mitk::ExtendedToftsModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr || - dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool isNum2CXMFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; - bool isSLFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr || - dynamic_cast<mitk::TwoStepLinearModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; m_Controls.groupAIF->setVisible(isToftsFactory || is2CXMFactory); m_Controls.groupDescBrix->setVisible(isDescBrixFactory); - m_Controls.groupNum2CXM->setVisible(isNum2CXMFactory); - m_Controls.groupConcentration->setVisible(isToftsFactory || is2CXMFactory || isSLFactory); + m_Controls.groupConcentration->setVisible(isToftsFactory || is2CXMFactory ); m_Controls.groupBox_FitConfiguration->setVisible(m_selectedModelFactory); m_Controls.groupBox->setEnabled(!m_FittingInProgress); m_Controls.comboModel->setEnabled(!m_FittingInProgress); m_Controls.groupAIF->setEnabled(!m_FittingInProgress); m_Controls.groupDescBrix->setEnabled(!m_FittingInProgress); m_Controls.groupNum2CXM->setEnabled(!m_FittingInProgress); m_Controls.groupConcentration->setEnabled(!m_FittingInProgress); m_Controls.groupBox_FitConfiguration->setEnabled(!m_FittingInProgress); m_Controls.radioROIbased->setEnabled(m_selectedMask.IsNotNull()); m_Controls.btnModelling->setEnabled(m_selectedImage.IsNotNull() && m_selectedModelFactory.IsNotNull() && !m_FittingInProgress && CheckModelSettings()); m_Controls.spinBox_baselineStartTimeStep->setEnabled(m_Controls.radioButtonTurboFlash->isChecked() || m_Controls.radioButton_absoluteEnhancement->isChecked() || m_Controls.radioButton_relativeEnchancement->isChecked() || m_Controls.radioButtonUsingT1viaVFA->isChecked()); m_Controls.spinBox_baselineEndTimeStep->setEnabled(m_Controls.radioButton_absoluteEnhancement->isChecked() || m_Controls.radioButton_relativeEnchancement->isChecked() || m_Controls.radioButtonUsingT1viaVFA->isChecked() || m_Controls.radioButtonTurboFlash->isChecked()); } void MRPerfusionView::OnModellSet(int index) { m_selectedModelFactory = nullptr; if (index > 0) { if (static_cast<ModelFactoryStackType::size_type>(index) <= m_FactoryStack.size() ) { m_selectedModelFactory = m_FactoryStack[index - 1]; } else { MITK_WARN << "Invalid model index. Index outside of the factory stack. Factory stack size: "<< m_FactoryStack.size() << "; invalid index: "<< index; } } if (m_selectedModelFactory) { this->m_modelConstraints = dynamic_cast<mitk::SimpleBarrierConstraintChecker*> (m_selectedModelFactory->CreateDefaultConstraints().GetPointer()); m_Controls.initialValuesManager->setInitialValues(m_selectedModelFactory->GetParameterNames(), m_selectedModelFactory->GetDefaultInitialParameterization()); if (this->m_modelConstraints.IsNull()) { this->m_modelConstraints = mitk::SimpleBarrierConstraintChecker::New(); } m_Controls.constraintManager->setChecker(this->m_modelConstraints, this->m_selectedModelFactory->GetParameterNames()); } UpdateGUIControls(); } std::string MRPerfusionView::GetFitName() const { std::string fitName = m_Controls.lineFitName->text().toStdString(); if (fitName.empty()) { fitName = m_Controls.lineFitName->placeholderText().toStdString(); } return fitName; } std::string MRPerfusionView::GetDefaultFitName() const { std::string defaultName = "undefined model"; if (this->m_selectedModelFactory.IsNotNull()) { defaultName = this->m_selectedModelFactory->GetClassID(); } if (this->m_Controls.radioPixelBased->isChecked()) { defaultName += "_pixel"; } else { defaultName += "_roi"; } return defaultName; } void MRPerfusionView::OnModellingButtonClicked() { //check if all static parameters set if (m_selectedModelFactory.IsNotNull() && CheckModelSettings()) { m_HasGeneratedNewInput = false; m_HasGeneratedNewInputAIF = false; mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr; mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr; bool isDescBrixFactory = dynamic_cast<mitk::DescriptivePharmacokineticBrixModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool is3LinearFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; - bool is2LinearFactory = dynamic_cast<mitk::TwoStepLinearModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; bool isExtToftsFactory = dynamic_cast<mitk::ExtendedToftsModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isStanToftsFactory = dynamic_cast<mitk::StandardToftsModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool isNum2CXMFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; if (isDescBrixFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateDescriptiveBrixModel_PixelBased(fitSession, generator); } else { GenerateDescriptiveBrixModel_ROIBased(fitSession, generator); } } - else if (is2LinearFactory) - { - if (this->m_Controls.radioPixelBased->isChecked()) - { - GenerateLinearModelFit_PixelBased<mitk::TwoStepLinearModelParameterizer>(fitSession, generator); - } - else - { - GenerateLinearModelFit_ROIBased<mitk::TwoStepLinearModelParameterizer>(fitSession, generator); - } - } - else if (is3LinearFactory) - { - if (this->m_Controls.radioPixelBased->isChecked()) - { - GenerateLinearModelFit_PixelBased<mitk::ThreeStepLinearModelParameterizer>(fitSession, generator); - } - else - { - GenerateLinearModelFit_ROIBased<mitk::ThreeStepLinearModelParameterizer>(fitSession, generator); - } - } else if (isStanToftsFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased<mitk::StandardToftsModelParameterizer>(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased<mitk::StandardToftsModelParameterizer>(fitSession, generator); } } else if (isExtToftsFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased<mitk::ExtendedToftsModelParameterizer>(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased<mitk::ExtendedToftsModelParameterizer>(fitSession, generator); } } else if (is2CXMFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased<mitk::TwoCompartmentExchangeModelParameterizer>(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased<mitk::TwoCompartmentExchangeModelParameterizer>(fitSession, generator); } } - else if (isNum2CXMFactory) - { - if (this->m_Controls.radioPixelBased->isChecked()) - { - GenerateAIFbasedModelFit_PixelBased<mitk::NumericTwoCompartmentExchangeModelParameterizer>(fitSession, - generator); - } - else - { - GenerateAIFbasedModelFit_ROIBased<mitk::NumericTwoCompartmentExchangeModelParameterizer>(fitSession, - generator); - } - } //add other models with else if if (generator.IsNotNull() && fitSession.IsNotNull()) { m_FittingInProgress = true; UpdateGUIControls(); DoFit(fitSession, generator); } else { QMessageBox box; box.setText("Fitting error!"); box.setInformativeText("Could not establish fitting job. Error when setting ab generator, model parameterizer or session info."); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } else { QMessageBox box; box.setText("Static parameters for model are not set!"); box.setInformativeText("Some static parameters, that are needed for calculation are not set and equal to zero. Modeling not possible"); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } void MRPerfusionView::OnNodeSelectionChanged(QList<mitk::DataNode::Pointer>/*nodes*/) { m_selectedMaskNode = nullptr; m_selectedMask = nullptr; if (m_Controls.timeSeriesNodeSelector->GetSelectedNode().IsNotNull()) { this->m_selectedNode = m_Controls.timeSeriesNodeSelector->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); if (m_selectedImage) { this->m_Controls.initialValuesManager->setReferenceImageGeometry(m_selectedImage->GetGeometry()); } else { this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr); } } else { this->m_selectedNode = nullptr; this->m_selectedImage = nullptr; this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr); } if (m_Controls.maskNodeSelector->GetSelectedNode().IsNotNull()) { this->m_selectedMaskNode = m_Controls.maskNodeSelector->GetSelectedNode(); this->m_selectedMask = dynamic_cast<mitk::Image*>(m_selectedMaskNode->GetData()); if (this->m_selectedMask.IsNotNull() && this->m_selectedMask->GetTimeSteps() > 1) { MITK_INFO << "Selected mask has multiple timesteps. Only use first timestep to mask model fit. Mask name: " << m_Controls.maskNodeSelector->GetSelectedNode()->GetName(); mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedMask = maskedImageTimeSelector->GetOutput(); } } if (m_selectedMask.IsNull()) { this->m_Controls.radioPixelBased->setChecked(true); } if (this->m_selectedImage.IsNotNull()) { m_Controls.spinBox_baselineStartTimeStep->setMaximum((this->m_selectedImage->GetDimension(3))-1); m_Controls.spinBox_baselineEndTimeStep->setMaximum((this->m_selectedImage->GetDimension(3)) - 1); } UpdateGUIControls(); } bool MRPerfusionView::CheckModelSettings() const { bool ok = true; - //check wether any model is set at all. Otherwise exit with false + //check whether any model is set at all. Otherwise exit with false if (m_selectedModelFactory.IsNotNull()) { bool isDescBrixFactory = dynamic_cast<mitk::DescriptivePharmacokineticBrixModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool is3LinearFactory = dynamic_cast<mitk::ThreeStepLinearModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; - bool is2LinearFactory = dynamic_cast<mitk::TwoStepLinearModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; bool isToftsFactory = dynamic_cast<mitk::StandardToftsModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr|| dynamic_cast<mitk::ExtendedToftsModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool isNum2CXMFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; if (isDescBrixFactory) { //if all static parameters for this model are set, exit with true, Otherwise exit with false ok = m_Controls.injectiontime->value() > 0; } - else if (is3LinearFactory || is2LinearFactory) - { - if (this->m_Controls.radioButtonTurboFlash->isChecked() ) - { - ok = ok && (m_Controls.recoverytime->value() > 0); - ok = ok && (m_Controls.relaxationtime->value() > 0); - ok = ok && (m_Controls.relaxivity->value() > 0); - ok = ok && (m_Controls.AifRecoverytime->value() > 0); - ok = ok && CheckBaselineSelectionSettings(); - - } - else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked() - || this->m_Controls.radioButton_relativeEnchancement->isChecked() ) - { - ok = ok && (m_Controls.factorSpinBox->value() > 0); - ok = ok && CheckBaselineSelectionSettings(); - } - else if (this->m_Controls.radioButtonUsingT1viaVFA->isChecked() ) - { - ok = ok && (m_Controls.FlipangleSpinBox->value() > 0); - ok = ok && (m_Controls.TRSpinBox->value() > 0); - ok = ok && (m_Controls.RelaxivitySpinBox->value() > 0); - ok = ok && (m_Controls.PDWImageNodeSelector->GetSelectedNode().IsNotNull()); - ok = ok && CheckBaselineSelectionSettings(); - } - else if (this->m_Controls.radioButtonNoConversion->isChecked()) - { - ok = true; - } - else - { - ok = false; - } - } - else if (isToftsFactory || is2CXMFactory || isNum2CXMFactory) + else if (isToftsFactory || is2CXMFactory) { if (this->m_Controls.radioAIFImage->isChecked()) { ok = ok && m_Controls.AIFMaskNodeSelector->GetSelectedNode().IsNotNull(); if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { ok = ok && m_Controls.AIFImageNodeSelector->GetSelectedNode().IsNotNull(); } } else if (this->m_Controls.radioAIFFile->isChecked()) { ok = ok && (this->AIFinputGrid.size() != 0) && (this->AIFinputFunction.size() != 0); } else { ok = false; } if (this->m_Controls.radioButtonTurboFlash->isChecked() ) { ok = ok && (m_Controls.recoverytime->value() > 0); ok = ok && (m_Controls.relaxationtime->value() > 0); ok = ok && (m_Controls.relaxivity->value() > 0); ok = ok && (m_Controls.AifRecoverytime->value() > 0); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked() || this->m_Controls.radioButton_relativeEnchancement->isChecked() ) { ok = ok && (m_Controls.factorSpinBox->value() > 0); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButtonUsingT1viaVFA->isChecked() ) { ok = ok && (m_Controls.FlipangleSpinBox->value() > 0); ok = ok && (m_Controls.TRSpinBox->value() > 0); ok = ok && (m_Controls.RelaxivitySpinBox->value() > 0); ok = ok && (m_Controls.PDWImageNodeSelector->GetSelectedNode().IsNotNull()); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButtonNoConversion->isChecked()) { ok = ok && true; } else { ok = false; } - if (isNum2CXMFactory) - { - ok = ok && (this->m_Controls.odeStepSize->value() > 0); - } - } - //add other models as else if and check wether all needed static parameters are set + //add other models as else if and check whether all needed static parameters are set else { ok = false; } if (this->m_Controls.radioButton_StartParameters->isChecked() && !this->m_Controls.initialValuesManager->hasValidInitialValues()) { std::string warning = "Warning. Invalid start parameters. At least one parameter as an invalid image setting as source."; MITK_ERROR << warning; m_Controls.infoBox->append(QString("") + QString::fromStdString(warning) + QString("")); ok = false; }; } else { ok = false; } return ok; } bool MRPerfusionView::CheckBaselineSelectionSettings() const { return m_Controls.spinBox_baselineStartTimeStep->value() <= m_Controls.spinBox_baselineEndTimeStep->value(); } void MRPerfusionView::ConfigureInitialParametersOfParameterizer(mitk::ModelParameterizerBase* parameterizer) const { if (m_Controls.radioButton_StartParameters->isChecked()) { //use user defined initial parameters mitk::InitialParameterizationDelegateBase::Pointer paramDelegate = m_Controls.initialValuesManager->getInitialParametrizationDelegate(); parameterizer->SetInitialParameterizationDelegate(paramDelegate); } } void MRPerfusionView::GenerateDescriptiveBrixModel_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); mitk::DescriptivePharmacokineticBrixModelParameterizer::Pointer modelParameterizer = mitk::DescriptivePharmacokineticBrixModelParameterizer::New(); //Model configuration (static parameters) can be done now modelParameterizer->SetTau(m_Controls.injectiontime->value()); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(this->m_selectedImage); imageTimeSelector->SetTimeNr(0); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::DescriptivePharmacokineticBrixModelParameterizer::BaseImageType::Pointer baseImage; mitk::CastToItkImage(imageTimeSelector->GetOutput(), baseImage); modelParameterizer->SetBaseImage(baseImage); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = m_selectedMask->GetUID(); } fitGenerator->SetDynamicImage(m_selectedImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); } void MRPerfusionView::GenerateDescriptiveBrixModel_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::Pointer modelParameterizer = mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::New(); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(m_selectedImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Model configuration (static parameters) can be done now modelParameterizer->SetTau(m_Controls.injectiontime->value()); modelParameterizer->SetBaseValue(roiSignal[0]); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage)); generator = fitGenerator.GetPointer(); std::string roiUID = this->m_selectedMask->GetUID(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } template <typename TParameterizer> void MRPerfusionView::GenerateLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = this->m_selectedMask->GetUID(); } fitGenerator->SetDynamicImage(m_selectedImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); } template <typename TParameterizer> void MRPerfusionView::GenerateLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(m_selectedImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Model configuration (static parameters) can be done now this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage)); generator = fitGenerator.GetPointer(); std::string roiUID = this->m_selectedMask->GetUID(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } template <typename TParameterizer> void MRPerfusionView::GenerateAIFbasedModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); PrepareConcentrationImage(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid; GetAIF(aif, aifTimeGrid); modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); - mitk::NumericTwoCompartmentExchangeModelParameterizer* numTCXParametrizer = - dynamic_cast<mitk::NumericTwoCompartmentExchangeModelParameterizer*> - (modelParameterizer.GetPointer()); - - if (numTCXParametrizer) - { - numTCXParametrizer->SetODEINTStepSize(this->m_Controls.odeStepSize->value()); - } //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = this->m_selectedMask->GetUID(); } fitGenerator->SetDynamicImage(this->m_inputImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, this->m_inputImage, mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } template <typename TParameterizer> void MRPerfusionView::GenerateAIFbasedModelFit_ROIBased( mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); PrepareConcentrationImage(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid; GetAIF(aif, aifTimeGrid); modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); - mitk::NumericTwoCompartmentExchangeModelParameterizer* numTCXParametrizer = - dynamic_cast<mitk::NumericTwoCompartmentExchangeModelParameterizer*> - (modelParameterizer.GetPointer()); - - if (numTCXParametrizer) - { - numTCXParametrizer->SetODEINTStepSize(this->m_Controls.odeStepSize->value()); - } //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(this->m_inputImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(this->m_inputImage)); generator = fitGenerator.GetPointer(); std::string roiUID = this->m_selectedMask->GetUID(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, this->m_inputImage, mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); infoSignal.clear(); for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } void MRPerfusionView::DoFit(const mitk::modelFit::ModelFitInfo* fitSession, mitk::ParameterFitImageGeneratorBase* generator) { this->m_Controls.infoBox->append(QString("" + QString("Fitting Data Set . . .") + QString (""))); ///////////////////////// //create job and put it into the thread pool mitk::modelFit::ModelFitResultNodeVectorType additionalNodes; if (m_HasGeneratedNewInput) { additionalNodes.push_back(m_inputNode); } if (m_HasGeneratedNewInputAIF) { additionalNodes.push_back(m_inputAIFNode); } ParameterFitBackgroundJob* pJob = new ParameterFitBackgroundJob(generator, fitSession, this->m_selectedNode, additionalNodes); pJob->setAutoDelete(true); connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnJobError(QString))); connect(pJob, SIGNAL(Finished()), this, SLOT(OnJobFinished())); connect(pJob, SIGNAL(ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), this, SLOT(OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), Qt::BlockingQueuedConnection); connect(pJob, SIGNAL(JobProgress(double)), this, SLOT(OnJobProgress(double))); connect(pJob, SIGNAL(JobStatusChanged(QString)), this, SLOT(OnJobStatusChanged(QString))); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); } MRPerfusionView::MRPerfusionView() : m_FittingInProgress(false), m_HasGeneratedNewInput(false), m_HasGeneratedNewInputAIF(false) { m_selectedImage = nullptr; m_selectedMask = nullptr; mitk::ModelFactoryBase::Pointer factory = mitk::DescriptivePharmacokineticBrixModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); - factory = mitk::TwoStepLinearModelFactory::New().GetPointer(); - m_FactoryStack.push_back(factory); - factory = mitk::ThreeStepLinearModelFactory::New().GetPointer(); - m_FactoryStack.push_back(factory); factory = mitk::StandardToftsModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::ExtendedToftsModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::TwoCompartmentExchangeModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); - factory = mitk::NumericTwoCompartmentExchangeModelFactory::New().GetPointer(); - m_FactoryStack.push_back(factory); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image"); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isLegacyMask = mitk::NodePredicateAnd::New(isImage, isBinary); mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3); mitk::NodePredicateOr::Pointer isMask = mitk::NodePredicateOr::New(isLegacyMask, isLabelSet); mitk::NodePredicateAnd::Pointer isNoMask = mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isMask)); mitk::NodePredicateAnd::Pointer is3DImage = mitk::NodePredicateAnd::New(isImage, is3D, isNoMask); this->m_IsMaskPredicate = mitk::NodePredicateAnd::New(isMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); this->m_IsNoMaskImagePredicate = mitk::NodePredicateAnd::New(isNoMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); auto isDynamicData = mitk::NodePredicateFunction::New([](const mitk::DataNode* node) { return (node && node->GetData() && node->GetData()->GetTimeSteps() > 1); }); auto modelFitResultRelationRule = mitk::ModelFitResultRelationRule::New(); auto isNoModelFitNodePredicate = mitk::NodePredicateNot::New(modelFitResultRelationRule->GetConnectedSourcesDetector()); this->m_isValidPDWImagePredicate = mitk::NodePredicateAnd::New(is3DImage, isNoModelFitNodePredicate); this->m_isValidTimeSeriesImagePredicate = mitk::NodePredicateAnd::New(isDynamicData, isImage, isNoMask); } void MRPerfusionView::OnJobFinished() { this->m_Controls.infoBox->append(QString("Fitting finished.")); this->m_FittingInProgress = false; this->UpdateGUIControls(); }; void MRPerfusionView::OnJobError(QString err) { MITK_ERROR << err.toStdString().c_str(); m_Controls.infoBox->append(QString("") + err + QString("")); }; void MRPerfusionView::OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results, const ParameterFitBackgroundJob* pJob) { //Store the resulting parameter fit image via convenience helper function in data storage //(handles the correct generation of the nodes and their properties) mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), results, pJob->GetParentNode()); //this stores the concentration image and AIF concentration image, if generated for this fit in the storage. //if not generated for this fit, relevant nodes are empty. mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), pJob->GetAdditionalRelevantNodes(), pJob->GetParentNode()); }; void MRPerfusionView::OnJobProgress(double progress) { QString report = QString("Progress. ") + QString::number(progress); this->m_Controls.infoBox->append(report); }; void MRPerfusionView::OnJobStatusChanged(QString info) { this->m_Controls.infoBox->append(info); } void MRPerfusionView::InitModelComboBox() const { this->m_Controls.comboModel->clear(); this->m_Controls.comboModel->addItem(tr("No model selected")); for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin(); pos != m_FactoryStack.end(); ++pos) { this->m_Controls.comboModel->addItem(QString::fromStdString((*pos)->GetClassID())); } this->m_Controls.comboModel->setCurrentIndex(0); }; mitk::DataNode::Pointer MRPerfusionView::GenerateConcentrationNode(mitk::Image* image, const std::string& nodeName) const { if (!image) { mitkThrow() << "Cannot generate concentration node. Passed image is null. parameter name: "; } mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetData(image); result->SetName(nodeName); result->SetVisibility(true); return result; }; mitk::Image::Pointer MRPerfusionView::ConvertConcentrationImage(bool AIFMode) { //Compute Concentration image mitk::ConcentrationCurveGenerator::Pointer concentrationGen = mitk::ConcentrationCurveGenerator::New(); if (m_Controls.checkDedicatedAIFImage->isChecked() && AIFMode) { concentrationGen->SetDynamicImage(this->m_selectedAIFImage); } else { concentrationGen->SetDynamicImage(this->m_selectedImage); } concentrationGen->SetisTurboFlashSequence(IsTurboFlashSequenceFlag()); concentrationGen->SetAbsoluteSignalEnhancement(m_Controls.radioButton_absoluteEnhancement->isChecked()); concentrationGen->SetRelativeSignalEnhancement(m_Controls.radioButton_relativeEnchancement->isChecked()); concentrationGen->SetUsingT1Map(m_Controls.radioButtonUsingT1viaVFA->isChecked()); if (IsTurboFlashSequenceFlag()) { if (AIFMode) { concentrationGen->SetRecoveryTime(m_Controls.AifRecoverytime->value()); } else { concentrationGen->SetRecoveryTime(m_Controls.recoverytime->value()); } concentrationGen->SetRelaxationTime(m_Controls.relaxationtime->value()); concentrationGen->SetRelaxivity(m_Controls.relaxivity->value()); concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value()); concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value()); } else if (this->m_Controls.radioButtonUsingT1viaVFA->isChecked()) { concentrationGen->SetRecoveryTime(m_Controls.TRSpinBox->value()); concentrationGen->SetRelaxivity(m_Controls.RelaxivitySpinBox->value()); concentrationGen->SetT10Image(dynamic_cast<mitk::Image*>(m_Controls.PDWImageNodeSelector->GetSelectedNode()->GetData())); concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value()); concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value()); //Convert Flipangle from degree to radiant double alpha = m_Controls.FlipangleSpinBox->value()/360*2* boost::math::constants::pi<double>(); concentrationGen->SetFlipAngle(alpha); } else { concentrationGen->SetFactor(m_Controls.factorSpinBox->value()); concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value()); concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value()); } mitk::Image::Pointer concentrationImage = concentrationGen->GetConvertedImage(); return concentrationImage; } void MRPerfusionView::GetAIF(mitk::AIFBasedModelBase::AterialInputFunctionType& aif, mitk::AIFBasedModelBase::AterialInputFunctionType& aifTimeGrid) { if (this->m_Controls.radioAIFFile->isChecked()) { aif.clear(); aifTimeGrid.clear(); aif.SetSize(AIFinputFunction.size()); aifTimeGrid.SetSize(AIFinputGrid.size()); aif.fill(0.0); aifTimeGrid.fill(0.0); itk::Array<double>::iterator aifPos = aif.begin(); for (std::vector<double>::const_iterator pos = AIFinputFunction.begin(); pos != AIFinputFunction.end(); ++pos, ++aifPos) { *aifPos = *pos; } itk::Array<double>::iterator gridPos = aifTimeGrid.begin(); for (std::vector<double>::const_iterator pos = AIFinputGrid.begin(); pos != AIFinputGrid.end(); ++pos, ++gridPos) { *gridPos = *pos; } } else if (this->m_Controls.radioAIFImage->isChecked()) { aif.clear(); aifTimeGrid.clear(); mitk::AterialInputFunctionGenerator::Pointer aifGenerator = mitk::AterialInputFunctionGenerator::New(); //Hematocrit level aifGenerator->SetHCL(this->m_Controls.HCLSpinBox->value()); //mask settings this->m_selectedAIFMaskNode = m_Controls.AIFMaskNodeSelector->GetSelectedNode(); this->m_selectedAIFMask = dynamic_cast<mitk::Image*>(this->m_selectedAIFMaskNode->GetData()); if (this->m_selectedAIFMask->GetTimeSteps() > 1) { MITK_INFO << "Selected AIF mask has multiple timesteps. Only use first timestep to mask model fit. AIF Mask name: " << m_selectedAIFMaskNode->GetName() ; mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedAIFMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedAIFMask = maskedImageTimeSelector->GetOutput(); } if (this->m_selectedAIFMask.IsNotNull()) { aifGenerator->SetMask(this->m_selectedAIFMask); } //image settings if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { this->m_selectedAIFImageNode = m_Controls.AIFImageNodeSelector->GetSelectedNode(); this->m_selectedAIFImage = dynamic_cast<mitk::Image*>(this->m_selectedAIFImageNode->GetData()); } else { this->m_selectedAIFImageNode = m_selectedNode; this->m_selectedAIFImage = m_selectedImage; } this->PrepareAIFConcentrationImage(); aifGenerator->SetDynamicImage(this->m_inputAIFImage); aif = aifGenerator->GetAterialInputFunction(); aifTimeGrid = aifGenerator->GetAterialInputFunctionTimeGrid(); } else { - mitkThrow() << "Cannot generate AIF. View is in a invalide state. No AIF mode selected."; + mitkThrow() << "Cannot generate AIF. View is in a invalid state. No AIF mode selected."; } } void MRPerfusionView::LoadAIFfromFile() { QFileDialog dialog; dialog.setNameFilter(tr("Images (*.csv")); QString fileName = dialog.getOpenFileName(); m_Controls.aifFilePath->setText(fileName); std::string m_aifFilePath = fileName.toStdString(); //Read Input typedef boost::tokenizer< boost::escaped_list_separator<char> > Tokenizer; ///////////////////////////////////////////////////////////////////////////////////////////////// //AIF Data std::ifstream in1(m_aifFilePath.c_str()); if (!in1.is_open()) { this->m_Controls.infoBox->append(QString("Could not open AIF File!")); } std::vector< std::string > vec1; std::string line1; while (getline(in1, line1)) { Tokenizer tok(line1); vec1.assign(tok.begin(), tok.end()); this->AIFinputGrid.push_back(convertToDouble(vec1[0])); this->AIFinputFunction.push_back(convertToDouble(vec1[1])); } } void MRPerfusionView::PrepareConcentrationImage() { mitk::Image::Pointer concentrationImage = this->m_selectedImage; mitk::DataNode::Pointer concentrationNode = this->m_selectedNode; m_HasGeneratedNewInput = false; if (!this->m_Controls.radioButtonNoConversion->isChecked()) { concentrationImage = this->ConvertConcentrationImage(false); concentrationNode = GenerateConcentrationNode(concentrationImage, "Concentration"); m_HasGeneratedNewInput = true; } m_inputImage = concentrationImage; m_inputNode = concentrationNode; } void MRPerfusionView::PrepareAIFConcentrationImage() { mitk::Image::Pointer concentrationImage = this->m_selectedImage; mitk::DataNode::Pointer concentrationNode = this->m_selectedNode; m_HasGeneratedNewInputAIF = false; if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { concentrationImage = this->m_selectedAIFImage; concentrationNode = this->m_selectedAIFImageNode; } if (!this->m_Controls.radioButtonNoConversion->isChecked()) { if (!IsTurboFlashSequenceFlag() && !this->m_Controls.checkDedicatedAIFImage->isChecked()) { if (m_inputImage.IsNull()) { mitkThrow() << "Cannot get AIF concentration image. Invalid view state. Input image is not defined yet, but should be."; } //we can directly use the concentration input image/node (generated by GetConcentrationImage) also for the AIF concentrationImage = this->m_inputImage; concentrationNode = this->m_inputNode; } else { concentrationImage = this->ConvertConcentrationImage(true); concentrationNode = GenerateConcentrationNode(concentrationImage, "AIF Concentration"); m_HasGeneratedNewInputAIF = true; } } m_inputAIFImage = concentrationImage; m_inputAIFNode = concentrationNode; } mitk::ModelFitFunctorBase::Pointer MRPerfusionView::CreateDefaultFitFunctor( const mitk::ModelParameterizerBase* parameterizer) const { mitk::LevenbergMarquardtModelFitFunctor::Pointer fitFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::Pointer chi2 = mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("Chi^2", chi2); if (m_Controls.checkBox_Constraints->isChecked()) { fitFunctor->SetConstraintChecker(m_modelConstraints); } mitk::ModelBase::Pointer refModel = parameterizer->GenerateParameterizedModel(); ::itk::LevenbergMarquardtOptimizer::ScalesType scales; scales.SetSize(refModel->GetNumberOfParameters()); scales.Fill(1.0); fitFunctor->SetScales(scales); fitFunctor->SetDebugParameterMaps(m_Controls.checkDebug->isChecked()); return fitFunctor.GetPointer(); } diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui index be5a4f0665..b4e0cb396d 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui @@ -1,745 +1,745 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>MRPerfusionViewControls</class> <widget class="QWidget" name="MRPerfusionViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>489</width> <height>1124</height> </rect> </property> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <property name="sizeConstraint"> <enum>QLayout::SetDefaultConstraint</enum> </property> <item> <layout class="QVBoxLayout" name="verticalLayout_2"> <property name="spacing"> <number>4</number> </property> <property name="sizeConstraint"> <enum>QLayout::SetDefaultConstraint</enum> </property> <item> <layout class="QGridLayout" name="gridLayout_6"> <item row="0" column="0"> <widget class="QLabel" name="timeSeriesLabel"> <property name="text"> <string>Selected Time Series:</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="maskLabel"> <property name="text"> <string>Selected Mask:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QmitkSingleNodeSelectionWidget" name="timeSeriesNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="1" column="1"> <widget class="QmitkSingleNodeSelectionWidget" name="maskNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <widget class="QGroupBox" name="groupBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> <property name="title"> <string>Fitting strategy</string> </property> <layout class="QHBoxLayout" name="horizontalLayout_3"> <property name="spacing"> <number>5</number> </property> <property name="sizeConstraint"> <enum>QLayout::SetMinAndMaxSize</enum> </property> <property name="leftMargin"> <number>5</number> </property> <property name="topMargin"> <number>5</number> </property> <property name="rightMargin"> <number>5</number> </property> <property name="bottomMargin"> <number>5</number> </property> <item> <widget class="QRadioButton" name="radioPixelBased"> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="text"> <string>Pixel based</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioROIbased"> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="text"> <string>ROI based</string> </property> </widget> </item> </layout> </widget> </item> </layout> </item> <item> <widget class="QComboBox" name="comboModel"> <item> <property name="text"> - <string>Select pharmacokinetic modell...</string> + <string>Select pharmacokinetic model...</string> </property> </item> </widget> </item> <item> <widget class="QGroupBox" name="groupAIF"> <property name="title"> <string>AIF Mask:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <widget class="QRadioButton" name="radioAIFImage"> <property name="text"> <string>Select AIF from Image:</string> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout_3"> <property name="leftMargin"> <number>20</number> </property> <item row="0" column="0"> <widget class="QLabel" name="labelAIFMask"> <property name="text"> <string>AIF Mask:</string> </property> </widget> </item> <item row="2" column="0"> <widget class="QCheckBox" name="checkDedicatedAIFImage"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Dedicated AIF Image:</string> </property> </widget> </item> <item row="0" column="2"> <widget class="QmitkSingleNodeSelectionWidget" name="AIFMaskNodeSelector" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="2" column="2"> <widget class="QmitkSingleNodeSelectionWidget" name="AIFImageNodeSelector" native="true"> <property name="enabled"> <bool>false</bool> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <property name="spacing"> <number>0</number> </property> <item> <widget class="QRadioButton" name="radioAIFFile"> <property name="text"> <string>Select AIF from File: </string> </property> </widget> </item> <item> <widget class="QLineEdit" name="aifFilePath"/> </item> <item> <widget class="QPushButton" name="btnAIFFile"> <property name="enabled"> <bool>false</bool> </property> <property name="text"> <string>Browse</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_6"> <property name="topMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label"> <property name="text"> <string>Hematocrit Level [ ]:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="HCLSpinBox"> <property name="maximum"> <double>1.000000000000000</double> </property> <property name="singleStep"> <double>0.010000000000000</double> </property> </widget> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupDescBrix"> <property name="title"> <string>Descriptive Brix-Model Parameters:</string> </property> <layout class="QFormLayout" name="formLayout"> <property name="fieldGrowthPolicy"> <enum>QFormLayout::AllNonFixedFieldsGrow</enum> </property> <item row="0" column="0"> <widget class="QLabel" name="lableInjectionTime"> <property name="text"> <string>Injection Time [min]: </string> </property> </widget> </item> <item row="0" column="1"> <widget class="QDoubleSpinBox" name="injectiontime"/> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupNum2CXM"> <property name="title"> <string>Numeric Two Compartment Exchange Model Parameters:</string> </property> <layout class="QGridLayout" name="gridLayout_2"> <item row="0" column="0"> <widget class="QLabel" name="Label"> <property name="text"> <string>ODE Int Step Size [s]: </string> </property> </widget> </item> <item row="0" column="1"> <widget class="QDoubleSpinBox" name="odeStepSize"> <property name="decimals"> <number>3</number> </property> <property name="singleStep"> <double>0.001000000000000</double> </property> <property name="value"> <double>0.050000000000000</double> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_FitConfiguration"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Expanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="title"> <string>Model Fit Configuration</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QToolBox" name="toolboxConfiguration"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <widget class="QWidget" name="groupStartParameter"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>459</width> <height>84</height> </rect> </property> <attribute name="label"> <string>Start parameter</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <widget class="QRadioButton" name="radioButton_StartParameters"> <property name="text"> <string>Enter Fit Starting Parameters</string> </property> </widget> </item> <item> <widget class="QmitkInitialValuesManagerWidget" name="initialValuesManager" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="MinimumExpanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> </widget> </item> </layout> </widget> <widget class="QWidget" name="groupConstraints"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>459</width> <height>232</height> </rect> </property> <attribute name="label"> <string>Constraints</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_9"> <item> <widget class="QCheckBox" name="checkBox_Constraints"> <property name="text"> <string>Enter Constraints for Fit Parameters</string> </property> </widget> </item> <item> <widget class="QmitkSimpleBarrierManagerWidget" name="constraintManager" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="MinimumExpanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>200</height> </size> </property> </widget> </item> </layout> </widget> <widget class="QWidget" name="groupConcentration"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>449</width> <height>397</height> </rect> </property> <attribute name="label"> <string>Conversion: Signal to Concentration</string> </attribute> <layout class="QHBoxLayout" name="horizontalLayout_8"> <item> <layout class="QVBoxLayout" name="concentrationOptionsLayout"> <property name="topMargin"> <number>10</number> </property> <item> <widget class="QRadioButton" name="radioButtonNoConversion"> <property name="text"> <string>No Signal Conversion</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioButton_absoluteEnhancement"> <property name="text"> <string>Absolute Signal Enhancement</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioButton_relativeEnchancement"> <property name="text"> <string>Relative Signal Enhancement</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioButtonUsingT1viaVFA"> <property name="text"> <string>Using T1 Map via Variable Flip Angle</string> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioButtonTurboFlash"> <property name="text"> <string>TurboFLASH Sequence</string> </property> </widget> </item> <item> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </item> <item> <layout class="QVBoxLayout" name="concentrationSettingsLayout"> <item> <widget class="QGroupBox" name="groupBoxEnhancement"> <property name="title"> <string>Enhancement Parameters:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <widget class="QLabel" name="label_Faktor"> <property name="text"> <string>Conversion Factor k:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="factorSpinBox"/> </item> <item> <widget class="QLabel" name="label_baselineRange"> <property name="text"> <string>Baseline Range Selection:</string> </property> <property name="alignment"> <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout_4"> <item row="0" column="1"> <widget class="QSpinBox" name="spinBox_baselineStartTimeStep"/> </item> <item row="0" column="0"> <widget class="QLabel" name="label_baselineStartTimeStep"> <property name="text"> <string>Start Time Frame</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="label_baselineEndTimeStep"> <property name="text"> <string>End Time Frame</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QSpinBox" name="spinBox_baselineEndTimeStep"/> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_T1MapviaVFA"> <property name="title"> <string>T1 Map via Variable Flip Angle Parameters:</string> </property> <layout class="QGridLayout" name="gridLayout_5"> <item row="1" column="0"> <widget class="QLabel" name="label_7"> <property name="text"> <string>Flip Angle [ ° ] : </string> </property> </widget> </item> <item row="0" column="0"> <widget class="QLabel" name="label_6"> <property name="text"> <string>Repetition Time TR [ms] :</string> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label_9"> <property name="text"> <string>Relaxivity [mM⁻¹ s⁻¹] : </string> </property> </widget> </item> <item row="1" column="1"> <widget class="QDoubleSpinBox" name="FlipangleSpinBox"/> </item> <item row="2" column="1"> <widget class="QDoubleSpinBox" name="RelaxivitySpinBox"/> </item> <item row="3" column="0"> <widget class="QLabel" name="label_8"> <property name="text"> <string>Proton Density Weighted Image :</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QDoubleSpinBox" name="TRSpinBox"> <property name="maximum"> <double>10000.000000000000000</double> </property> </widget> </item> <item row="3" column="1"> <widget class="QmitkSingleNodeSelectionWidget" name="PDWImageNodeSelector" native="true"/> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBoxTurboFlash"> <property name="enabled"> <bool>true</bool> </property> <property name="title"> <string>Turbo FLASH Parameters:</string> </property> <layout class="QGridLayout" name="gridLayout"> <item row="1" column="0"> <widget class="QLabel" name="lable_TRec"> <property name="text"> <string>Recovery Time [s]:</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QDoubleSpinBox" name="relaxationtime"/> </item> <item row="0" column="0"> <widget class="QLabel" name="label_25"> <property name="text"> <string>AIF Recovery Time [s]:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QDoubleSpinBox" name="AifRecoverytime"/> </item> <item row="3" column="1"> <widget class="QDoubleSpinBox" name="relaxivity"/> </item> <item row="2" column="0"> <widget class="QLabel" name="label_T10"> <property name="text"> <string>Relaxation Time [s]:</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QDoubleSpinBox" name="recoverytime"/> </item> <item row="3" column="0"> <widget class="QLabel" name="label__alpha"> <property name="text"> <string>Relaxivity [ ]:</string> </property> </widget> </item> </layout> </widget> </item> </layout> </item> </layout> </widget> </widget> </item> </layout> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_7"> <property name="topMargin"> <number>5</number> </property> <item> <widget class="QLabel" name="label_5"> <property name="text"> <string>Fitting name:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="lineFitName"> <property name="toolTip"> <string><html><head/><body>Name/prefix that should be used for the fitting results.May be explicitly defined by the user.</body></html></string> </property> <property name="statusTip"> <string/> </property> <property name="placeholderText"> <string>default fit name</string> </property> </widget> </item> </layout> </item> <item> <widget class="QPushButton" name="btnModelling"> <property name="text"> <string>Start Modelling</string> </property> </widget> </item> <item> <widget class="QCheckBox" name="checkDebug"> <property name="text"> <string>Generate debug parameter images</string> </property> </widget> </item> <item> <widget class="QTextEdit" name="infoBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Maximum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="readOnly"> <bool>true</bool> </property> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Expanding</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkSimpleBarrierManagerWidget</class> <extends>QWidget</extends> <header>QmitkSimpleBarrierManagerWidget.h</header> </customwidget> <customwidget> <class>QmitkInitialValuesManagerWidget</class> <extends>QWidget</extends> <header>QmitkInitialValuesManagerWidget.h</header> </customwidget> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header>QmitkSingleNodeSelectionWidget.h</header> <container>1</container> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicView.cpp index 9e4a74c8c1..5b5eadb97b 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicView.cpp +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicView.cpp @@ -1,946 +1,923 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "PETDynamicView.h" #include "mitkWorkbenchUtil.h" #include "mitkAterialInputFunctionGenerator.h" #include "mitkOneTissueCompartmentModelFactory.h" #include "mitkOneTissueCompartmentModelParameterizer.h" #include "mitkExtendedOneTissueCompartmentModelFactory.h" #include "mitkExtendedOneTissueCompartmentModelParameterizer.h" #include "mitkTwoTissueCompartmentFDGModelFactory.h" #include "mitkTwoTissueCompartmentFDGModelParameterizer.h" #include "mitkTwoTissueCompartmentModelFactory.h" #include "mitkTwoTissueCompartmentModelParameterizer.h" -#include "mitkNumericTwoTissueCompartmentModelFactory.h" -#include "mitkNumericTwoTissueCompartmentModelParameterizer.h" - #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateOr.h> #include <mitkPixelBasedParameterFitImageGenerator.h> #include <mitkROIBasedParameterFitImageGenerator.h> #include <mitkLevenbergMarquardtModelFitFunctor.h> #include <mitkSumOfSquaredDifferencesFitCostFunction.h> #include <mitkSquaredDifferencesFitCostFunction.h> #include <mitkChiSquareFitCostFunction.h> #include <mitkReducedChiSquareFitCostFunction.h> #include <mitkSimpleBarrierConstraintChecker.h> #include <mitkModelFitResultHelper.h> #include <mitkImageTimeSelector.h> #include <mitkMaskedDynamicImageStatisticsGenerator.h> #include <mitkExtractTimeGrid.h> #include <mitkInitialParameterizationDelegateBase.h> #include <QMessageBox> #include <QThreadPool> #include <QmitkDataStorageComboBox.h> #include <QFileDialog> #include <boost/tokenizer.hpp> // Includes for image casting between ITK and MITK #include <mitkImage.h> #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include <itkImage.h> #include <itkImageRegionIterator.h> #include <iostream> const std::string PETDynamicView::VIEW_ID = "org.mitk.views.pharmacokinetics.pet"; inline double convertToDouble(const std::string& data) { std::istringstream stepStream(data); double value = 0.0; stepStream >> value; return value; } void PETDynamicView::SetFocus() { m_Controls.btnModelling->setFocus(); } void PETDynamicView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_Controls.btnModelling->setEnabled(false); m_Controls.errorMessageLabel->hide(); this->InitModelComboBox(); connect(m_Controls.btnModelling, SIGNAL(clicked()), this, SLOT(OnModellingButtonClicked())); connect(m_Controls.comboModel, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int))); connect(m_Controls.radioPixelBased, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); //AIF setting m_Controls.groupAIF->hide(); m_Controls.btnAIFFile->setEnabled(false); m_Controls.btnAIFFile->setEnabled(false); m_Controls.radioAIFImage->setChecked(true); m_Controls.comboAIFMask->SetDataStorage(this->GetDataStorage()); m_Controls.comboAIFMask->SetPredicate(m_IsMaskPredicate); m_Controls.comboAIFMask->setVisible(true); m_Controls.comboAIFMask->setEnabled(true); m_Controls.comboAIFImage->SetDataStorage(this->GetDataStorage()); m_Controls.comboAIFImage->SetPredicate(m_IsNoMaskImagePredicate); m_Controls.comboAIFImage->setEnabled(false); m_Controls.checkDedicatedAIFImage->setEnabled(true); m_Controls.HCLSpinBox->setValue(0.0); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFMask, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.labelAIFMask, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFMask, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFImage, SLOT(setVisible(bool))); connect(m_Controls.checkDedicatedAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFImage, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.btnAIFFile, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.aifFilePath, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.btnAIFFile, SIGNAL(clicked()), this, SLOT(LoadAIFfromFile())); //Model fit configuration m_Controls.groupBox_FitConfiguration->hide(); m_Controls.checkBox_Constraints->setEnabled(false); m_Controls.constraintManager->setEnabled(false); m_Controls.initialValuesManager->setEnabled(false); m_Controls.initialValuesManager->setDataStorage(this->GetDataStorage()); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.initialValuesManager, SIGNAL(initialValuesChanged(void)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), m_Controls.initialValuesManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setVisible(bool))); UpdateGUIControls(); } void PETDynamicView::UpdateGUIControls() { m_Controls.lineFitName->setPlaceholderText(QString::fromStdString(this->GetDefaultFitName())); m_Controls.lineFitName->setEnabled(!m_FittingInProgress); m_Controls.checkBox_Constraints->setEnabled(m_modelConstraints.IsNotNull()); bool is1TCMFactory = dynamic_cast<mitk::OneTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isExt1TCMFactory = dynamic_cast<mitk::ExtendedOneTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isFDGCMFactory = dynamic_cast<mitk::TwoTissueCompartmentFDGModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast<mitk::TwoTissueCompartmentModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr || - dynamic_cast<mitk::NumericTwoTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; m_Controls.groupAIF->setVisible(is1TCMFactory || isExt1TCMFactory || isFDGCMFactory || is2TCMFactory); m_Controls.groupBox_FitConfiguration->setVisible(m_selectedModelFactory); m_Controls.groupBox->setEnabled(!m_FittingInProgress); m_Controls.comboModel->setEnabled(!m_FittingInProgress); m_Controls.groupAIF->setEnabled(!m_FittingInProgress); m_Controls.groupBox_FitConfiguration->setEnabled(!m_FittingInProgress); m_Controls.radioROIbased->setEnabled(m_selectedMask.IsNotNull()); m_Controls.btnModelling->setEnabled(m_selectedImage.IsNotNull() && m_selectedModelFactory.IsNotNull() && !m_FittingInProgress && CheckModelSettings()); } //void PETDynamicView::OnModelSettingChanged() //{ // bool ok = m_selectedImage.IsNotNull() && m_selectedModelFactory.IsNotNull() && !m_FittingInProgress && CheckModelSettings(); // m_Controls.btnModelling->setEnabled(ok); //} void PETDynamicView::OnModellSet(int index) { m_selectedModelFactory = nullptr; if (index > 0) { if (static_cast<ModelFactoryStackType::size_type>(index) <= m_FactoryStack.size() ) { m_selectedModelFactory = m_FactoryStack[index - 1]; } else { MITK_WARN << "Invalid model index. Index outside of the factory stack. Factory stack size: "<< m_FactoryStack.size() << "; invalid index: "<< index; } } if (m_selectedModelFactory) { this->m_modelConstraints = dynamic_cast<mitk::SimpleBarrierConstraintChecker*> (m_selectedModelFactory->CreateDefaultConstraints().GetPointer()); m_Controls.initialValuesManager->setInitialValues(m_selectedModelFactory->GetParameterNames(), m_selectedModelFactory->GetDefaultInitialParameterization()); if (this->m_modelConstraints.IsNull()) { this->m_modelConstraints = mitk::SimpleBarrierConstraintChecker::New(); } m_Controls.constraintManager->setChecker(this->m_modelConstraints, this->m_selectedModelFactory->GetParameterNames()); } m_Controls.checkBox_Constraints->setEnabled(m_modelConstraints.IsNotNull()); UpdateGUIControls(); } std::string PETDynamicView::GetFitName() const { std::string fitName = m_Controls.lineFitName->text().toStdString(); if (fitName.empty()) { fitName = m_Controls.lineFitName->placeholderText().toStdString(); } return fitName; } std::string PETDynamicView::GetDefaultFitName() const { std::string defaultName = "undefined model"; if (this->m_selectedModelFactory.IsNotNull()) { defaultName = this->m_selectedModelFactory->GetClassID(); } if (this->m_Controls.radioPixelBased->isChecked()) { defaultName += "_pixel"; } else { defaultName += "_roi"; } return defaultName; } void PETDynamicView::OnModellingButtonClicked() { //check if all static parameters set if (m_selectedModelFactory.IsNotNull() && CheckModelSettings()) { mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr; mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr; bool isOTCFactory = dynamic_cast<mitk::OneTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isextOTCFactory = dynamic_cast<mitk::ExtendedOneTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isFDGFactory = dynamic_cast<mitk::TwoTissueCompartmentFDGModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isTTCFactory = dynamic_cast<mitk::TwoTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool isNumTTCFactory = dynamic_cast<mitk::NumericTwoTissueCompartmentModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; if (isOTCFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::OneTissueCompartmentModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::OneTissueCompartmentModelParameterizer>(fitSession, generator); } } else if (isextOTCFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::ExtendedOneTissueCompartmentModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::ExtendedOneTissueCompartmentModelParameterizer>(fitSession, generator); } } else if (isFDGFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::TwoTissueCompartmentFDGModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::TwoTissueCompartmentFDGModelParameterizer>(fitSession, generator); } } else if (isTTCFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateModelFit_PixelBased<mitk::TwoTissueCompartmentModelParameterizer>(fitSession, generator); } else { GenerateModelFit_ROIBased<mitk::TwoTissueCompartmentModelParameterizer>(fitSession, generator); } } - else if (isNumTTCFactory) - { - if (this->m_Controls.radioPixelBased->isChecked()) - { - GenerateModelFit_PixelBased<mitk::NumericTwoTissueCompartmentModelParameterizer>(fitSession, - generator); - } - else - { - GenerateModelFit_ROIBased<mitk::NumericTwoTissueCompartmentModelParameterizer>(fitSession, - generator); - } - } //add other models with else if if (generator.IsNotNull() && fitSession.IsNotNull()) { m_FittingInProgress = true; DoFit(fitSession, generator); } else { QMessageBox box; box.setText("Fitting error!"); box.setInformativeText("Could not establish fitting job. Error when setting ab generator, model parameterizer or session info."); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } else { QMessageBox box; box.setText("Static parameters for model are not set!"); box.setInformativeText("Some static parameters, that are needed for calculation are not set and equal to zero. Modeling not possible"); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } void PETDynamicView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList<mitk::DataNode::Pointer>& selectedNodes) { m_selectedMaskNode = nullptr; m_selectedMask = nullptr; m_Controls.errorMessageLabel->setText(""); m_Controls.masklabel->setText("No (valid) mask selected."); m_Controls.timeserieslabel->setText("No (valid) series selected."); QList<mitk::DataNode::Pointer> nodes = selectedNodes; if (nodes.size() > 0 && this->m_IsNoMaskImagePredicate->CheckNode(nodes.front())) { this->m_selectedNode = nodes.front(); auto selectedImage = dynamic_cast<mitk::Image*>(this->m_selectedNode->GetData()); m_Controls.timeserieslabel->setText((this->m_selectedNode->GetName()).c_str()); if (selectedImage != this->m_selectedImage) { if (selectedImage) { this->m_Controls.initialValuesManager->setReferenceImageGeometry(selectedImage->GetGeometry()); } else { this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr); } } this->m_selectedImage = selectedImage; nodes.pop_front(); } else { this->m_selectedNode = nullptr; this->m_selectedImage = nullptr; this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr); } if (nodes.size() > 0 && this->m_IsMaskPredicate->CheckNode(nodes.front())) { this->m_selectedMaskNode = nodes.front(); this->m_selectedMask = dynamic_cast<mitk::Image*>(this->m_selectedMaskNode->GetData()); if (this->m_selectedMask->GetTimeSteps() > 1) { MITK_INFO << "Selected mask has multiple timesteps. Only use first timestep to mask model fit. Mask name: " << m_selectedMaskNode->GetName(); mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedMask = maskedImageTimeSelector->GetOutput(); } m_Controls.masklabel->setText((this->m_selectedMaskNode->GetName()).c_str()); } if (m_selectedMask.IsNull()) { this->m_Controls.radioPixelBased->setChecked(true); } m_Controls.errorMessageLabel->show(); UpdateGUIControls(); } bool PETDynamicView::CheckModelSettings() const { bool ok = true; - //check wether any model is set at all. Otherwise exit with false + //check whether any model is set at all. Otherwise exit with false if (m_selectedModelFactory.IsNotNull()) { bool isOTCFactory = dynamic_cast<mitk::OneTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isextOTCFactory = dynamic_cast<mitk::ExtendedOneTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isFDGFactory = dynamic_cast<mitk::TwoTissueCompartmentFDGModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; bool isTTCFactory = dynamic_cast<mitk::TwoTissueCompartmentModelFactory*> (m_selectedModelFactory.GetPointer()) != nullptr; - bool isNumTTCFactory = dynamic_cast<mitk::NumericTwoTissueCompartmentModelFactory*> - (m_selectedModelFactory.GetPointer()) != nullptr; - if (isOTCFactory || isextOTCFactory || isFDGFactory || isTTCFactory || isNumTTCFactory) + if (isOTCFactory || isextOTCFactory || isFDGFactory || isTTCFactory) { if (this->m_Controls.radioAIFImage->isChecked()) { ok = ok && m_Controls.comboAIFMask->GetSelectedNode().IsNotNull(); if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { ok = ok && m_Controls.comboAIFImage->GetSelectedNode().IsNotNull(); } } else if (this->m_Controls.radioAIFFile->isChecked()) { ok = ok && (this->AIFinputGrid.size() != 0) && (this->AIFinputFunction.size() != 0); } else { ok = false; } } - //add other models as else if and check wether all needed static parameters are set + //add other models as else if and check whether all needed static parameters are set else { ok = false; } if (this->m_Controls.radioButton_StartParameters->isChecked() && !this->m_Controls.initialValuesManager->hasValidInitialValues()) { std::string warning = "Warning. Invalid start parameters. At least one parameter as an invalid image setting as source."; MITK_ERROR << warning; m_Controls.infoBox->append(QString("") + QString::fromStdString(warning) + QString("")); ok = false; }; } else { ok = false; } return ok; } void PETDynamicView::ConfigureInitialParametersOfParameterizer(mitk::ModelParameterizerBase* parameterizer) const { if (m_Controls.radioButton_StartParameters->isChecked()) { //use user defined initial parameters mitk::InitialParameterizationDelegateBase::Pointer paramDelegate = m_Controls.initialValuesManager->getInitialParametrizationDelegate(); parameterizer->SetInitialParameterizationDelegate(paramDelegate); } } template <typename TParameterizer> void PETDynamicView::GenerateModelFit_PixelBased( mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::TimeGridType aifTimeGrid; GetAIF(aif, aifTimeGrid); //Model configuration (static parameters) can be done now modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = m_selectedMask->GetUID(); } fitGenerator->SetDynamicImage(this->m_selectedImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } template <typename TParameterizer> void PETDynamicView::GenerateModelFit_ROIBased( mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); //Compute AIF mitk::AterialInputFunctionGenerator::Pointer aifGenerator = mitk::AterialInputFunctionGenerator::New(); aifGenerator->SetDynamicImage(this->m_selectedImage); aifGenerator->SetMask(this->m_selectedAIFMask); mitk::AIFBasedModelBase::AterialInputFunctionType aif = aifGenerator->GetAterialInputFunction(); mitk::AIFBasedModelBase::TimeGridType aifTimeGrid = aifGenerator->GetAterialInputFunctionTimeGrid(); //Model configuration (static parameters) can be done now modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(m_selectedImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage)); generator = fitGenerator.GetPointer(); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { roiUID = m_selectedMask->GetUID(); } //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); infoSignal.clear(); for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } void PETDynamicView::DoFit(const mitk::modelFit::ModelFitInfo* fitSession, mitk::ParameterFitImageGeneratorBase* generator) { std::stringstream message; message << "" << "Fitting Data Set . . ." << ""; m_Controls.errorMessageLabel->setText(message.str().c_str()); m_Controls.errorMessageLabel->show(); ///////////////////////// //create job and put it into the thread pool ParameterFitBackgroundJob* pJob = new ParameterFitBackgroundJob(generator, fitSession, this->m_selectedNode); pJob->setAutoDelete(true); connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnJobError(QString))); connect(pJob, SIGNAL(Finished()), this, SLOT(OnJobFinished())); connect(pJob, SIGNAL(ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), this, SLOT(OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), Qt::BlockingQueuedConnection); connect(pJob, SIGNAL(JobProgress(double)), this, SLOT(OnJobProgress(double))); connect(pJob, SIGNAL(JobStatusChanged(QString)), this, SLOT(OnJobStatusChanged(QString))); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); } PETDynamicView::PETDynamicView() : m_FittingInProgress(false) { m_selectedImage = nullptr; m_selectedMask = nullptr; mitk::ModelFactoryBase::Pointer factory = mitk::OneTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::ExtendedOneTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::TwoTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::TwoTissueCompartmentFDGModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); - factory = mitk::NumericTwoTissueCompartmentModelFactory::New().GetPointer(); - m_FactoryStack.push_back(factory); + mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image"); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isLegacyMask = mitk::NodePredicateAnd::New(isImage, isBinary); mitk::NodePredicateOr::Pointer isMask = mitk::NodePredicateOr::New(isLegacyMask, isLabelSet); mitk::NodePredicateAnd::Pointer isNoMask = mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isMask)); this->m_IsMaskPredicate = mitk::NodePredicateAnd::New(isMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); this->m_IsNoMaskImagePredicate = mitk::NodePredicateAnd::New(isNoMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); } void PETDynamicView::OnJobFinished() { this->m_Controls.infoBox->append(QString("Fitting finished")); this->m_FittingInProgress = false; }; void PETDynamicView::OnJobError(QString err) { MITK_ERROR << err.toStdString().c_str(); m_Controls.infoBox->append(QString("") + err + QString("")); }; void PETDynamicView::OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results, const ParameterFitBackgroundJob* pJob) { //Store the resulting parameter fit image via convenience helper function in data storage //(handles the correct generation of the nodes and their properties) mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), results, pJob->GetParentNode()); m_Controls.errorMessageLabel->setText(""); m_Controls.errorMessageLabel->hide(); }; void PETDynamicView::OnJobProgress(double progress) { QString report = QString("Progress. ") + QString::number(progress); this->m_Controls.infoBox->append(report); }; void PETDynamicView::OnJobStatusChanged(QString info) { this->m_Controls.infoBox->append(info); } void PETDynamicView::InitModelComboBox() const { this->m_Controls.comboModel->clear(); this->m_Controls.comboModel->addItem(tr("No model selected")); for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin(); pos != m_FactoryStack.end(); ++pos) { this->m_Controls.comboModel->addItem(QString::fromStdString((*pos)->GetClassID())); } this->m_Controls.comboModel->setCurrentIndex(0); }; mitk::ModelFitFunctorBase::Pointer PETDynamicView::CreateDefaultFitFunctor( const mitk::ModelParameterizerBase* parameterizer) const { mitk::LevenbergMarquardtModelFitFunctor::Pointer fitFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); mitk::SumOfSquaredDifferencesFitCostFunction::Pointer evaluation = mitk::SumOfSquaredDifferencesFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("sum_diff^2", evaluation); mitk::ChiSquareFitCostFunction::Pointer chi2 = mitk::ChiSquareFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("Chi^2", chi2); mitk::ReducedChiSquareFitCostFunction::Pointer redchi2 = mitk::ReducedChiSquareFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("redChi^2", redchi2); if (m_Controls.checkBox_Constraints->isChecked()) { fitFunctor->SetConstraintChecker(m_modelConstraints); } mitk::ModelBase::Pointer refModel = parameterizer->GenerateParameterizedModel(); ::itk::LevenbergMarquardtOptimizer::ScalesType scales; scales.SetSize(refModel->GetNumberOfParameters()); scales.Fill(1.0); fitFunctor->SetScales(scales); return fitFunctor.GetPointer(); } void PETDynamicView::GetAIF(mitk::AIFBasedModelBase::AterialInputFunctionType& aif, mitk::AIFBasedModelBase::AterialInputFunctionType& aifTimeGrid) { if (this->m_Controls.radioAIFFile->isChecked()) { aif.clear(); aifTimeGrid.clear(); aif.SetSize(AIFinputFunction.size()); aifTimeGrid.SetSize(AIFinputGrid.size()); aif.fill(0.0); aifTimeGrid.fill(0.0); itk::Array<double>::iterator aifPos = aif.begin(); for (std::vector<double>::const_iterator pos = AIFinputFunction.begin(); pos != AIFinputFunction.end(); ++pos, ++aifPos) { *aifPos = *pos; } itk::Array<double>::iterator gridPos = aifTimeGrid.begin(); for (std::vector<double>::const_iterator pos = AIFinputGrid.begin(); pos != AIFinputGrid.end(); ++pos, ++gridPos) { *gridPos = *pos; } } else if (this->m_Controls.radioAIFImage->isChecked()) { aif.clear(); aifTimeGrid.clear(); mitk::AterialInputFunctionGenerator::Pointer aifGenerator = mitk::AterialInputFunctionGenerator::New(); //Hematocrit level aifGenerator->SetHCL(this->m_Controls.HCLSpinBox->value()); //mask settings this->m_selectedAIFMaskNode = m_Controls.comboAIFMask->GetSelectedNode(); this->m_selectedAIFMask = dynamic_cast<mitk::Image*>(this->m_selectedAIFMaskNode->GetData()); if (this->m_selectedAIFMask->GetTimeSteps() > 1) { MITK_INFO << "Selected AIF mask has multiple timesteps. Only use first timestep to mask model fit. AIF Mask name: " << m_selectedAIFMaskNode->GetName() ; mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedAIFMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedAIFMask = maskedImageTimeSelector->GetOutput(); } if (this->m_selectedAIFMask.IsNotNull()) { aifGenerator->SetMask(this->m_selectedAIFMask); } //image settings if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { this->m_selectedAIFImageNode = m_Controls.comboAIFImage->GetSelectedNode(); this->m_selectedAIFImage = dynamic_cast<mitk::Image*>(this->m_selectedAIFImageNode->GetData()); } else { this->m_selectedAIFImageNode = m_selectedNode; this->m_selectedAIFImage = m_selectedImage; } aifGenerator->SetDynamicImage(this->m_selectedAIFImage); aif = aifGenerator->GetAterialInputFunction(); aifTimeGrid = aifGenerator->GetAterialInputFunctionTimeGrid(); } else { - mitkThrow() << "Cannot generate AIF. View is in a invalide state. No AIF mode selected."; + mitkThrow() << "Cannot generate AIF. View is in a invalid state. No AIF mode selected."; } } void PETDynamicView::LoadAIFfromFile() { QFileDialog dialog; dialog.setNameFilter(tr("Images (*.csv")); QString fileName = dialog.getOpenFileName(); m_Controls.aifFilePath->setText(fileName); std::string m_aifFilePath = fileName.toStdString(); //Read Input typedef boost::tokenizer< boost::escaped_list_separator<char> > Tokenizer; ///////////////////////////////////////////////////////////////////////////////////////////////// //AIF Data std::ifstream in1(m_aifFilePath.c_str()); if (!in1.is_open()) { m_Controls.errorMessageLabel->setText("Could not open AIF File!"); } std::vector< std::string > vec1; std::string line1; while (getline(in1, line1)) { Tokenizer tok(line1); vec1.assign(tok.begin(), tok.end()); // if (vec1.size() < 3) continue; this->AIFinputGrid.push_back(convertToDouble(vec1[0])); this->AIFinputFunction.push_back(convertToDouble(vec1[1])); } } diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicViewControls.ui b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicViewControls.ui index 7d15ec19da..ab1f608646 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicViewControls.ui +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.pet/src/internal/PETDynamicViewControls.ui @@ -1,325 +1,325 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>PETDynamicViewControls</class> <widget class="QWidget" name="PETDynamicViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>745</width> <height>898</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QLabel" name="label_2"> <property name="text"> <string>Selected Time Series:</string> </property> </widget> </item> <item> <widget class="QLabel" name="timeserieslabel"> <property name="text"> <string>No series selected.</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <item> <widget class="QLabel" name="label_3"> <property name="text"> <string>Selected Mask:</string> </property> </widget> </item> <item> <widget class="QLabel" name="masklabel"> <property name="text"> <string>No mask selected.</string> </property> </widget> </item> </layout> </item> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> <string>Fitting strategy</string> </property> <layout class="QHBoxLayout" name="horizontalLayout_3"> <property name="spacing"> <number>5</number> </property> <property name="margin"> <number>5</number> </property> <item> <widget class="QRadioButton" name="radioPixelBased"> <property name="text"> <string>Pixel based</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item> <widget class="QRadioButton" name="radioROIbased"> <property name="text"> <string>ROI based</string> </property> </widget> </item> </layout> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <item> <widget class="QLabel" name="label_4"> <property name="text"> <string>Message</string> </property> </widget> </item> <item> <widget class="QLabel" name="errorMessageLabel"> <property name="text"> <string>-</string> </property> </widget> </item> </layout> </item> </layout> </item> <item> <widget class="QComboBox" name="comboModel"> <item> <property name="text"> - <string>Select pharmacokinetic modell...</string> + <string>Select pharmacokinetic model...</string> </property> </item> </widget> </item> <item> <widget class="QGroupBox" name="groupAIF"> <property name="title"> <string>AIF Mask:</string> </property> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <widget class="QRadioButton" name="radioAIFImage"> <property name="text"> <string>Select AIF from Image:</string> </property> </widget> </item> <item> <layout class="QGridLayout" name="gridLayout"> <item row="0" column="0"> <widget class="QLabel" name="labelAIFMask"> <property name="text"> <string>AIF Mask:</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QCheckBox" name="checkDedicatedAIFImage"> <property name="text"> <string>Dedicated AIF Image:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QmitkDataStorageComboBox" name="comboAIFMask" native="true"/> </item> <item row="1" column="1"> <widget class="QmitkDataStorageComboBox" name="comboAIFImage" native="true"/> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_5"> <item> <widget class="QRadioButton" name="radioAIFFile"> <property name="text"> <string>Select AIF from File:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="aifFilePath"/> </item> <item> <widget class="QPushButton" name="btnAIFFile"> <property name="text"> <string>Browse</string> </property> </widget> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_6"> <item> <widget class="QLabel" name="label"> <property name="text"> <string>Whole Blood to Plasma Correction:</string> </property> </widget> </item> <item> <widget class="QDoubleSpinBox" name="HCLSpinBox"/> </item> </layout> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="groupBox_FitConfiguration"> <property name="title"> <string>Model Fit Configuration</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QToolBox" name="toolBox"> <property name="currentIndex"> <number>1</number> </property> <widget class="QWidget" name="groupStartParameter"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>701</width> <height>129</height> </rect> </property> <property name="toolTip"> <string/> </property> <property name="whatsThis"> <string/> </property> <attribute name="label"> <string>Start Parameters</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <widget class="QRadioButton" name="radioButton_StartParameters"> <property name="text"> <string>Enter parameter starting values manually:</string> </property> </widget> </item> <item> <widget class="QmitkInitialValuesManagerWidget" name="initialValuesManager" native="true"/> </item> </layout> </widget> <widget class="QWidget" name="groupConstraints"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>701</width> <height>129</height> </rect> </property> <attribute name="label"> <string>Constraints</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <widget class="QCheckBox" name="checkBox_Constraints"> <property name="text"> <string>Enter Constraints for Fit Parameters</string> </property> </widget> </item> <item> <widget class="QmitkSimpleBarrierManagerWidget" name="constraintManager" native="true"/> </item> </layout> </widget> </widget> </item> </layout> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_7"> <property name="leftMargin"> <number>0</number> </property> <property name="topMargin"> <number>0</number> </property> <item> <widget class="QLabel" name="label_5"> <property name="text"> <string>Fitting name:</string> </property> </widget> </item> <item> <widget class="QLineEdit" name="lineFitName"/> </item> </layout> </item> <item> <widget class="QPushButton" name="btnModelling"> <property name="text"> <string>Start Modelling</string> </property> </widget> </item> <item> <widget class="QTextEdit" name="infoBox"> <property name="readOnly"> <bool>true</bool> </property> </widget> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkSimpleBarrierManagerWidget</class> <extends>QWidget</extends> <header>QmitkSimpleBarrierManagerWidget.h</header> </customwidget> <customwidget> <class>QmitkInitialValuesManagerWidget</class> <extends>QWidget</extends> <header>QmitkInitialValuesManagerWidget.h</header> </customwidget> <customwidget> <class>QmitkDataStorageComboBox</class> <extends>QWidget</extends> <header location="global">QmitkDataStorageComboBox.h</header> </customwidget> </customwidgets> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp index 9a250cb94a..64cef01de2 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp @@ -1,1000 +1,880 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include <QMessageBox> #include "mitkWorkbenchUtil.h" #include "PerfusionDataSimulationView.h" #include "itkUnaryFunctorImageFilter.h" #include <boost/tokenizer.hpp> #include "mitkImageCast.h" #include "mitkImageTimeSelector.h" #include "mitkITKImageImport.h" #include "mitkGaussianNoiseFunctor.h" #include "mitkTwoCompartmentExchangeModel.h" #include "mitkTwoCompartmentExchangeModelParameterizer.h" #include "mitkTwoCompartmentExchangeModelFactory.h" -#include "mitkNumericTwoCompartmentExchangeModel.h" -#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" -#include "mitkNumericTwoCompartmentExchangeModelFactory.h" #include "mitkExtendedToftsModel.h" #include "mitkExtendedToftsModelFactory.h" #include "mitkExtendedToftsModelParameterizer.h" #include "mitkTwoTissueCompartmentModel.h" #include "mitkTwoTissueCompartmentModelParameterizer.h" #include "mitkTwoTissueCompartmentModelFactory.h" #include "mitkOneTissueCompartmentModel.h" #include "mitkOneTissueCompartmentModelParameterizer.h" #include "mitkOneTissueCompartmentModelFactory.h" #include "mitkModelSignalImageGenerator.h" #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateDataType.h> #include "mitkSimpleFunctorBase.h" #include "mitkArbitraryTimeGeometry.h" #include <iostream> #include <QFileDialog> const std::string PerfusionDataSimulationView::VIEW_ID = "org.mitk.views.pharmacokinetics.simulation"; inline double convertToDouble(const std::string& data) { std::istringstream stepStream(data); stepStream.imbue(std::locale("C")); double value = 0.0; if (!(stepStream >> value) || !(stepStream.eof())) { mitkThrow() << "Cannot convert string to double. String: " << data; } return value; } inline double FindeMaxConcentration(std::vector<double> Concentration) { double maximum = Concentration[0]; for (std::vector<double>::size_type i =0; i<Concentration.size(); ++i) { maximum = std::max(maximum, Concentration[i]); } return maximum; } void PerfusionDataSimulationView::SetFocus() { m_Controls.GenerateBtn->setFocus(); } void PerfusionDataSimulationView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_Controls.GenerateBtn->setEnabled(false); m_Controls.groupBox_TM->hide(); m_Controls.groupBox_2CXM->hide(); m_Controls.groupBox_2TCM->hide(); m_Controls.groupBox_1TCM->hide(); m_Controls.groupBox_CNR->hide(); this->InitModelComboBox(); /** #2 @todo Reduce code ? */ m_Controls.comboBox_F->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_F->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_PS->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_PS->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_fp->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_fp->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_fi->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_fi->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_Ktrans->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_Ktrans->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_vp->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_vp->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_ve->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_ve->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K1->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K1->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K2->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K2->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K3->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K3->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K4->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K4->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_VB->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_VB->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_k1->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_k1->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_k2->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_k2->SetPredicate(m_IsNotABinaryImagePredicate); connect(m_Controls.AifFileBtn, SIGNAL(clicked()), this, SLOT(LoadAIFFile())); connect(m_Controls.ModelSelection, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int))); connect(m_Controls.GenerateBtn, SIGNAL(clicked()), this, SLOT(OnGenerateDataButtonClicked())); connect(m_Controls.comboBox_F, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_PS, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_fp, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_fi, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_VB, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K1, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K2, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K3, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K4, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_k1, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_k2, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_Ktrans, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_vp, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_ve, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.CNRSpinBox, SIGNAL(valueChanged(double)),this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.NoiseCheckBox, SIGNAL(stateChanged(int)),this, SLOT(OnSimulationConfigurationChanged())); // UpdateDataSelection(); } void PerfusionDataSimulationView::UpdateDataSelection() { } //void PerfusionDataSimulationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, // const QList<mitk::DataNode::Pointer>& selectedNodes) //{ // UpdateDataSelection(); // m_Controls.GenerateBtn->setEnabled(CheckModelSettings()); //} void PerfusionDataSimulationView::OnSimulationConfigurationChanged() { // UpdateDataSelection(); m_Controls.groupBox_CNR->setVisible(m_Controls.NoiseCheckBox->isChecked()); this->m_CNR = m_Controls.CNRSpinBox->value(); m_Controls.GenerateBtn->setEnabled( CheckModelSettings() ); } void PerfusionDataSimulationView::OnModellSet(int index) { m_selectedModelFactory = nullptr; if (index > 0) { if (static_cast<ModelFactoryStackType::size_type>(index) <= m_FactoryStack.size() ) { m_selectedModelFactory = m_FactoryStack[index - 1]; } else { MITK_WARN << "Invalid model index. Index outside of the factory stack. Factory stack size: "<< m_FactoryStack.size() << "; invalid index: "<< index; } } bool isToftsFactory = dynamic_cast<mitk::ExtendedToftsModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; - bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; + bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast<mitk::TwoTissueCompartmentModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool is1TCMFactory = dynamic_cast<mitk::OneTissueCompartmentModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; m_Controls.groupBox_TM->setVisible(isToftsFactory); m_Controls.groupBox_2CXM->setVisible(is2CXMFactory ); m_Controls.groupBox_2TCM->setVisible(is2TCMFactory ); m_Controls.groupBox_1TCM->setVisible(is1TCMFactory ); m_Controls.GenerateBtn->setEnabled( CheckModelSettings() ); // UpdateDataSelection(); } bool PerfusionDataSimulationView::CheckModelSettings() { bool ok = true; if(m_selectedModelFactory.IsNull()) { return false; } if(this->m_AterialInputFunction.GetSize() == 0 || this->m_TimeGrid.GetSize() == 0) { return false; } bool isToftsFactory = dynamic_cast<mitk::ExtendedToftsModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; - bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; + bool is2CXMFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast<mitk::TwoTissueCompartmentModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool is1TCMFactory = dynamic_cast<mitk::OneTissueCompartmentModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; if(isToftsFactory) { ok = ok && m_Controls.comboBox_Ktrans->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_vp->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_ve->GetSelectedNode().IsNotNull(); } else if(is2CXMFactory) { ok = ok && m_Controls.comboBox_F->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_PS->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_fp->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_fi->GetSelectedNode().IsNotNull(); } else if(is2TCMFactory) { ok = ok && m_Controls.comboBox_K1->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_K2->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_K3->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_K4->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_VB->GetSelectedNode().IsNotNull(); } else if(is1TCMFactory) { ok = ok && m_Controls.comboBox_k1->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_k2->GetSelectedNode().IsNotNull(); } else { return false; } if(m_Controls.NoiseCheckBox->isChecked()) { if(m_CNR !=0 && m_MaxConcentration !=0) { this->m_Sigma = m_MaxConcentration/m_CNR; } if(m_Sigma==0) { return false; } } return ok; } void PerfusionDataSimulationView::InitModelComboBox() const { this->m_Controls.ModelSelection->clear(); this->m_Controls.ModelSelection->addItem(tr("No model selected")); for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin(); pos != m_FactoryStack.end(); ++pos) { this->m_Controls.ModelSelection->addItem(QString::fromStdString((*pos)->GetClassID())); } this->m_Controls.ModelSelection->setCurrentIndex(0); }; void PerfusionDataSimulationView::LoadAIFFile() { QFileDialog dialog; dialog.setNameFilter(tr("Images (*.csv")); QString fileName = dialog.getOpenFileName(); m_Controls.AifFilePath->setText( fileName ); std::string aifFilePath = fileName.toStdString(); //Read Input typedef boost::tokenizer< boost::escaped_list_separator<char> > Tokenizer; ///////////////////////////////////////////////////////////////////////////////////////////////// //AIF Data std::vector<double> inputFunction; std::vector<double> inputGrid; std::ifstream in1(aifFilePath.c_str()); if(!in1.is_open()) { m_Controls.errorMessageLabel->setText("Could not open AIF File!"); } std::vector< std::string > vec1; std::string line1; while (getline(in1,line1)) { Tokenizer tok(line1); vec1.assign(tok.begin(),tok.end()); // if (vec1.size() < 3) continue; inputGrid.push_back(convertToDouble(vec1[0])); inputFunction.push_back(convertToDouble(vec1[1])); } this->m_MaxConcentration = FindeMaxConcentration(inputFunction); itk::Array<double> aif; itk::Array<double> grid; aif.SetSize(inputFunction.size()); grid.SetSize(inputGrid.size()); aif.fill(0.0); grid.fill(0.0); itk::Array<double>::iterator aifPos = aif.begin(); for(std::vector<double>::const_iterator pos = inputFunction.begin(); pos != inputFunction.end(); ++pos, ++aifPos) { *aifPos = *pos; } itk::Array<double>::iterator gridPos = grid.begin(); for(std::vector<double>::const_iterator pos = inputGrid.begin(); pos != inputGrid.end(); ++pos, ++gridPos) { *gridPos = *pos; } this->m_AterialInputFunction = aif; this->m_TimeGrid = grid; m_Controls.GenerateBtn->setEnabled( CheckModelSettings() ); // UpdateDataSelection(); } -/** @todo #2 Same function for Numeric and analytic version of FillParameterMap2CXM +/** @todo #2 Same function for analytic version of FillParameterMap2CXM */ void PerfusionDataSimulationView::FillParameterMap2CXM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_F->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_F,m_selectedImage)); m_selectedNode = m_Controls.comboBox_PS->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_PS,m_selectedImage)); m_selectedNode = m_Controls.comboBox_fp->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_vp,m_selectedImage)); m_selectedNode = m_Controls.comboBox_fi->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_ve,m_selectedImage)); this->m_ParameterImageMap = stack; } -void PerfusionDataSimulationView::FillParameterMapNumeric2CXM() -{ - ParameterMapType stack; - - mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_F->GetSelectedNode(); - mitk::Image::Pointer m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_F,m_selectedImage)); - - m_selectedNode = m_Controls.comboBox_PS->GetSelectedNode(); - m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_PS,m_selectedImage)); - - m_selectedNode = m_Controls.comboBox_fp->GetSelectedNode(); - m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_vp,m_selectedImage)); - - m_selectedNode = m_Controls.comboBox_fi->GetSelectedNode(); - m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_ve,m_selectedImage)); - - this->m_ParameterImageMap = stack; - -} void PerfusionDataSimulationView::FillParameterMapETM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_Ktrans->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::ExtendedToftsModel::NAME_PARAMETER_Ktrans,m_selectedImage)); m_selectedNode = m_Controls.comboBox_vp->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::ExtendedToftsModel::NAME_PARAMETER_vp,m_selectedImage)); m_selectedNode = m_Controls.comboBox_ve->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::ExtendedToftsModel::NAME_PARAMETER_ve,m_selectedImage)); this->m_ParameterImageMap = stack; } void PerfusionDataSimulationView::FillParameterMap2TCM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_K1->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_K1,m_selectedImage)); m_selectedNode = m_Controls.comboBox_K2->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k2,m_selectedImage)); m_selectedNode = m_Controls.comboBox_K3->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k3,m_selectedImage)); m_selectedNode = m_Controls.comboBox_K4->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k4,m_selectedImage)); m_selectedNode = m_Controls.comboBox_VB->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_VB,m_selectedImage)); + stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_vb,m_selectedImage)); this->m_ParameterImageMap = stack; } void PerfusionDataSimulationView::FillParameterMap1TCM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_k1->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::OneTissueCompartmentModel::NAME_PARAMETER_k1,m_selectedImage)); + stack.insert(std::make_pair(mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1,m_selectedImage)); m_selectedNode = m_Controls.comboBox_k2->GetSelectedNode(); m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2,m_selectedImage)); this->m_ParameterImageMap = stack; } void PerfusionDataSimulationView::OnGenerateDataButtonClicked() { mitk::Image::Pointer m_DynamicImage = mitk::Image::New(); bool isToftsFactory = dynamic_cast<mitk::ExtendedToftsModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool isPhysBrixFactory = dynamic_cast<mitk::TwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; - bool isNumPhysBrixFactory = dynamic_cast<mitk::NumericTwoCompartmentExchangeModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast<mitk::TwoTissueCompartmentModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; bool is1TCMFactory = dynamic_cast<mitk::OneTissueCompartmentModelFactory*>(m_selectedModelFactory.GetPointer()) != nullptr; if(isToftsFactory) { this->FillParameterMapETM(); m_DynamicImage = this->GenerateETModelData(); } if (isPhysBrixFactory) { this->FillParameterMap2CXM(); m_DynamicImage = this->Generate2CXModelData(); } - if (isNumPhysBrixFactory) - { - this->FillParameterMapNumeric2CXM(); - m_DynamicImage = this->GenerateNumeric2CXModelData(); - } if (is2TCMFactory) { this->FillParameterMap2TCM(); m_DynamicImage = this->Generate2TCModelData(); } if (is1TCMFactory) { this->FillParameterMap1TCM(); m_DynamicImage = this->Generate1TCModelData(); } mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); std::string nameOfResultImage = "SimulationData_"; nameOfResultImage.append(m_selectedModelFactory->GetModelDisplayName()); resultNode->SetProperty("name", mitk::StringProperty::New(nameOfResultImage) ); resultNode->SetData(m_DynamicImage); // set data of new node this->GetDataStorage()->Add(resultNode); } mitk::Image::Pointer PerfusionDataSimulationView::Generate2CXModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::TwoCompartmentExchangeModelParameterizer::Pointer modelParameterizer = mitk::TwoCompartmentExchangeModelParameterizer::New(); /** @todo #2 necessary? Generator need to have a map with Parameters in order of Model in order to pass vector parameters correctly to Model. - * I wanted to make it independend from the order the images are passed on + * I wanted to make it independent from the order the images are passed on */ for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_F) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_F, pos->second); } if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_PS) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_PS, pos->second); } if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_ve) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_ve, pos->second); } if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_vp) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_vp, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image<double,3> ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast<mitk::ArbitraryTimeGeometry*> (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor<double,double> NoiseFunctorType; typedef itk::UnaryFunctorImageFilter<ImageType,ImageType, NoiseFunctorType > NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } -/** @todo #2 Synergie? Function implementation for every Model to complicated? - */ -mitk::Image::Pointer PerfusionDataSimulationView::GenerateNumeric2CXModelData() -{ -mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); -mitk::NumericTwoCompartmentExchangeModelParameterizer::Pointer modelParameterizer = mitk::NumericTwoCompartmentExchangeModelParameterizer::New(); - -for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) -{ - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_F) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_F, pos->second); - } - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_PS) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_PS, pos->second); - } - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_ve) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_ve, pos->second); - } - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_vp) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_vp, pos->second); - } -} - -modelParameterizer->SetAIF(this->m_AterialInputFunction); -modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); -modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); -modelParameterizer->SetODEINTStepSize(0.05); - -generator->SetParameterizer(modelParameterizer); - -mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); - - -mitk::Image::Pointer resultImage = mitk::Image::New(); -if(m_Controls.NoiseCheckBox->isChecked()) -{ - typedef itk::Image<double,3> ImageType; - - mitk::Image::Pointer tempImage = mitk::Image::New(); - tempImage->Initialize(generatedImage); - - mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast<mitk::ArbitraryTimeGeometry*> (generatedImage->GetTimeGeometry()); - - tempImage->SetTimeGeometry(timeGeometry); - - ImageType::Pointer itkImage = ImageType::New(); - mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); - imageTimeSelector->SetInput(generatedImage); - - for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) - { - imageTimeSelector->SetTimeNr(i); - imageTimeSelector->UpdateLargestPossibleRegion(); - - mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); - - mitk::CastToItkImage(mitkInputImage, itkImage ); - - typedef mitk::GaussianNoiseFunctor<double,double> NoiseFunctorType; - typedef itk::UnaryFunctorImageFilter<ImageType,ImageType, NoiseFunctorType > NoiseFilterType; - NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); - NoiseFunctorType noiseFunctor; - noiseFunctor.SetMean(0.0); - noiseFunctor.SetSigma(this->m_Sigma); - noiseFilter->SetFunctor(noiseFunctor); - - noiseFilter->SetInput(itkImage); - - mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); - - mitk::ImageReadAccessor accessor(outputImage); - tempImage->SetVolume(accessor.GetData(), i); - } - - resultImage = tempImage->Clone(); -} -else -{ - resultImage = generatedImage; -} -return resultImage; -} mitk::Image::Pointer PerfusionDataSimulationView::GenerateETModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::ExtendedToftsModelParameterizer::Pointer modelParameterizer = mitk::ExtendedToftsModelParameterizer::New(); for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::ExtendedToftsModel::NAME_PARAMETER_Ktrans) { generator->SetParameterInputImage(mitk::ExtendedToftsModel::POSITION_PARAMETER_Ktrans, pos->second); } if(pos->first == mitk::ExtendedToftsModel::NAME_PARAMETER_vp) { generator->SetParameterInputImage(mitk::ExtendedToftsModel::POSITION_PARAMETER_vp, pos->second); } if(pos->first == mitk::ExtendedToftsModel::NAME_PARAMETER_ve) { generator->SetParameterInputImage(mitk::ExtendedToftsModel::POSITION_PARAMETER_ve, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image<double,3> ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast<mitk::ArbitraryTimeGeometry*> (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor<double,double> NoiseFunctorType; typedef itk::UnaryFunctorImageFilter<ImageType,ImageType, NoiseFunctorType > NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } mitk::Image::Pointer PerfusionDataSimulationView::Generate2TCModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::TwoTissueCompartmentModelParameterizer::Pointer modelParameterizer = mitk::TwoTissueCompartmentModelParameterizer::New(); for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_K1) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_K1, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k2) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k2, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k3) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k3, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k4) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k4, pos->second); } - if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_VB) + if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_vb) { - generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_VB, pos->second); + generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_vb, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image<double,3> ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast<mitk::ArbitraryTimeGeometry*> (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor<double,double> NoiseFunctorType; typedef itk::UnaryFunctorImageFilter<ImageType,ImageType, NoiseFunctorType > NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } mitk::Image::Pointer PerfusionDataSimulationView::Generate1TCModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::OneTissueCompartmentModelParameterizer::Pointer modelParameterizer = mitk::OneTissueCompartmentModelParameterizer::New(); for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { - if(pos->first == mitk::OneTissueCompartmentModel::NAME_PARAMETER_k1) + if(pos->first == mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1) { - generator->SetParameterInputImage(mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k1, pos->second); + generator->SetParameterInputImage(mitk::OneTissueCompartmentModel::POSITION_PARAMETER_K1, pos->second); } if(pos->first == mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2) { generator->SetParameterInputImage(mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k2, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image<double,3> ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast<mitk::ArbitraryTimeGeometry*> (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor<double,double> NoiseFunctorType; typedef itk::UnaryFunctorImageFilter<ImageType,ImageType, NoiseFunctorType > NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } PerfusionDataSimulationView::PerfusionDataSimulationView() { m_Sigma = 0; m_CNR=0; m_MaxConcentration=0; m_selectedModelFactory = nullptr; mitk::ModelFactoryBase::Pointer factory = mitk::ExtendedToftsModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::TwoCompartmentExchangeModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); - factory = mitk::NumericTwoCompartmentExchangeModelFactory::New().GetPointer(); - m_FactoryStack.push_back(factory); factory = mitk::TwoTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::OneTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); m_IsNotABinaryImagePredicate = mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType<mitk::Image>::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true))), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); } diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h index 7956d413f1..27cf365e0a 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h @@ -1,114 +1,112 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef PerfusionDataSimulationView_h #define PerfusionDataSimulationView_h #include <QString> #include <QmitkAbstractView.h> #include "ui_PerfusionDataSimulationViewControls.h" #include "mitkModelBase.h" #include <mitkModelFactoryBase.h> #include "itkArray.h" #include "mitkImage.h" #include <mitkImage.h> /*! * @brief Test Plugin for SUV calculations of PET images */ class PerfusionDataSimulationView : public QmitkAbstractView { Q_OBJECT public: /*! @brief The view's unique ID - required by MITK */ static const std::string VIEW_ID; PerfusionDataSimulationView(); protected slots: /*! * @brief Is triggered of the update button is clicked and the selected node should get the (new) iso level set. */ void OnGenerateDataButtonClicked(); void LoadAIFFile(); void OnModellSet(int); void OnSimulationConfigurationChanged(); void UpdateDataSelection(); protected: typedef std::map<std::string, mitk::Image::Pointer> ParameterMapType; // Overridden base class functions /*! * @brief Sets up the UI controls and connects the slots and signals. Gets * called by the framework to create the GUI at the right time. * @param[in,out] parent The parent QWidget, as this class itself is not a QWidget * subclass. */ void CreateQtPartControl(QWidget* parent) override; /*! * @brief Sets the focus to the plot curve button. Gets called by the framework to set the * focus on the right widget. */ void SetFocus() override; void InitModelComboBox() const; mitk::Image::Pointer Generate2CXModelData(); - mitk::Image::Pointer GenerateNumeric2CXModelData(); mitk::Image::Pointer GenerateETModelData(); void FillParameterMap2CXM(); - void FillParameterMapNumeric2CXM(); void FillParameterMapETM(); ///////////////////// dynamic PET Models/////////////// mitk::Image::Pointer Generate2TCModelData(); mitk::Image::Pointer Generate1TCModelData(); void FillParameterMap2TCM(); void FillParameterMap1TCM(); bool CheckModelSettings(); // Variables /*! @brief The view's UI controls */ Ui::PerfusionDataSimulationViewControls m_Controls; mitk::DataNode::Pointer m_selectedNode; ParameterMapType m_ParameterImageMap; itk::Array<double> m_AterialInputFunction; itk::Array<double> m_TimeGrid; mitk::ModelFactoryBase::Pointer m_selectedModelFactory; private: typedef std::vector<mitk::ModelFactoryBase::Pointer> ModelFactoryStackType; ModelFactoryStackType m_FactoryStack; mitk::NodePredicateBase::Pointer m_IsNotABinaryImagePredicate; double m_CNR, m_MaxConcentration, m_Sigma; }; #endif diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp index e3911c8ce6..e7bec0d4df 100644 --- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp +++ b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp @@ -1,286 +1,286 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "PointSetInteractionMultispectrum.h" #include "QmitkPointListWidget.h" #include "QmitkRenderWindow.h" // Qt #include <QMessageBox> #include <QApplication> #include <qwt_plot.h> #include <qwt_plot_curve.h> #include <qwt_plot_grid.h> #include <qwt_symbol.h> #include <qwt_legend.h> #include <QColor> #include <QString> //mitk image #include <mitkImage.h> #include <mitkImagePixelReadAccessor.h> // MITK #include "mitkITKImageImport.h" #include "mitkProperties.h" #include "mitkColorProperty.h" #include "mitkImageCast.h" #include <mitkVector.h> #include <mitkPoint.h> #include <mitkImageStatisticsHolder.h> // ITK #include <itkConnectedThresholdImageFilter.h> const std::string PointSetInteractionMultispectrum::VIEW_ID = "org.mitk.views.pointsetinteractionmultispectrum"; PointSetInteractionMultispectrum::PointSetInteractionMultispectrum() : m_PointListWidget(nullptr) { } void PointSetInteractionMultispectrum::SetFocus() { m_Controls.buttonPerformImageProcessing->setFocus(); } void PointSetInteractionMultispectrum::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect(m_Controls.buttonPerformImageProcessing, SIGNAL(clicked()), this, SLOT(DoImageProcessing())); //! [cpp-createqtpartcontrol] // create a QmitkPointListWidget and add it to the widget created from .ui file m_PointListWidget = new QmitkPointListWidget(); m_Controls.verticalLayout->addWidget(m_PointListWidget, 1); // retrieve a possibly existing IRenderWindowPart if (mitk::IRenderWindowPart* renderWindowPart = GetRenderWindowPart()) { // let the point set widget know about the render window part (crosshair updates) RenderWindowPartActivated(renderWindowPart); } // create a new DataNode containing a PointSet with some interaction m_PointSet = mitk::PointSet::New(); mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New(); pointSetNode->SetData(m_PointSet); pointSetNode->SetName("points for displaying reflectance."); pointSetNode->SetProperty("helper object", mitk::BoolProperty::New(true)); pointSetNode->SetProperty("layer", mitk::IntProperty::New(1024)); // add the pointset to the data storage (for rendering and access by other modules) GetDataStorage()->Add(pointSetNode); // tell the GUI widget about the point set m_PointListWidget->SetPointSetNode(pointSetNode); //! [cpp-createqtpartcontrol] m_Plot = new QwtPlot(); } void PointSetInteractionMultispectrum::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*source*/, const QList<mitk::DataNode::Pointer>& nodes) { // iterate all selected objects, adjust warning visibility foreach( mitk::DataNode::Pointer node, nodes ){ if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) ) { m_Controls.labelWarning->setVisible( false ); m_Controls.buttonPerformImageProcessing->setEnabled( true ); return; } } m_Controls.labelWarning->setVisible( true ); m_Controls.buttonPerformImageProcessing->setEnabled( false ); } void PointSetInteractionMultispectrum::RenderWindowPartActivated( mitk::IRenderWindowPart* renderWindowPart) { // let the point set widget know about the slice navigation controllers // in the active render window part (crosshair updates) foreach(QmitkRenderWindow* renderWindow, renderWindowPart->GetQmitkRenderWindows().values()) { m_PointListWidget->AddSliceNavigationController(renderWindow->GetSliceNavigationController()); } } void PointSetInteractionMultispectrum::RenderWindowPartDeactivated( mitk::IRenderWindowPart* renderWindowPart) { foreach(QmitkRenderWindow* renderWindow, renderWindowPart->GetQmitkRenderWindows().values()) { m_PointListWidget->RemoveSliceNavigationController(renderWindow->GetSliceNavigationController()); } } void PointSetInteractionMultispectrum::DoImageProcessing() { QList<mitk::DataNode::Pointer> DataManagerNodes = this->GetDataManagerSelection(); if (DataManagerNodes.empty()) return; mitk::DataNode* DataManagerNode = DataManagerNodes.front(); if (!DataManagerNode) { // Nothing selected. Inform the user and return QMessageBox::information( nullptr, "Template", "Please load and select an image before starting image processing."); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image). // notice that this is the 'BaseData' type. mitk::BaseData* data = DataManagerNode->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast<mitk::Image*>(data); if (image) { //! [cpp-doimageprocessing] // So we have an image. Let's see if the user has set some seed points already if (m_PointSet->GetSize() == 0) { // no points there. Not good for region growing QMessageBox::information( nullptr, "Reflectance display functionality", "Please set some points inside the image first.\n" "(hold Shift key and click left mouse button inside the image.)"); return; } // plot the reflectances // PlotReflectance(m_PointSet, DataManagerNodes); //! [cpp-doimageprocessing] } } } void PointSetInteractionMultispectrum::PlotReflectance(mitk::PointSet::Pointer m_PointSet, QList<mitk::DataNode::Pointer> dataManagerNodes) { - mitk::PointSet::PointsIterator PtIterator; // The point iterator in the PointSet, which gets accesss to each point. + mitk::PointSet::PointsIterator PtIterator; // The point iterator in the PointSet, which gets access to each point. mitk::Point3D Point; // The extracted point. Notice that a point has three components (x, y, z). itk::Index<3> index; // The 3D index, which is converted from the world coordinate - itk::Index<2> index2; // The truncated version of the 3D index, for which only the first two componets are extracted. + itk::Index<2> index2; // The truncated version of the 3D index, for which only the first two components are extracted. itk::VectorImage<double, 2>::Pointer itkImage; // The itk vector image. This is used since the mitk::Image could not handle multi-channel images well. // //////////////// Qwt window configuration ///////////////////////////////////////////// delete m_Plot; m_Plot = new QwtPlot(); // create a new plot // m_Plot->setAxisAutoScale(QwtPlot::xBottom); // automatical scale -x // m_Plot->setAxisAutoScale(QwtPlot::yLeft); // automatical scale -y // m_Plot->setTitle("Multispectral Reflectance"); // set the plot title // m_Plot->setCanvasBackground(Qt::white); // set the background color // m_Plot->insertLegend(new QwtLegend()); // set the legend // QwtPlotGrid* grid = new QwtPlotGrid(); // set the grid // grid->attach(m_Plot); // set the grid // m_Controls.verticalLayout->addWidget(m_Plot, 1); // put the plot into the workbench // // the number of the plotted curve int curveIdx = 0; // iterate selected datanodes: for (auto node = dataManagerNodes.begin(); node != dataManagerNodes.end(); ++node) { mitk::BaseData* data = node->GetPointer()->GetData(); // the current number of examined data point: int pointIdx = 0; if (data) { std::string curveNameString = ""; node->GetPointer()->GetStringProperty("name", curveNameString); curveNameString += " point "; // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast<mitk::Image*>(data); if (image) { // convert the MITK image to the ITK image // mitk::CastToItkImage(image, itkImage); ////////////////////////// main loop ///////////////////////////////// int reflectanceIdx; itk::VariableLengthVector<double> reflectance; int channels; // The loop goes through each point in the point set // for (PtIterator = m_PointSet->Begin(0); PtIterator != m_PointSet->End(0); PtIterator++) { // extract the reflectance on a given pixel // Point = PtIterator.Value(); image->GetGeometry(0)->WorldToIndex(Point, index); index2[0] = index[0]; index2[1] = index[1]; reflectance = itkImage->GetPixel(index2); channels = reflectance.GetNumberOfElements(); // plot the reflectance dynamically // // create colors for each element in pointset. // "randomly" select colors for each added point by multiplying with prime. QColor curveColor((200 + (41 * curveIdx)) % 255, (89 * curveIdx) % 255, (37 * curveIdx) % 255); QString curveName(curveNameString.c_str()); curveName.append(QString::number(pointIdx)); QPolygonF qwtPoints; QwtPlotCurve* curve = new QwtPlotCurve(); curve->setTitle(curveName); curve->setPen(curveColor, 4); curve->setRenderHint(QwtPlotItem::RenderAntialiased, true); QwtSymbol *symbol = new QwtSymbol(QwtSymbol::Ellipse, QBrush(Qt::yellow), QPen(Qt::black, 2), QSize(10, 10)); for (reflectanceIdx = 0; reflectanceIdx < channels; reflectanceIdx++) { qwtPoints<< QPointF((double) reflectanceIdx,reflectance.GetElement(reflectanceIdx)); } curve->setSamples(qwtPoints); curve->setSymbol(symbol); curve->attach(m_Plot); m_Plot->show(); ++curveIdx; ++pointIdx; } } } } } diff --git a/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp b/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp index 8927b738ff..653fa848a0 100644 --- a/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp +++ b/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp @@ -1,453 +1,453 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkPreprocessingResamplingView.h" // QT includes (GUI) #include <qlabel.h> #include <qspinbox.h> #include <qpushbutton.h> #include <qcheckbox.h> #include <qgroupbox.h> #include <qradiobutton.h> #include <qmessagebox.h> // Berry includes (selection service) #include <berryISelectionService.h> #include <berryIWorkbenchWindow.h> // MITK includes (GUI) #include "QmitkDataNodeSelectionProvider.h" #include "mitkDataNodeObject.h" // MITK includes (general) #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateDimension.h" #include "mitkNodePredicateAnd.h" #include "mitkImageTimeSelector.h" #include "mitkVectorImageMapper2D.h" #include "mitkProperties.h" #include "mitkLevelWindowProperty.h" #include <mitkTimeNavigationController.h> // Includes for image casting between ITK and MITK #include "mitkImageCast.h" #include "mitkITKImageImport.h" // ITK includes (general) #include <itkVectorImage.h> #include <itkImageFileWriter.h> // Resampling #include <itkResampleImageFilter.h> #include <itkNearestNeighborInterpolateImageFunction.h> #include <itkBSplineInterpolateImageFunction.h> #include <itkCastImageFilter.h> #include <itkLinearInterpolateImageFunction.h> #include <itkRescaleIntensityImageFilter.h> #include <itkShiftScaleImageFilter.h> // STD #include <cmath> // Convenient Definitions typedef itk::Image<double, 3> ImageType; typedef itk::Image<unsigned char, 3> SegmentationImageType; typedef itk::Image<double, 3> DoubleImageType; typedef itk::Image<itk::Vector<float,3>, 3> VectorImageType; typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType; typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType2; typedef itk::CastImageFilter< ImageType, DoubleImageType > ImagePTypeToFloatPTypeCasterType; typedef itk::LinearInterpolateImageFunction< ImageType, double > LinearInterpolatorType; typedef itk::NearestNeighborInterpolateImageFunction< ImageType, double > NearestInterpolatorType; typedef itk::BSplineInterpolateImageFunction<ImageType, double> BSplineInterpolatorType; QmitkPreprocessingResampling::QmitkPreprocessingResampling() : QmitkAbstractView(), m_Controls(nullptr), m_SelectedImageNode(nullptr), m_TimeStepperAdapter(nullptr) { } QmitkPreprocessingResampling::~QmitkPreprocessingResampling() { } void QmitkPreprocessingResampling::CreateQtPartControl(QWidget *parent) { if (m_Controls == nullptr) { m_Controls = new Ui::QmitkPreprocessingResamplingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); mitk::NodePredicateDataType::Pointer imagePredicate = mitk::NodePredicateDataType::New("Image"); } m_SelectedImageNode = mitk::DataStorageSelection::New(this->GetDataStorage(), false); // Setup Controls this->m_Controls->cbParam4->clear(); this->m_Controls->cbParam4->insertItem(LINEAR, "Linear"); this->m_Controls->cbParam4->insertItem(NEAREST, "Nearest neighbor"); this->m_Controls->cbParam4->insertItem(SPLINE, "B-Spline"); } void QmitkPreprocessingResampling::CreateConnections() { if ( m_Controls ) { connect((QObject*)(m_Controls->btnDoIt), SIGNAL(clicked()), (QObject*) this, SLOT(StartButtonClicked())); connect((QObject*)(m_Controls->buttonExecuteOnMultipleImages), SIGNAL(clicked()), (QObject*) this, SLOT(StartMultipleImagesButtonClicked())); connect( (QObject*)(m_Controls->cbParam4), SIGNAL( activated(int) ), this, SLOT( SelectInterpolator(int) ) ); } } void QmitkPreprocessingResampling::InternalGetTimeNavigationController() { auto* timeNavigationController = mitk::RenderingManager::GetInstance()->GetTimeNavigationController(); if(nullptr != timeNavigationController) { m_TimeStepperAdapter = new QmitkStepperAdapter(m_Controls->timeSliceNavigationWidget, timeNavigationController->GetStepper()); } } void QmitkPreprocessingResampling::SetFocus() { } //datamanager selection changed void QmitkPreprocessingResampling::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& nodes) { ResetOneImageOpPanel(); //any nodes there? if (!nodes.empty()) { // reset GUI m_Controls->timeSliceNavigationWidget->setEnabled(false); m_Controls->leImage1->setText(tr("Select an Image in Data Manager")); m_SelectedNodes.clear(); for (mitk::DataNode* _DataNode : nodes) { m_SelectedImageNode->RemoveAllNodes(); *m_SelectedImageNode = _DataNode; mitk::Image::Pointer tempImage = dynamic_cast<mitk::Image*>(m_SelectedImageNode->GetNode()->GetData()); //no image if (tempImage.IsNull() || (tempImage->IsInitialized() == false)) { if (m_SelectedNodes.size() < 1) { m_Controls->leImage1->setText(tr("Not an image.")); } continue; } //2D image if (tempImage->GetDimension() < 3) { if (m_SelectedNodes.size() < 1) { m_Controls->leImage1->setText(tr("2D images are not supported.")); } continue; } if (m_SelectedNodes.size() < 1) { m_Controls->leImage1->setText(QString(m_SelectedImageNode->GetNode()->GetName().c_str())); mitk::Vector3D aSpacing = tempImage->GetGeometry()->GetSpacing(); std::string text("x-spacing (" + std::to_string(aSpacing[0]) + ")"); m_Controls->tlParam1->setText(text.c_str()); text = "y-spacing (" + std::to_string(aSpacing[1]) + ")"; m_Controls->tlParam2->setText(text.c_str()); text = "z-spacing (" + std::to_string(aSpacing[2]) + ")"; m_Controls->tlParam3->setText(text.c_str()); if (tempImage->GetDimension() > 3) { // try to retrieve the TNC (for 4-D Processing ) this->InternalGetTimeNavigationController(); m_Controls->timeSliceNavigationWidget->setEnabled(true); m_Controls->tlTime->setEnabled(true); } } m_SelectedNodes.push_back(_DataNode); } if (m_SelectedNodes.size() > 0) { *m_SelectedImageNode = m_SelectedNodes[0]; } ResetParameterPanel(); } } void QmitkPreprocessingResampling::ResetOneImageOpPanel() { m_Controls->tlTime->setEnabled(false); m_Controls->btnDoIt->setEnabled(false); m_Controls->buttonExecuteOnMultipleImages->setEnabled(false); m_Controls->cbHideOrig->setEnabled(false); m_Controls->leImage1->setText(tr("Select an Image in Data Manager")); m_Controls->tlParam1->setText("x-spacing"); m_Controls->tlParam1->setText("y-spacing"); m_Controls->tlParam1->setText("z-spacing"); } void QmitkPreprocessingResampling::ResetParameterPanel() { m_Controls->btnDoIt->setEnabled(true); m_Controls->buttonExecuteOnMultipleImages->setEnabled(true); m_Controls->cbHideOrig->setEnabled(true); } void QmitkPreprocessingResampling::ResetTwoImageOpPanel() { } void QmitkPreprocessingResampling::StartMultipleImagesButtonClicked() { for (auto currentSelectedNode : m_SelectedNodes) { m_SelectedImageNode->RemoveAllNodes(); *m_SelectedImageNode = currentSelectedNode; StartButtonClicked(); } } void QmitkPreprocessingResampling::StartButtonClicked() { if(!m_SelectedImageNode->GetNode()) return; this->BusyCursorOn(); mitk::Image::Pointer newImage; try { newImage = dynamic_cast<mitk::Image*>(m_SelectedImageNode->GetNode()->GetData()); } catch ( std::exception &e ) { - QString exceptionString = tr("An error occured during image loading:\n"); + QString exceptionString = tr("An error occurred during image loading:\n"); exceptionString.append( e.what() ); QMessageBox::warning( nullptr, "Preprocessing - Resampling: ", exceptionString , QMessageBox::Ok, QMessageBox::NoButton ); this->BusyCursorOff(); return; } // check if input image is valid, casting does not throw exception when casting from 'NULL-Object' if ( (! newImage) || (newImage->IsInitialized() == false) ) { this->BusyCursorOff(); QMessageBox::warning( nullptr, "Preprocessing - Resampling", tr("Input image is broken or not initialized. Returning."), QMessageBox::Ok, QMessageBox::NoButton ); return; } // check if operation is done on 4D a image time step if(newImage->GetDimension() > 3) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(newImage); timeSelector->SetTimeNr(m_Controls->timeSliceNavigationWidget->GetPos()); timeSelector->Update(); newImage = timeSelector->GetOutput(); } // check if image or vector image ImageType::Pointer itkImage = ImageType::New(); VectorImageType::Pointer itkVecImage = VectorImageType::New(); int isVectorImage = newImage->GetPixelType().GetNumberOfComponents(); if(isVectorImage > 1) { CastToItkImage( newImage, itkVecImage ); } else { CastToItkImage( newImage, itkImage ); } std::stringstream nameAddition(""); double dparam1 = m_Controls->dsbParam1->value(); double dparam2 = m_Controls->dsbParam2->value(); double dparam3 = m_Controls->dsbParam3->value(); try{ std::string selectedInterpolator; ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New(); switch (m_SelectedInterpolation) { case LINEAR: { LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Linear"; break; } case NEAREST: { NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Nearest"; break; } case SPLINE: { BSplineInterpolatorType::Pointer interpolator = BSplineInterpolatorType::New(); interpolator->SetSplineOrder(3); resampler->SetInterpolator(interpolator); selectedInterpolator = "B-Spline"; break; } default: { LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Linear"; break; } } resampler->SetInput( itkImage ); resampler->SetOutputOrigin( itkImage->GetOrigin() ); ImageType::SizeType input_size = itkImage->GetLargestPossibleRegion().GetSize(); ImageType::SpacingType input_spacing = itkImage->GetSpacing(); ImageType::SizeType output_size; ImageType::SpacingType output_spacing; if (dparam1 > 0) { output_size[0] = std::ceil(input_size[0] * (input_spacing[0] / dparam1)); output_spacing[0] = dparam1; } else { output_size[0] = std::ceil(input_size[0] * (-1.0 / dparam1)); output_spacing[0] = -1.0*input_spacing[0] * dparam1; } if (dparam2 > 0) { output_size[1] = std::ceil(input_size[1] * (input_spacing[1] / dparam2)); output_spacing[1] = dparam2; } else { output_size[1] = std::ceil(input_size[1] * (-1.0 / dparam2)); output_spacing[1] = -1.0*input_spacing[1] * dparam2; } if (dparam3 > 0) { output_size[2] = std::ceil(input_size[2] * (input_spacing[2] / dparam3)); output_spacing[2] = dparam3; } else { output_size[2] = std::ceil(input_size[2] * (-1.0 / dparam3)); output_spacing[2] = -1.0*input_spacing[2] * dparam3; } resampler->SetSize( output_size ); resampler->SetOutputSpacing( output_spacing ); resampler->SetOutputDirection( itkImage->GetDirection() ); resampler->UpdateLargestPossibleRegion(); ImageType::Pointer resampledImage = resampler->GetOutput(); newImage = mitk::ImportItkImage( resampledImage )->Clone(); nameAddition << "_Resampled_" << selectedInterpolator; std::cout << "Resampling successful." << std::endl; } catch (...) { this->BusyCursorOff(); QMessageBox::warning(nullptr, "Warning", "Problem when applying filter operation. Check your input..."); return; } newImage->DisconnectPipeline(); // adjust level/window to new image mitk::LevelWindow levelwindow; levelwindow.SetAuto( newImage ); mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); levWinProp->SetLevelWindow( levelwindow ); // compose new image name std::string name = m_SelectedImageNode->GetNode()->GetName(); if (name.find(".nrrd") == name.size() -5 ) { name = name.substr(0,name.size() -5); } name.append( nameAddition.str() ); // create final result MITK data storage node mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetProperty( "levelwindow", levWinProp ); result->SetProperty( "name", mitk::StringProperty::New( name.c_str() ) ); result->SetData( newImage ); // for vector images, a different mapper is needed if(isVectorImage > 1) { mitk::VectorImageMapper2D::Pointer mapper = mitk::VectorImageMapper2D::New(); result->SetMapper(1,mapper); } // add new image to data storage and set as active to ease further processing GetDataStorage()->Add( result, m_SelectedImageNode->GetNode() ); if ( m_Controls->cbHideOrig->isChecked() == true ) m_SelectedImageNode->GetNode()->SetProperty( "visible", mitk::BoolProperty::New(false) ); // show the results mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->BusyCursorOff(); } void QmitkPreprocessingResampling::SelectInterpolator(int interpolator) { switch (interpolator) { case 0: { m_SelectedInterpolation = LINEAR; break; } case 1: { m_SelectedInterpolation = NEAREST; break; } case 2: { m_SelectedInterpolation = SPLINE; } } } diff --git a/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox b/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox index 2450b2f9c7..407d6d01d7 100644 --- a/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox +++ b/Plugins/org.mitk.gui.qt.properties/documentation/UserManual/PropertiesView.dox @@ -1,57 +1,57 @@ /** \page org_mitk_views_properties The Properties View \imageMacro{properties-dox.svg,"Icon of the Properties View.",2.00} \tableofcontents \section org_mitk_views_propertiesOverview Overview The Properties View allows you to inspect and change properties of a selected data node and its attached data. This View is only for advanced users and developers, as it is easy to alter the program state in unexpected ways. It can be considered as a complete exposure of parts of the backend that are usually supposed to be accessed only through dedicated frontend components like the color or opacity widgets in the context menu of a data node in the Data Manager View. \section org_mitk_views_propertiesUsage Usage \imageMacro{view.png,"The Properties View.",12.00} \subsection org_mitk_views_propertiesUsagePropertyListTypes Property list types After you selected a data node, the Property View allows you to switch between several property lists that are attached to the selected data node and its actual data. By default, you see the common data node property list. There are two types of property lists: data node property lists and data property lists. Data node property lists consist of properties that the application attaches mainly for rendering settings. They are not intrinsically part of the actual data and are only persisted when saving the MITK scene as a whole. A typical example of such a property is "visible", which decides if the data should be rendered or hidden. The common data node property list is applied to all render windows but there are also render window specific data node property lists. -Any property that is found in both the common list and a render window specific list is overriden by the latter one. +Any property that is found in both the common list and a render window specific list is overridden by the latter one. For example, if you want to hide an image only in the 3d render window but show it in all other render windows, you check "visible" in the common list, add the same property to the 3d render window specific list, and uncheck it there. There is only a single data property list. It represents the true metadata of the selected data like DICOM tags of a DICOM image. When saving specific data, most data properties are written to the data file, as long as the selected file format supports metadata. A popular example is the NRRD image format that allows to save custom key value pairs in text format in the file header. Not all data properties are meant for persistence, though. To check if a certain data property will be written to a metadata-enabled file format, click on it in the properties tree view and check if there is a save icon at the bottom in the additional property info box. \subsection org_mitk_views_propertiesUsageFilter Filter Property lists can be quite large and complex, shown as a tree structure in the Properties View. To quickly find properties of interest you can use the filter text box, which will filter the properties while you type. \subsection org_mitk_views_propertiesUsageEditProperties Edit properties Most property value types like numbers, strings, boolean values, or colors can be edited by either clicking or double-clicking in the Value column. For example, to edit color properties, double-click on the colored Value cell. You can either enter a color by name like "yellow", in hex notation like "#ffff00" (or abbreviated "#ff0"), or click on the "..." button to open a color picker dialog. \subsection org_mitk_views_propertiesUsagePropertyInfos Additional property information Some properties have additional information attached like a description, aliases, or a persistence flag. This information is shown at the bottom of the Properties View. When no additional information is available, the additional property info box is hidden. */ diff --git a/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox b/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox index 73d1ecb6af..836355173e 100644 --- a/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox +++ b/Plugins/org.mitk.gui.qt.python/documentation/UserManual/QmitkPython.dox @@ -1,33 +1,33 @@ /** \page org_mitk_views_python The Python Plugin Available sections: - \ref org_mitk_views_pythonOverview - \ref org_mitk_views_pythonUsage - \ref org_mitk_views_pythonConsole - \ref org_mitk_views_pythonSnippets \section org_mitk_views_pythonOverview Overview The Python view provides the graphical front end to run Python code through the mitkPython module. Furthermore the SimpleITK/VTK/OpenCV Python wrapping can be used. Images and surfaces in the DataManager can be transferred via a drag & drop mechanism into the MITK Python Console. \section org_mitk_views_pythonUsage Transfer data -Images and surfaces can be tranferred from the data manger into the python console. To transfer an image or +Images and surfaces can be transferred from the data manager into the python console. To transfer an image or surface simply drag it from the data manager into the Variable Stack view, as shown in Figure. A new entry will appear in the Variable Stack, as soon as the data is transferred. As soon as the entry is available the object can be accessed and modified in the python console. Three dimensional images will be copied in-memory to python via numpy and a SimpleITK image object is created with the same properties. When a two dimensional image is transferred the user can choose to transfer it as an OpenCV image object. Surfaces are fully memory mapped as a vtkPolyData object. To transfer an image or surface from the python runtime to the data manager just double click on the corresponding entry in the Variable Stack View. \imageMacro{MitkPythonPluginView.png,"Screenshot of the MITK Python Plugin",6} \section org_mitk_views_pythonConsole Console The Python console can be used for interactive programming. All items in the data storage can be accessed in the python console. The console can also be used to load python scripts and run them. \section org_mitk_views_pythonSnippets Snippets The python plugin contains some code snippets of SimpleITK/VTK/OpenCV that can be run in the python console. Snippets can be modified and saved by the user. */ diff --git a/Plugins/org.mitk.gui.qt.python/plugin.xml b/Plugins/org.mitk.gui.qt.python/plugin.xml index 9629c07384..bf93663d87 100644 --- a/Plugins/org.mitk.gui.qt.python/plugin.xml +++ b/Plugins/org.mitk.gui.qt.python/plugin.xml @@ -1,21 +1,21 @@ <?xml version="1.0" encoding="UTF-8"?> <?eclipse version="3.0"?> <plugin> <extension point="org.blueberry.ui.views"> <view id="org.mitk.views.python" name="Python Console" category="General" icon="resources/Python.png" class="QmitkPythonView" > - <description>Allow the acces of python from MITK</description> + <description>Allow the access of python from MITK</description> <keywordReference id="org.mitk.views.python.Keyword"/> </view> </extension> <extension point="org.blueberry.ui.keywords"> <keyword label="Python" id="org.mitk.views.python.Keyword"/> <keyword label="Scripting" id="org.mitk.views.python.Keyword"/> <keyword label="Programming" id="org.mitk.views.python.Keyword"/> <keyword label="Automatic" id="org.mitk.views.python.Keyword"/> </extension> </plugin> diff --git a/Plugins/org.mitk.gui.qt.remeshing/src/internal/QmitkRemeshingViewControls.ui b/Plugins/org.mitk.gui.qt.remeshing/src/internal/QmitkRemeshingViewControls.ui index 105b8e2ba4..fd84d7772f 100644 --- a/Plugins/org.mitk.gui.qt.remeshing/src/internal/QmitkRemeshingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.remeshing/src/internal/QmitkRemeshingViewControls.ui @@ -1,244 +1,244 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkRemeshingViewControls</class> <widget class="QWidget" name="QmitkRemeshingViewControls"> <property name="enabled"> <bool>true</bool> </property> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>253</width> <height>573</height> </rect> </property> <property name="windowTitle"> <string>Remeshing</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <layout class="QGridLayout" name="gridLayout"> <item row="0" column="0"> <widget class="QLabel" name="surfaceLabel"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Surface</string> </property> </widget> </item> <item row="0" column="1" colspan="2"> <widget class="QmitkSingleNodeSelectionWidget" name="selectionWidget" native="true"> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="densityLabel"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Density</string> </property> </widget> </item> <item row="1" column="1"> <widget class="QSlider" name="densitySlider"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>100</number> </property> <property name="pageStep"> <number>10</number> </property> <property name="value"> <number>100</number> </property> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item row="1" column="2"> <widget class="QSpinBox" name="densitySpinBox"> <property name="suffix"> <string>%</string> </property> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>100</number> </property> <property name="singleStep"> <number>1</number> </property> <property name="value"> <number>100</number> </property> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="remeshingLabel"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Remeshing</string> </property> </widget> </item> <item row="2" column="1" colspan="2"> <widget class="QComboBox" name="remeshingComboBox"> <item> <property name="text"> <string>Adaptive</string> </property> </item> <item> <property name="text"> <string>Regular</string> </property> </item> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="qualityLabel"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Quality</string> </property> </widget> </item> <item row="3" column="1" colspan="2"> <widget class="QComboBox" name="qualityComboBox"> <property name="currentIndex"> <number>0</number> </property> <item> <property name="text"> <string>Medium (fast)</string> </property> </item> <item> <property name="text"> <string>High (slow)</string> </property> </item> <item> <property name="text"> <string>Maximum (very slow)</string> </property> </item> </widget> </item> <item row="4" column="1" colspan="2"> <widget class="QCheckBox" name="preserveEdgesCheckBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>Preserve Edges</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> </layout> </item> <item> <widget class="QPushButton" name="remeshPushButton"> <property name="enabled"> <bool>true</bool> </property> <property name="text"> <string>Remesh</string> </property> <property name="icon"> <iconset resource="../../resources/Remeshing.qrc"> <normaloff>:/Remeshing/RemeshingIcon.svg</normaloff>:/Remeshing/RemeshingIcon.svg</iconset> </property> <property name="iconSize"> <size> <width>24</width> <height>24</height> </size> </property> </widget> </item> <item> <widget class="QLabel" name="explanationLabel"> <property name="text"> - <string><html><head/><body>Density: The density of the resulting surface compared to the input surface. For example, a density of 50% will effectively halve the number of vertices. It's not uncommen to choose values as low as 10% for overly dense input surfaces. The minimum number of output vertices is at least 100, though.Remeshing: Adaptive remeshing results in higher density in curvy areas and less density in flat areas. This remeshing strategy can preserve fine shape details even when the overall density is heavily reduced. Regular remeshing evenly distributes the density regardless of the local shape of the surface.Quality: While medium quality is sufficient for the vast majority of use cases, you can increase this setting to further optimize the mesh quality in terms of uniformly shaped triangles. However, computation time and memory consumption increase dramatically compared to very small improvements.Preserve Edges: If the input surface contains holes or edges, they will be preserved very accurately by default at the cost of less uniform triangles at their direct neighborhood.</body></html></string> + <string><html><head/><body>Density: The density of the resulting surface compared to the input surface. For example, a density of 50% will effectively halve the number of vertices. It's not uncommon to choose values as low as 10% for overly dense input surfaces. The minimum number of output vertices is at least 100, though.Remeshing: Adaptive remeshing results in higher density in curvy areas and less density in flat areas. This remeshing strategy can preserve fine shape details even when the overall density is heavily reduced. Regular remeshing evenly distributes the density regardless of the local shape of the surface.Quality: While medium quality is sufficient for the vast majority of use cases, you can increase this setting to further optimize the mesh quality in terms of uniformly shaped triangles. However, computation time and memory consumption increase dramatically compared to very small improvements.Preserve Edges: If the input surface contains holes or edges, they will be preserved very accurately by default at the cost of less uniform triangles at their direct neighborhood.</body></html></string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> <container>1</container> </customwidget> </customwidgets> <tabstops> <tabstop>densitySpinBox</tabstop> <tabstop>preserveEdgesCheckBox</tabstop> <tabstop>remeshPushButton</tabstop> </tabstops> <resources> <include location="../../resources/Remeshing.qrc"/> </resources> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index 1e18045728..a50a2fa578 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,439 +1,467 @@ /** \page org_mitk_views_segmentation The Segmentation View \imageMacro{segmentation-dox.svg,"Icon of the Segmentation View",2.00} \tableofcontents \section org_mitk_views_segmentationoverview Overview Segmentation is the act of separating an image into foreground and background subsets by manual or automated delineation, while the foreground is defined to be part of the segmentation. Such a segmented image subset is also called a label as it typically labels a specific region of interest. A multilabel segmentation may contain multiple labels organized in distinct groups. You can create multiple labels for different regions of interest contained within a single segmentation image. Labels in the same group cannot overlap each other but labels from different groups may overlap. The MITK Segmentation Plugin allows you to create multilabel segmentations of anatomical and pathological structures in medical images. The plugin consists of three views: <ul> <li> Segmentation View: Manual and (semi-)automatic segmentation <li> \subpage org_mitk_views_segmentationutilities : Post-processing of segmentations <li> \subpage org_mitk_views_segmentationtasklist : Optimized workflow for batches of segmentation tasks based on a user-defined task list </ul> In this user guide, the features of the Segmentation View are described. For an introduction to the Segmentation Utilities or Segmentation Task List, refer to the respective user guides. \imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation View", 16.00} \section org_mitk_views_segmentationtechnicalissues Image and segmentation prerequisites The Segmentation View has a few prerequisites regarding segmentations and their reference image: <ul> <li> Images must be two or three-dimensional and may be either static or dynamic, e.g., are time-resolved resp. have different pixel values for different time steps. <li> Images must be single-valued, i.e. CT, MRI or ultrasound. Images from color doppler or photographic (RGB) images are only partially supported (please be aware that some tools might not be compatible with this image type). <li> Segmentations must be congruent to their reference images. </ul> \section org_mitk_views_segmentationdataselection Image selection and creating new segmentations To select a reference image for a new segmentation, click on the Image widget in the Data selection section at the very top of the Segmentation View. Choose an image from the displayed list of Data Manager images. Once an image is selected, a new segmentation for this reference image can be created by clicking the button right next to the Segmentation widget in the Data selection section. A new multilabel segmentation with an initial, empty label is automatically generated if not set otherwise in the preferences. The new segmentation will be added to the Data Manager as a child node of its reference image node. It is automatically selected and can be edited in the Segmentation View right away. Instead of creating a new segmentation, an existing segmentation can be selected and edited as well. The selection list of existing segmentations for a certain reference image consists of matching/congruent segmentations only. \imageMacro{"QmitkSegmentation_DataSelection.png","Data selection and creating new segmentations",12} \section org_mitk_views_segmentationgroups Groups Segmentation images consist of at least a single group called "Group 0" in which the first default label is created. More groups can be added and removed but there will always be at least a single group. Labels of the same group cannot overlap each other. Labels of different groups may overlap each other. For example, you could segment the whole heart as "Heart" label in "Group 0", add "Group 1" and create multiple labels of the anatomical details of the heart in that group. Naturally, all these labels lie within the extents of the "Heart" label of "Group 0" but in principle they are completely independent of "Group 0". Some pixels are now labelled twice, e.g., as "Heart" and "Left ventricle". Since the labels of "Group 1" cannot overlap each other, it is impossible to accidentally label a pixel as both "Left ventricle" and "Right ventricle". If you would like to segment even more details you could create "Group 2" to have up to three labels per pixel. Nevertheless, groups are technically a flat data structure and cannot contain nested groups. It is all about possibly overlapping labels from distinct groups and spatially exclusive, non-overlapping labels within the same group. \imageMacro{"QmitkSegmentation_Groups.png","Groups",10} \section org_mitk_views_segmentationlabelinstances Labels vs. label instances The Segmentation View supports label instances. That is, segmenting multiple distributed entities of the same thing like metastases for example. A label, as we used the term before, is already a single instance of itself but it may consist of multiple label instances. If a label consists of multiple label instances, they each show their own distinct pixel value in square brackets as a clue for distinction and identification. It is important to understand that this number is not a separate, consequtive index for each label. It is just the plain pixel value of the label instance, which is unique across all label instances of the whole segmentation. \imageMacro{"QmitkSegmentation_LabelInstances.png","Label instances",10} \section org_mitk_views_segmentationlock_color_visibility Unlocking, changing color of, and hiding label instances Label instances are locked by default: label instances from the same group cannot accidentally override pixels from other label instances. Locked label instances behave like cookie cutters for other label instances of the same group. You can unlock label instances to remove that protection from other label instances of the same group. Their pixel contents can then be overridden by other label instances of the same group. Remember that label instances from distinct groups do not interact with each other. They can always overlap (not override) each other. You can also change the color of label instances as well as show (default) or hide their pixel contents. The icons at the right side of the rows of the groups and labels widget reflect their state in all these regards. Renaming of labels and label instances can be found in their content menu as shown further below. \imageMacro{"QmitkSegmentation_LockColorVisibility.png","Unlocking\, changing color of\, and hiding label instances",10} \section org_mitk_views_segmentationcontextmenus Context menus Actions for organization of groups, labels, and label instances (as well as other operations) can be also found in their right-click context menus. \imageMacro{"QmitkSegmentation_ContextMenus.png","Context menus of groups\, labels\, and label instances",12} Most actions available in these context menus are self-explanatory or were already described above by other means of access like the tool button bar for adding and removing groups, labels, and label instances. Labels and label instances can be renamed, while groups have fixed names. Note that renaming a label instance will make a separate label out of it, since all instances of the same label share a single common name. Clear content only clears the pixels of a label instance but won't delete the actual label instance. Groups can be locked and unlocked as a whole from their context menu, while label instances can be directly locked and unlocked outside the context menu as decribed further below. \section org_mitk_views_segmentationlabelsuggestions Label name and color suggestions When renaming label instances or creating new label instances with enforced manual naming in the Segmentation preferences, entering names is supported by auto-completion for common label names. -The list of predefined label names and colors for the auto-completion feature can be either extented or replaced by a custom list of label name and color suggestions. +The list of predefined label names and colors for the auto-completion feature can be either extended or replaced by a custom list of label name and color suggestions. This custom list must be specified as a JSON file, just containing an array of objects, each with a mandatory "name" string and an optional "color" string. The JSON file can be set in the Segmentation preferences as well as a few options on how to apply these suggestions. \section org_mitk_views_segmentationlabelpresets Saving and loading label set presets Label set presets are useful to share a certain style or scheme between different segmentation sessions or to provide templates for new segmentation sessions. The properties of all label instances in all groups like their names, colors, and visibilities are saved as a label set preset by clicking on the 'Save label set preset' button. Label set presets are applied to any segmentation session by clicking on the 'Load label set preset' button. If a label instance for a certain value already exists, its properties are overridden by the preset. If a label instance for a certain value does not yet exist, an empty label instance with the label properties of the preset is created. The actual pixel contents of label instances are unaffected as label set presets only store label properties. \imageMacro{QmitkSegmentation_Preset.png,"Saving and loading label set presets", 10.00} -\subsection org_mitk_views_segmentationdefaultlabelpresets Applying label set presets by default +If you work on a repetitive segmentation task, manually loading the same label set preset for each and every new segmentation can be tedious. +To streamline your workflow, you can set a default label set preset in the Segmentation preferences (Ctrl+P). When set, this label set preset will be applied to all new segmentations instead of creating the default red "Label 1" label instance. -If you work on a repetetive segmentation task, manually loading the same label set preset for each and every new segmentation can be tedious. +If you work on a repetitive segmentation task, manually loading the same label set preset for each and every new segmentation can be tedious. To streamline your workflow, you can set a default label set preset in the Segmentation preferences (Ctrl+P). When set, this label set preset will be applied to all new segmentations instead of creating the default red "Label 1" label instance. \section org_mitk_views_segmentationpreferences Preferences The Segmentation Plugin offers a number of preferences which can be set via the MITK Workbench application preferences (Ctrl+P): \imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00} <ul> <li> Compact view: Hide the tool button texts to save some space on screen (6 instead of 4 buttons per row) <li> 2D display: Draw segmentations as as outlines or transparent overlays <li> Data node selection mode: Hide everything but the selected segmentation and its reference image <li> Default label set preset: Start a new segmentation with this preset instead of a default label <li> Label creation: Assign default names and colors to new label instances or ask users for name and color <li> Label suggestions: Specify custom suggestions for label names and colors </ul> \section org_mitk_views_segmentationtooloverview Segmentation tool overview MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools. The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only require a small amount of user interaction, i.e. placing seed points or setting / adjusting parameters. You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50} \section org_mitk_views_segmentation2dsegmentation 2D segmentation tools With 2D manual contouring you define which voxels are part of the segmentation and which are not. This allows you to create segmentations of any structures of interest in an image. You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation. To start using one of the editing tools, click its button from the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one.\n If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). All of the editing tools work by the same principle: using the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal), moving the mouse while holding the mouse button and releasing the button to finish the editing action. Multi-step undo and redo is fully supported by all editing tools by using the application-wide undo / redo buttons in the toolbar. Remark: Clicking and moving the mouse in any of the 2D render windows will move the crosshair that defines what part of the image is displayed. This behavior is disabled as long as any of the manual segmentation tools are active - otherwise you might have a hard time concentrating on the contour you are drawing. \subsection org_mitk_views_segmentationaddsubtracttools Add and subtract tools \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and subtract tools",7.70} Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation. Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted). \subsection org_mitk_views_segmentationlassotool Lasso tool \imageMacro{QmitkSegmentation_Lasso.png,"Lasso tool",7.70} The tool is a more advanced version of the add/subtract tool. It offers you the following features: <ol> <li> Generating a polygon segmentation (click left mouse button to set ancor point) <li> Freehand contouring (like the add tool; press left mouse button while moving the mouse) <li> Move ancor points (select an ancor point, press left mouse button while moving the mouse) <li> Add new ancor points (press CTRL while click left mouse to add an ancor to the contour) <li> Delete an ancor point (press Del while ancor point is selected) <li> Segmentation can be added to the label (Add mode) or subtracted (Subtract mode) </ol> To start a segmentation double left click where the first ancor point should be. To end the segmentation double left click where the last ancor point should be. Please note that: <ul> <li> feature 3-6 are only available, if auto confirm is *not* activated <li> feature 3-5 is not available for freehand contour segments </ul> \subsection org_mitk_views_segmentationpaintwipetools Paint and wipe tools \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and wipe tools",7.68} Use the Size slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped). \subsection org_mitk_views_segmentationregiongrowingtool Region growing tool \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region growing tool",3.81} Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This allows to quickly create segmentations of structures that have a good contrast to surrounding tissue. The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged. Moving the mouse up / down is different from left / right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. The tool will select more or less pixels, corresponding to the changing gray value range. \if THISISNOTIMPLEMENTEDATTHEMOMENT A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \imageMacro{QmitkSegmentation_Leakage.png,"Leakage correction feature of the region growing tool",11.28} \endif \subsection org_mitk_views_segmentationfilltool Fill tool \imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill tool",3.81} Left-click inside a region/segmentation to flood fill all connected pixels that have the same label with the active label. This tool will only work on regions of unlocked labels or on regions that are not labeled at all. \subsection org_mitk_views_segmentationerasetool Erase tool \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase tool",3.79} This tool removes a connected part of pixels that form a segmentation. You may use it to remove single segmented regions (left-click on specific segmentation) or to clear a whole slice at once (left-click at the non-labeled background). This tool will only work and regions of unlocked labels or on regions of the active label. \subsection org_mitk_views_segmentationclosetool Close tool \imageMacro{QmitkSegmentation_IMGIconClose.png,"Close tool",3.79} Left-click inside the region/segmentation to fill all "holes" (pixels labelled with another label or no label) inside the region. Therefore this tool behaves like a local closing operation. This tool will not work, when a non-labeled region is selected and holes of locked labels will not be filled. \remark This tool always uses the label of the selected region (even if this label is not the active label). Therefore you can use this tool on regions of the active label and of none locked labels (without the need to change the active label). \subsection org_mitk_views_segmentationlivewiretool Live wire tool \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live wire tool",3.01} The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00} The tool handling is the same like the Lasso tool (see for more info), except it generates live wire contours instead of straight lines. +\subsection org_mitk_views_segmentationSegmentAnything Segment Anything Tool + +\imageMacro{QmitkSegmentation_nnUnetTool.png,"Segment Anything tool",10.00} + +\imageMacro{QmitkSegmentation_SAMTool.png,"Segment Anything tool",10.00} + +The Segment Anything Tool is a deep learning-based interactive segmentation tool. Originally created by MetaAI, MITK presents this model for medical image segmentation tasks. +The tool requires that you have Python 3 installed and available on your machine. Note: On Debian/Ubuntu systems, you need to install git, python3-pip, python3-venv package using the following command: `apt install git python3-pip python3-venv`. For best experience, your machine should be ideally equipped with a CUDA-enabled GPU. +For a detailed explanation of what this algorithm is able to, please refer to https://ai.facebook.com/research/publications/segment-anything/ +Any adjustments to the \subpage org_mitk_editors_stdmultiwidget_Levelwindow setting impacts the segmentation. However, any applied color maps are ignored. + +\subsubsection org_mitk_views_segmentationSegmentAnythingWorkflow Workflow: + -# Install Segment Anything: Goto Preferences (Cntl+P) > Segment Anything and click "Install Segment Anything" to install Segment Anything (version: 1.0). + The installation process implicitly creates a python virtual environment using the Python located in "System Python" in an MITK mainitained directory. Make sure you have a working internet connection. This might take a while. It is a one time job, though. + Once installed, the "Install Segment Anything" button is grayed out. + \imageMacro{QmitkSegmentation_SAMTool_Preferences.png,"Segment Anything Preferences",10.00} + + -# Note: If Python is not listed by MITK in "System Python", click "Select..." in the dropdown to choose an unlisted installation of Python. Note that, while selecting an arbitrary environment folder, only select the base folder, e.g. "/usr/bin/". + No need to navigate all the way into "../usr/bin/python3", for example. + -# Select a specific model type in the "Model Type" dropdown. The default is "vit_b" for low memory footprint. However, more larger models "vit_l" and "vit_h" are also available for selection. + -# Select inference hardware, i.e. any GPU or CPU. This is internally equivalent to setting the CUDA_VISIBLE_DEVICES environment variable. + -# Click "OK" to save the preference settings. + -# Goto Segmentation View > 2D tools > Segment Anything. + -# Click "Initialize Segment Anything" to start the tool backend. This will invoke downloading of the selected model type from the internet. This might take a while. It is a one time job, though. + -# Once the tool is initialized, Press SHIFT+Left Click on any of the 3 render windows to start click guided segmentation on that slice. + -# Press SHIFT+Right Click for negative clicks to adjust the preview mask on the render window. + \subsection org_mitk_views_segmentationinterpolation 2D and 3D Interpolation Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices. The segmentation view offers two helpful features to mitigate this drawback: <ul> <li> 2D Interpolation <li> 3D Interpolation </ul> The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that <ul> <li> has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND <li> is completely clear of a manual segmentation, i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice. </ul> \imageMacro{QmitkSegmentation_2DInterpolation.png,"2D interpolation usage",3.01} Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation. To confirm single slices, click the Confirm for single slice button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting Confirm for all slices. The 3D interpolation creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D interpolation usage",16.00} You can accept the interpolation result by clicking the Confirm-button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background. Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation. You can navigate between the drawn contours by clicking on the corresponding position nodes in the data manager which are stored as sub-nodes of the selected segmentation. If you do not want to see these nodes just uncheck the Show Position Nodes checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since undo / redo is not yet working for 3D interpolation. The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area. \section org_mitk_views_segmentation3dsegmentation 3D segmentation tools The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the Confirm button of the selected tool. The following 3D tools are available: \subsection org_mitk_views_segmentation3dthresholdtool 3D Threshold tool The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_views_segmentation3dulthresholdTool 3D upper / lower threshold tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold interval will be labeled as part of the segmentation. \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D upper / lower threshold tool",10.00} \subsection org_mitk_views_segmentation3dotsutool 3D Otsu tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_views_segmentation3dgrowcuttool 3D GrowCut tool The 3D GrowCut tool uses previously created segmentation labels (e.g. by the "Add"-tool) stored in the segmentation layer 0. The GrowCut tool will use these segmentation labels to create a seedimage that will serve as input to the algorithm. As an advanced setting option, a Distance penalty can be set, which increases the cohesion in the immediate surroundings of the initial labels. Based on the seedimage and the Distance penalty, a growing is started, which includes all areas that are not initially assigned to a specific label. During this process, initially unassigned areas are assigned to the best fitting labels. After the segmentation process, the user can decide which newly generated labels should be confirmed. \imageMacro{QmitkSegmentation_3DGrowCutTool.png,"3D GrowCut tool",16.00} \subsection org_mitk_views_segmentationpickingtool Picking Tool The Picking tool offers two modes that allow you to manipulate "islands" within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within your image but you are just interested in one special region. - Picking mode: Allows you to select certain "islands". When the pick is confirmed, the complete content of the active label will be removed except the pick. This mode is beneficial if you have a lot segmentation noise and want to pick the relevant parts and dismiss the rest. Hint: You can also pick from other labels, but this will only work if these labels are unlocked. - Relabel mode: Allows you to select certain "islands". When the pick is confirmed, it will be relabeled and added to the active label content. Hint: This mode ignores the locks of other labels, hence you do not need to unlock them explicitly. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \subsection org_mitk_views_segmentationnnUNetTool nnU-Net Tool (Ubuntu only) \imageMacro{QmitkSegmentation_nnUnetTool.png,"nnUNet tool",10.00} This tool provides a GUI to the deep learning-based segmentation algorithm called the nnU-Net v1. With this tool, you can get a segmentation mask predicted for the loaded image in MITK. Be ready with the pre-trained weights (a.k.a RESULTS_FOLDER) for your organ or task concerned, before using the tool. For a detailed explanation of the parameters and pre-trained weights folder structure etc., please refer to https://github.com/MIC-DKFZ/nnUNet. Remark: The tool assumes that you have a Python3 environment with nnU-Net v1 (pip) installed. Your machine should be also equipped with a CUDA enabled GPU. \subsubsection org_mitk_views_segmentationnnUNetToolWorkflow Workflow: -# Select the "Python Path" drop-down to see if MITK has automatically detected other Python environments. Click on a fitting environment for the nnUNet inference or click "Select" in the dropdown to choose an unlisted python environment. Note that, while selecting an arbitrary environment folder, only select the base folder, e.g. "myenv". No need to select all the way until "../myenv/bin/python", for example. -# Click on the "nnUNet Results Folder" directory icon to navigate to the results folder on your hard disk. This is equivalent to setting the RESULTS_FOLDER environment variable. If your results folder is as per the nnUNet required folder structure, the configuration, trainers, tasks and folds are automatically parsed and correspondingly loaded in the drop-down boxes as shown below. Note that MITK automatically checks for the RESULTS_FOLDER environment variable value and, if found, auto parses that directory when the tool is started. \imageMacro{QmitkSegmentation_nnUNet_Settings.png,"nnUNet Segmentation Settings",10} -# Choose your required Task-Configuration-Trainer-Planner-Fold parameters, sequentially. By default, all entries are selected inside the "Fold" dropdown (shown: "All"). Note that, even if you uncheck all entries from the "Fold" dropdown (shown: "None"), then too, all folds would be considered for inferencing. -# For ensemble predictions, you will get the option to select parameters irrespective on postprocessing files available in the ensembles folder of RESULTS_FOLDER. Note that, if a postprocessing json file exists for the selected combination then it will used for ensembling, by default. To choose not to, uncheck the "Use PostProcessing JSON" in the "Advanced" section. \imageMacro{QmitkSegmentation_nnUNet_ensemble.png,"nnUNet Segmentation Settings",10} -# If your task is trained with multi-modal inputs, then "Multi-Modal" checkbox is checked and the no.of modalities are preloaded and shown next to "Required Modalities". Instantly, as much node selectors with corresponding modality names should appear below to select the Data Manager along including a selector with preselected with the reference node. Now, select the image nodes in the node selectors accordingly for accurate inferencing. \imageMacro{QmitkSegmentation_nnUNet_multimodal.png,"nnUNet Multi Modal Settings",10.00} -# Click on "Preview". -# In the "Advanced" section, you can also activate other options like "Mixed Precision" and "Enable Mirroring" (for test time data augmentation) pertaining to nnUNet. \imageMacro{QmitkSegmentation_nnUNet_Advanced.png,"nnUNet Advanced Settings",10.00} -# Use "Advanced" > "GPU Id" combobox to change the preferred GPU for inferencing. This is internally equivalent to setting the CUDA_VISIBLE_DEVICES environment variable. -# Every inferred segmentation is cached to prevent a redundant computation. In case, a user doesn't wish to cache a Preview, uncheck the "Enable Caching" in the "Advanced" section. This will ensure that the current parameters will neither be checked against the existing cache nor a segmentation be loaded from it when Preview is clicked. -# You may always clear all the cached segmentations by clicking "Clear Cache" button. \subsubsection org_mitk_views_segmentationnnUNetToolMisc Miscellaneous: -# In case you want to reload/reparse the folders in the "nnUNet Results Folder", eg. after adding new tasks into it, you may do so without reselecting the folder again by clicking the "Refresh Results Folder" button. -# The "Advanced" > "GPU Id" combobox lists the Nvidia GPUs available by parsing the <tt>nvidia-smi</tt> utility output. In case your machine has Nvidia CUDA enabled GPUs but the <tt>nvidia-smi</tt> fails for some reason, the "GPU Id" combobox will show no entries. In such a situation, it's still possible to execute inferencing by manually entering the preferred GPU Id, eg. 0 in the combobox. -# The "Advanced" > "Available Models" lists the available pre-trained tasks for download. Make sure you have internet connection. Then, choose a Task from the dropdown and click the Download button. The pre-trained models for the selected Task will be downloaded and placed to the RESULTS_FOLDER directory automatically. -# In the RESULTS_FOLDER directory, inside the trainer-planner folder of every task, MITK keeps a "mitk_export.json" file for fast loading for multi-modal information. It is recommended not to delete this file(s) for a fast responsive UI. Tip: If multi-modal information shown on MITK is not correct for a given task, you may modify this JSON file and try again. \subsection org_mitk_views_segmentationTotalSegmentator TotalSegmentator Tool \imageMacro{QmitkSegmentation_nnUnetTool.png,"TotalSegmentator tool",10.00} This tool provides a GUI to the deep learning-based segmentation algorithm called the TotalSegmentator. With this tool, you can get a segmentation mask predicted for 104 classes in CT images, loaded in MITK. For a detailed explanation on tasks and supported classes etc., please refer to https://github.com/wasserth/TotalSegmentator The tool assumes that you have Python 3 installed and available on your machine. We recommend to install TotalSegmentator via MITK. The "Install TotalSegmentator" action implicitly creates a python virtual environment in an MITK mainitained directory. Note: on Debian/Ubuntu systems, you need to install the python3-venv package using the following command: `apt install python3-venv`. For best results, your machine should be ideally equipped with a CUDA-enabled GPU. \imageMacro{QmitkSegmentation_TotalsegmentatorTool.png, "TotalSegmentator Settings",5} \subsubsection org_mitk_views_segmentationTotalSegmentatorWorkflow Workflow: -# Install TotalSegmentator: Click "Install TotalSegmentator" to install TotalSegmentator (version: 1.5.5) in a virtual environment. Make sure you have a working internet connection. This might take a while. It is a one time job, though. Once installed, the "Install TotalSegmentator" button is grayed out. -# If Python is not found by MITK goto "Install Options" & select the "System Python Path" drop-down to see if MITK has automatically detected other Python environments. Click on a fitting Python installation for TotalSegmentator to use or click "Select" in the dropdown to choose an unlisted installation of Python. Note that, while selecting an arbitrary environment folder, only select the base folder, e.g. "/usr/bin/". No need to navigate all the way into "../usr/bin/python3", for example. -# Select a specific subtask in the "Tasks" drop-downs. The default is "total" for non-specific total segmentation. -# Click on "Run TotalSegmentator" for a preview. -# In the "Advanced" section, you can also activate other options like "Fast" for faster runtime and less memory requirements. Use "Fast" if you only have a CPU for inferencing. -# Use "Advanced" > "GPU Id" combobox to change the preferred GPU for inferencing. This is internally equivalent to setting the CUDA_VISIBLE_DEVICES environment variable. -# In case you want to use your own virtual environment containing TotalSegmentator, goto "Install Options" & check "Use Custom Installation" checkbox. Then, select the environment of your choice by using "Custom Env. Path". \section org_mitk_views_segmentationpostprocessing Additional things you can do with segmentations Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager. \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations",10.58} <ul> <li> Create polygon %model applies the marching cubes algorithm to the segmentation. This polygon %model can be used for visualization in 3D or other applications such as stereolithography (3D printing). <li> Create smoothed polygon %model uses smoothing in addition to the marching cubes algorithm, which creates models that do not follow the exact outlines of the segmentation, but look smoother. <li> Autocrop can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping. </ul> \section org_mitk_views_segmentationof3dtimages Segmentation of 3D+t images For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks. <ul> <li> Dynamic masks can be created on each time frame individually. <li> Static masks will be defined on one time frame and will be the same for all other time frames. </ul> In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted. \section org_mitk_views_segmentationtechnicaldetail Technical information for developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions. */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox index 2801ca67e4..a55ac22c09 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox @@ -1,84 +1,84 @@ /** \page org_mitk_views_segmentationutilities The Segmentation Utilities View \imageMacro{segmentation_utilities-dox.svg,"Icon of the Segmentation Utilities View",5.00} \imageMacro{QmitkSegmentationUtilities_Overview.png,"The Segmentation Utilities View",16.00} \tableofcontents \section org_mitk_views_segmentationUtilitiesManualOverview Overview The Segmentation Utilities View allows to postprocess existing segmentations. Currently five different operations exist: <ul> <li> \ref org_mitk_views_segmentationUtilitiesBooleanOperations <li> \ref org_mitk_views_segmentationUtilitiesContourToImage <li> \ref org_mitk_views_segmentationUtilitiesImageMasking <li> \ref org_mitk_views_segmentationUtilitiesMorphologicalOperations <li> \ref org_mitk_views_segmentationUtilitiesSurfaceToImage </ul> \section org_mitk_views_segmentationUtilitiesDataSelection Data Selection All postprocessing operations provide one or more selection widgets, which allow to select the data for the operation. \section org_mitk_views_segmentationUtilitiesBooleanOperations Boolean operations Boolean operations allows to perform the following fundamental operations on two segmentations: <ul> <li> Difference: Subtracts the second segmentation from the first segmentation. <li> Intersection: Extracts the overlapping areas of the two selected segmentations. <li> Union: Combines the two existing segmentations. </ul> The selected segmentations must have the same geometry (size, spacing, ...) in order for the operations to work correctly. The result will be stored in a new data node as a child node of the first selected segmentation. \imageMacro{QmitkSegmentationUtilities_BooleanOperations.png,"Boolean operations",6.00} \section org_mitk_views_segmentationUtilitiesContourToImage Contour to image Contour to image allows to create a segmentation out of a given contour-model. The operation requires a contour model set and a reference image. The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). \imageMacro{QmitkSegmentationUtilities_ContourToImage.png,"Contour to image",6.00} \section org_mitk_views_segmentationUtilitiesImageMasking Image masking Image masking allows to mask an image with either an existing segmentation or a surface. The operation requires an image and a segmentation or a surface. The result will be an image containing only the pixels that are covered by the respective mask. The default background pixel value is zero. It can be changed to the minimum existing pixel value of the image or to a custom pixel value. If the custom pixel value is out of the valid bounds of the pixel type, it is optionally clamped accordingly. \imageMacro{QmitkSegmentationUtilities_ImageMasking.png,"Image masking",6.00} \section org_mitk_views_segmentationUtilitiesMorphologicalOperations Morphological operations -Morphological operations are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modfied. +Morphological operations are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modified. The plugin provides a ball and a cross as structuring elements. The follow operations are available: <ul> <li> Dilation: Each labeled pixel within the segmentation will be dilated based on the selected structuring element. <li> Erosion: Each labeled pixel within the segmentation will be eroded based on the selected structuring element. <li> Opening: A dilation followed by an erosion, used for smoothing edges or eliminating small objects. <li> Closing: An erosion followed by an dilation, used for filling small holes. <li> Fill Holes: Fills bigger holes within a segmentation. </ul> \imageMacro{QmitkSegmentationUtilities_MorphologicalOperations.png,"Morphological operations",6.00} \section org_mitk_views_segmentationUtilitiesSurfaceToImage Surface to image Surface to image allows to create a segmentation out of a given surface. The operation requires a surface and a reference image. The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). \imageMacro{QmitkSegmentationUtilities_SurfaceToImage.png,"Surface to image",6.00} **/ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_SAMTool.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_SAMTool.png new file mode 100644 index 0000000000..e0cb76269d Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_SAMTool.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_SAMTool_Preferences.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_SAMTool_Preferences.png new file mode 100644 index 0000000000..06a07774e6 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_SAMTool_Preferences.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_Technical.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_Technical.dox index 346754a8f0..d8b04fb961 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_Technical.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_Technical.dox @@ -1,98 +1,98 @@ /** \page QmitkSegmentationTechnicalPage Technical design of QmitkSegmentation \li \ref QmitkSegmentationTechnicalPage2 \li \ref QmitkSegmentationTechnicalPage3 \li \ref QmitkSegmentationTechnicalPage4 \section QmitkSegmentationTechnicalPage2 Introduction QmitkSegmentation was designed for the liver resection planning project "ReLiver". The goal was a stable, well-documented, extensible, and testable re-implementation of a functionality called "ERIS", which was used for manual segmentation in 2D slices of 3D or 3D+t images. Re-implementation was chosen because it seemed to be easier to write documentation and tests for newly developed code. In addition, the old code had some design weaknesses (e.g. a monolithic class), which would be hard to maintain in the future. By now Segmentation is a well tested and easily extensible vehicle for all kinds of interactive segmentation applications. A separate page describes how you can extend Segmentation with new tools in a shared object (DLL): \ref toolextensions. \section QmitkSegmentationTechnicalPage3 Overview of tasks We identified the following major tasks: <ol> <li> Management of images: what is the original patient image, what images are the active segmentations? <li> Management of drawing tools: there is a set of drawing tools, one at a time is active, that is, someone has to decide which tool will receive mouse (and other) events. <li> Drawing tools: each tool can modify a segmentation in reaction to user interaction. To do so, the tools have to know about the relevant images. <li> Slice manipulation: drawing tools need to have means to extract a single slice from an image volume and to write a single slice back into an image volume. <li> Interpolation of unsegmented slices: some class has to keep track of all the segmentations in a volume and generate suggestions for missing slices. This should be possible in all three orthogonal slice direction. <li> Undo: Slice manipulations should be undoable, no matter whether a tool or the interpolation mechanism changed something. <li> GUI: Integration of everything. </ol> \section QmitkSegmentationTechnicalPage4 Classes involved The above blocks correspond to a number of classes. Here is an overview of all related classes with their responsibilities and relations: \imageMacro{QmitkSegmentation_InteractiveSegmentationClasses.png,"",16.00} <ol> <li> Management of images: mitk::ToolManager has a set of reference data (original images) and a second set of working data (segmentations). mitk::Tool objects know a ToolManager and can ask the manager for the currently relevant images. GUI and non-GUI classes are coupled by itk::Events (non-GUI to GUI) and direct method calls (GUI to non-GUI). <li> Management of drawing tools: As a second task, ToolManager manages all available tools and makes sure that one at a time is able to receive MITK events. The GUI for selecting tools is implemented in QmitkToolSelectionBox. <li> Drawing tools: Drawing tools all inherit from mitk::Tool, which is a mitk::StateMachine. There is a number of derivations from Tool, each offering some helper methods for specific sub-classes, like manipulation of 2D slices. Tools are instantiated through the itk::ObjectFactory, which means that there is also one factory for each tool (e.g. mitk::AddContourToolFactory). For the GUI representation, each tool has an identification, consisting of a name and an icon (XPM). The actual drawing methods are mainly implemented in mitk::SegTool2D (helper methods) and its sub-classes for region growing, freehand drawing, etc. <li> Slice manipulation: There are two ways to manipulate slices inside a 3D image volume. mitk::ExtractImageFilter retrieves a single 2D slice from a 3D volume. mitkVtkImageOverwrite replaces a slice inside a 3D volume with a second slice. These classes are used extensively by most of the tools to fulfill their task. <li> Interpolation of unsegmented slices: There are two classes involved in interpolation: mitk::SegmentationInterpolationController knows a mitk::Image (the segmentation) and scans its contents for slices with non-zero pixels. It keeps track of changes in the image and is always able to tell, which neighbors of a slice (in the three orthogonal slice directions) contain segmentations. The class also performs this interpolation for single slices on demand. Again, we have a second class responsible for the GUI: QmitkSlicesInterpolator enables/disables interpolation and offers to accept interpolations for one or all slices. <li> Undo: Undo functionality is implemented using mitk::DiffSliceOperation. mitk::SegTool2D::WriteSliceToVolume stores the original image and the modified slice to the undo stack as an mitk::DiffSliceOperation. When the user requests undo, this mitk::DiffSliceOperation will be executed by a singleton class DiffSliceOperationApplier. The operation itself observes the image, which it refers to, for itk::DeleteEvent, so no undo operation will be executed on/for images that have already been destroyed. <li> GUI: The top-level GUI is the view QmitkSegmentation, which is very thin in comparison to ERIS. There are -separate widgets for image and tool selection, for interpolation. Additionaly, +separate widgets for image and tool selection, for interpolation. Additionally, there are some methods to create, delete, crop, load and save segmentations. </ol> **/ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolExtensionsGeneralOverview.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolExtensionsGeneralOverview.dox index 47b868ad49..97e995e9bd 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolExtensionsGeneralOverview.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_ToolExtensionsGeneralOverview.dox @@ -1,182 +1,182 @@ /** \page toolextensions How to extend the Segmentation view with external tools \warning This documentation is outdated (see bug 19726). <ul> <li> \ref ToolExtensionsGeneralOverview2 </li> <li> \ref ToolExtensionsGeneralOverview3 </li> <ul> <li> \ref ToolExtensionsGeneralOverview31 </li> <li> \ref ToolExtensionsGeneralOverview32 </li> <li> \ref ToolExtensionsGeneralOverview33 </li> </ul> <li> \ref ToolExtensionsGeneralOverview4 </li> <li> \ref ToolExtensionsGeneralOverview5 </li> <li> \ref ToolExtensionsGeneralOverview6 </li> </ul> \section ToolExtensionsGeneralOverview2 Introduction The application for manual segmentation in MITK (Segmentation view) comes with a tool class framework that is extensible with new tools (description at \ref QmitkSegmentationTechnicalPage). The usual way to create new tools (since it is mostly used inside DKFZ) is to just add new files to the MITK source code tree. However, this requires to be familiar with the MITK build system and turnaround time during development might be long (recompiling parts of MITK again and again). For external users who just want to use MITK as a library and application, there is a way to create new segmentation tools in an MITK external project, which will compile the new tools into a shared object (DLL). Such shared objects can be loaded via the ITK object factory and its autoload feature on application startup. This document describes how to build such external extensions. Example files can be found in the MITK source code in the directory <tt>${MITK_SOURCE_DIR}/QApplications/ToolExtensionsExample/</tt>. \section ToolExtensionsGeneralOverview3 What might be part of an extension The extension concept assumes that you want to create one or several new interactive segmentation tools for Segmentation or another MITK view that uses the tools infrastructure. In the result you will create a shared object (DLL), which contains several tools and their GUI counterparts, plus optional code that your extension requires. The following sections shortly describe each of these parts. \subsection ToolExtensionsGeneralOverview31 Tool classes A tool is basically any subclass of mitk::Tool. Tools are created at runtime through the ITK object factory (so they inherit from itk::Object). Tools should handle the interaction part of a segmentation method, i.e. create seed points, draw contours, etc., in order to parameterize segmentation algorithms. Simple algorithms can even be part of a tool. A tools is identified by icon (XPM format), name (short string) and optionally a group name (e.g. the group name for Segmentation is "default"). There is a naming convention: you should put a tool called \c mitk::ExternalTool into files called \c mitkExternalTool.h and \c mitkExternalTool.cpp. This is \e required if you use the convenience macros described below, because there need to be ITK factories, which names are directly derived from the file names of the tools. For the example of mitk::ExternalTool there would be a factory called \c mitk::ExternalToolFactory in a file named \c mitkExternalToolFactory.cpp. \subsection ToolExtensionsGeneralOverview32 GUI classes for tools Tools are non-graphical classes that only implement interactions in renderwindows. However, some tools will need a means to allow the user to set some parameters -- a graphical user interface, GUI. In the Qt3 case, tool GUIs inherit from QmitkToolGUI, which is a mixture of QWidget and itk::Object. Tool GUIs are also created through the ITK object factory. Tools inform their GUIs about state changes by messages. Tool GUIs communicate with their associated tools via direct method calls (they know their tools). See mitk::BinaryThresholdTool for examples. Again a naming convention: if the convenience macros for tool extension shared objects are used, you have to put a tool GUI called \c QmitkExternalToolGUI into a files named \c QmitkExternalToolGUI.cpp and \c QmitkExternalToolGUI.h. The convenience macro will create a factory called \c QmitkExternalToolGUIFactory into a file named \c QmitkExternalToolGUIFactory.cpp. \subsection ToolExtensionsGeneralOverview33 Additional files If you are writing tools MITK externally, these tools might depend on additional files, e.g. segmentation algorithms. These can also be compiled into a tool extension shared object. \section ToolExtensionsGeneralOverview4 Writing a CMake file for a tool extension Summing up the last section, an example tool extension could comprise the following files: \verbatim mitkExternalTool.h \ mitkExternalTool.png >--- implementing mitk::ExternalTool (header, icon, implementation) mitkExternalTool.cpp / QmitkExternalToolGUI.h ,-- implementing a GUI for mitk::ExternalTool QmitkExternalToolGUI.cpp / externalalgorithm.h \ externalalgorithm.cpp \ externalalgorithmsolver.h >-- a couple of files (not related to MITK tools) externalalgorithmsolver.cpp / \endverbatim This should all be compiled into one shared object. Just like ITK, VTK and MITK we will use CMake for this purpose (I assume you either know or are willing to learn about <a href="htpp://www.cmake.org">www.cmake.org</a>) A CMake file for the above example would look like this: \code project( ExternalTool ) find_package(ITK) find_package(MITK) find_package(Qt3) add_definitions(${QT_DEFINITIONS}) set( TOOL_QT3GUI_FILES QmitkExternalToolGUI.cpp ) set( TOOL_FILES mitkExternalTool.cpp ) set( TOOL_ADDITIONAL_CPPS externalalgorithm.cpp externalalgorithmsolver.cpp ) set( TOOL_ADDITIONAL_MOC_H ) MITK_GENERATE_TOOLS_LIBRARY(mitkExternalTools) \endcode Basically, you only have to change the definitions of \c TOOL_FILES and, optionally, \c TOOL_QT3GUI_FILES, \c TOOL_ADDITIONAL_CPPS and \c TOOL_ADDITIONAL_MOC_H. For all .cpp files in \c TOOL_FILES and \c TOOL_QT3GUI_FILES there will be factories created assuming the naming conventions described in the sections above. Files listed in \c TOOL_ADDITIONAL_CPPS will just be compiled. Files listed in \c TOOL_ADDITIONAL_MOC_H will be run through Qts meta object compiler \c moc -- -this is neccessary for all objects that have the Q_OBJECT macro in their declaration. +this is necessary for all objects that have the Q_OBJECT macro in their declaration. \c moc will create new files that will also be compiled into the library. \section ToolExtensionsGeneralOverview5 Compiling the extension For compiling a tool extension, you will need a compiled version of MITK. We will assume MITK was compiled into /home/user/mitk/debug. You need to build MITK with BUILD_SHARED_CORE turned on! You build the tool extension just like any other CMake based project: \li know where your source code is (e.g. /home/user/mitk/tool-extension-src) \li change into the directory, where you want to compile the shared object (e.g. /home/user/mitk/tool-extension-debug) \li invoke cmake: <tt>ccmake /home/user/mitk/tool-extension-src</tt> \li configure (press c or the "configure" button) \li set the ITK_DIR variable to the directory, where you compiled ITK \li set the MITK_DIR variable to the directory, where you compiled MITK: <tt>/home/user/mitk/debug</tt> \li configure (press "c" or the "configure" button) \li generate (press "g" or the "generate" button) This should do it and leave you with a or project file or Makefile that you can compile (using make or VisualStudio). \section ToolExtensionsGeneralOverview6 Configuring ITK autoload If the compile succeeds, you will get a library mitkExternalTools.dll or libmitkExternalTools.so. This library exports a symbol \c itkLoad which is expected by the ITK object factory. On application startup the ITK object factory will search a list of directories from the environment variable \c ITK_AUTOLOAD_PATH. Set this environment variable to your binary directory (<tt>/home/user/mitk/tool-extension-debug</tt>). The ITK object factory will load all shared objects that it finds in the specified directories and will test if they contain a symbol (function pointer) \c itkLoad, which is expected to return a pointer to a itk::ObjectFactoryBase instance. If such a symbol is found, the returned factory will be registered with the ITK object factory. If you successfully followed all the steps above, MITK will find your mitk::ExternalTool on application startup, when the ITK object factory is asked to create all known instances of mitk::Tool. Furthermore, if your mitk::ExternalTool claims to be part of the "default" group, there will be a new icon in Segmentation, which activates your tool. Have fun! (And Windows users: welcome to the world of DLLs) **/ diff --git a/Plugins/org.mitk.gui.qt.segmentation/files.cmake b/Plugins/org.mitk.gui.qt.segmentation/files.cmake index c92f6fd02d..38abb65df5 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/files.cmake +++ b/Plugins/org.mitk.gui.qt.segmentation/files.cmake @@ -1,78 +1,81 @@ set(SRC_CPP_FILES QmitkSegmentationPreferencePage.cpp QmitkNewSegmentationDialog.cpp QmitkLabelSetWidget.cpp + QmitkSegmentAnythingPreferencePage.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkSegmentationView.cpp QmitkSegmentationUtilitiesView.cpp QmitkSegmentationTaskListView.cpp QmitkAutocropAction.cpp QmitkAutocropLabelSetImageAction.cpp QmitkCreatePolygonModelAction.cpp QmitkLoadMultiLabelPresetAction.cpp QmitkSaveMultiLabelPresetAction.cpp QmitkConvertSurfaceToLabelAction.cpp QmitkConvertMaskToLabelAction.cpp QmitkConvertToMultiLabelSegmentationAction.cpp QmitkCreateMultiLabelSegmentationAction.cpp Common/QmitkLabelsWidget.cpp Common/QmitkLayersWidget.cpp ) set(UI_FILES src/QmitkSegmentationPreferencePageControls.ui + src/QmitkSegmentAnythingPreferencePage.ui src/QmitkNewSegmentationDialog.ui src/QmitkLabelSetWidgetControls.ui src/internal/QmitkSegmentationViewControls.ui src/internal/QmitkSegmentationUtilitiesViewControls.ui src/internal/QmitkSegmentationTaskListView.ui src/internal/Common/QmitkLabelsWidgetControls.ui src/internal/Common/QmitkLayersWidgetControls.ui ) set(MOC_H_FILES src/QmitkSegmentationPreferencePage.h + src/QmitkSegmentAnythingPreferencePage.h src/QmitkNewSegmentationDialog.h src/QmitkLabelSetWidget.h src/internal/mitkPluginActivator.h src/internal/QmitkSegmentationView.h src/internal/QmitkSegmentationUtilitiesView.h src/internal/QmitkSegmentationTaskListView.h src/internal/QmitkAutocropAction.h src/internal/QmitkAutocropLabelSetImageAction.h src/internal/QmitkCreatePolygonModelAction.h src/internal/QmitkLoadMultiLabelPresetAction.h src/internal/QmitkSaveMultiLabelPresetAction.h src/internal/QmitkConvertSurfaceToLabelAction.h src/internal/QmitkConvertMaskToLabelAction.h src/internal/QmitkConvertToMultiLabelSegmentationAction.h src/internal/QmitkCreateMultiLabelSegmentationAction.h src/internal/Common/QmitkLabelsWidget.h src/internal/Common/QmitkLayersWidget.h ) set(CACHED_RESOURCE_FILES resources/segmentation.svg resources/segmentation_utilities.svg resources/SegmentationTaskListIcon.svg plugin.xml ) set(QRC_FILES resources/segmentation.qrc resources/SegmentationUtilities.qrc resources/SegmentationTaskList.qrc ) set(CPP_FILES) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.segmentation/plugin.xml b/Plugins/org.mitk.gui.qt.segmentation/plugin.xml index 70faf41d0e..d585f47707 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/plugin.xml +++ b/Plugins/org.mitk.gui.qt.segmentation/plugin.xml @@ -1,102 +1,105 @@ <?xml version="1.0" encoding="UTF-8"?> <?eclipse version="3.0"?> <plugin> <extension point="org.blueberry.ui.views"> <view id="org.mitk.views.segmentation" name="Segmentation" category="Segmentation" icon="resources/segmentation.svg" class="QmitkSegmentationView" > <description>Allows the segmentation of images using different tools.</description> <keywordReference id="org.mitk.views.segmentation.ViewKeyword"/> </view> <view id="org.mitk.views.segmentationutilities" name="Segmentation Utilities" category="Segmentation" class="QmitkSegmentationUtilitiesView" icon="resources/segmentation_utilities.svg" > <description>Edit segmentations using standard operations. </description> <keywordReference id="org.mitk.views.segmentationutilities.ViewKeyword"/> </view> <view id="org.mitk.views.segmentationtasklist" name="Segmentation Task List" category="Segmentation" class="QmitkSegmentationTaskListView" icon="resources/SegmentationTaskListIcon.svg" > <description>Create or edit a batch of segmentations according to a task list in a streamlined workflow.</description> <keywordReference id="org.mitk.views.segmentationtasklist.ViewKeyword"/> </view> </extension> <extension point="org.blueberry.ui.preferencePages"> <page id="org.mitk.gui.qt.application.SegmentationPreferencePage" name="Segmentation" class="QmitkSegmentationPreferencePage"> <keywordreference id="org.mitk.gui.qt.application.SegmentationPreferencePageKeywords"></keywordreference> + </page> + <page id="org.mitk.gui.qt.application.SegmentAnythingPreferencePage" name="Segment Anything" class="QmitkSegmentAnythingPreferencePage" category="org.mitk.gui.qt.application.SegmentationPreferencePage"> + <keywordreference id="org.mitk.gui.qt.application.SegmentationPreferencePageKeywords"></keywordreference> </page> </extension> <extension point="org.blueberry.ui.keywords"> <keyword id="org.mitk.gui.qt.application.SegmentationPreferencePageKeywords" label="data manager"></keyword> </extension> <extension point="org.mitk.gui.qt.datamanager.contextMenuActions"> <contextMenuAction nodeDescriptorName="Image" label="Create Segmentation" icon="" class="QmitkCreateMultiLabelSegmentationAction" /> <contextMenuAction nodeDescriptorName="Image" label="Convert to Segmentation" icon="" class="QmitkConvertToMultiLabelSegmentationAction" /> <contextMenuAction nodeDescriptorName="ImageMask" label="Create polygon model" icon="" smoothed="false" class="QmitkCreatePolygonModelAction" /> <contextMenuAction nodeDescriptorName="ImageMask" label="Create smoothed polygon model" icon="" smoothed = "true" class="QmitkCreatePolygonModelAction" /> <contextMenuAction nodeDescriptorName="ImageMask" label="Autocrop" icon="" class="QmitkAutocropAction" /> <contextMenuAction nodeDescriptorName="ImageMask" label="Convert to Label" icon="" class="QmitkConvertMaskToLabelAction" /> <contextMenuAction nodeDescriptorName="LabelSetImage" label="Create polygon model" icon="" smoothed="false" class="QmitkCreatePolygonModelAction" /> <contextMenuAction nodeDescriptorName="LabelSetImage" label="Create smoothed polygon model" icon="" smoothed = "true" class="QmitkCreatePolygonModelAction" /> <contextMenuAction nodeDescriptorName="LabelSetImage" label="Autocrop" icon="" class="QmitkAutocropLabelSetImageAction" /> <contextMenuAction nodeDescriptorName="LabelSetImage" label="Save LabelSet Preset" icon="" class="QmitkSaveMultiLabelPresetAction" /> <contextMenuAction nodeDescriptorName="LabelSetImage" label="Load LabelSet Preset" icon="" class="QmitkLoadMultiLabelPresetAction" /> <contextMenuAction nodeDescriptorName="Surface" label="Convert to Label" icon="" class="QmitkConvertSurfaceToLabelAction" /> </extension> <extension point="org.blueberry.ui.keywords"> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Segmentation" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Otsu" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Paint" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Wipe" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Region Growing" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Fill" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Erase" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Live Wire" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Fast Marching" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Threshold" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Picking" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Annotation annote" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Labeling" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="Tools" /> <keyword id="org.mitk.views.segmentation.ViewKeyword" label="nnUNet" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Segmentation" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Difference" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Intersection" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Union" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Image Masking" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface Masking" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Dilatation" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Erosion" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Closing" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Opening" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Fill Holes" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Morphological Operations" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Boolean Operations" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface to Image" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface creation" /> <keyword id="org.mitk.views.segmentationutilities.ViewKeyword" label="Surface operations" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="Segmentation" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="Task" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="Task List" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="Work List" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="To-do List" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="Workflow" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="Preset" /> <keyword id="org.mitk.views.segmentationtasklist.ViewKeyword" label="JSON" /> </extension> </plugin> diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h index d863238290..bf6dacb06b 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h @@ -1,171 +1,171 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkLabelSetWidget_h #define QmitkLabelSetWidget_h #include <org_mitk_gui_qt_segmentation_Export.h> #include <mitkColorSequenceRainbow.h> #include <mitkLabel.h> #include <mitkNumericTypes.h> #include <ui_QmitkLabelSetWidgetControls.h> class QmitkDataStorageComboBox; class QCompleter; namespace mitk { class LabelSetImage; class LabelSet; class Label; class DataStorage; class ToolManager; class DataNode; } class MITK_QT_SEGMENTATION QmitkLabelSetWidget : public QWidget { Q_OBJECT public: explicit QmitkLabelSetWidget(QWidget *parent = nullptr); ~QmitkLabelSetWidget() override; void SetDataStorage(mitk::DataStorage *storage); void UpdateControls(); virtual void setEnabled(bool enabled); QStringList &GetLabelStringList(); signals: /// \brief Send a signal when it was requested to go to a label. void goToLabel(const mitk::Point3D &); void LabelSetWidgetReset(); public slots: /** * @brief Updates the current labels in the label set widget table. For each label (widget item) the 'UpdateTableWidgetItem' is called. * * Updating means setting the color box of the table, setting the column with and fill it with the label name. * Furthermore the two push buttons for locking and showing/hiding the layer are checked/unchecked. * This functions only changes the appearance of the table widget and no render window update is necessary. */ void UpdateAllTableWidgetItems(); void UpdateAllTableWidgetItems(mitk::Label::PixelType); /** * @brief Resets the current labels in the label set widget table. For each label a widget item is inserted into the table. * * Resetting means removing all rows of the widget table and inserting new rows (labels) from the active label set (= layer) of the current working node. * The currently active label is selected and 'Number of labels' is set. * As this function is typically used after one label has been removed or the reference node has been changed (e.g.) the render windows have to be updated. */ void ResetAllTableWidgetItems(); void ResetAllTableWidgetItems(mitk::Label::PixelType); void SelectLabelByPixelValue(mitk::Label::PixelType pixelValue); private slots: // LabelSet dependent void OnOpacityChanged(int); void OnUnlockAllLabels(bool); void OnLockAllLabels(bool); void OnSetAllLabelsVisible(bool); void OnSetAllLabelsInvisible(bool); void OnSetOnlyActiveLabelVisible(bool); void OnRandomColor(bool); void OnRemoveLabel(bool); void OnRemoveLabels(bool); void OnRenameLabel(bool); void OnRenameLabelShortcutActivated(); void OnLockedButtonClicked(); void OnVisibleButtonClicked(); void OnColorButtonClicked(); void OnItemClicked(QTableWidgetItem *item); void OnItemDoubleClicked(QTableWidgetItem *item); void OnTableViewContextMenuRequested(const QPoint &); void InsertTableWidgetItem(mitk::Label *label); void UpdateTableWidgetItem(QTableWidgetItem *item); // reaction to "returnPressed" signal from ... void OnSearchLabel(); // reaction to the button "Change Label" void OnActiveLabelChanged(int pixelValue); - // LabelSetImage Dependet + // LabelSetImage Dependent void OnCreateDetailedSurface(bool); void OnCreateSmoothedSurface(bool); // reaction to the signal "createMask" from QmitkLabelSetTableWidget void OnCreateMask(bool); void OnCreateMasks(bool); // reaction to the signal "createCroppedMask" from QmitkLabelSetTableWidget void OnCreateCroppedMask(bool); void OnCombineAndCreateMask(bool); void OnCombineAndCreateSurface(bool); void OnEraseLabel(bool); void OnEraseLabels(bool); void OnMergeLabels(bool); // reaction to signal "labelListModified" from QmitkLabelSetTableWidget void OnLabelListModified(const QStringList &list); // reaction to the signal "toggleOutline" from QmitkLabelSetTableWidget void OnToggleOutline(bool); void OnRowsInserted(const QModelIndex&, int, int); void OnRowsRemoved(const QModelIndex&, int, int); private: enum TableColumns { NAME_COL = 0, LOCKED_COL, COLOR_COL, VISIBLE_COL }; void WaitCursorOn(); void WaitCursorOff(); void RestoreOverrideCursor(); void OnThreadedCalculationDone(); void InitializeTableWidget(); int GetPixelValueOfSelectedItem(); mitk::LabelSetImage *GetWorkingImage(); mitk::DataNode *GetWorkingNode(); Ui::QmitkLabelSetWidgetControls m_Controls; mitk::ColorSequenceRainbow m_ColorSequenceRainbow; mitk::DataStorage *m_DataStorage; QCompleter *m_Completer; mitk::ToolManager *m_ToolManager; QStringList m_OrganColors; QStringList m_LabelStringList; bool m_ProcessingManualSelection; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.cpp new file mode 100644 index 0000000000..3229b83a62 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.cpp @@ -0,0 +1,368 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "QmitkSegmentAnythingPreferencePage.h" + +#include <mitkCoreServices.h> +#include <mitkIPreferencesService.h> +#include <mitkIPreferences.h> +#include <mitkProcessExecutor.h> +#include <itkCommand.h> +#include <QmitkSegmentAnythingToolGUI.h> + +#include <QFileDialog> +#include <QmitkStyleManager.h> +#include <QDir> +#include <QDirIterator> + + +namespace +{ + mitk::IPreferences* GetPreferences() + { + auto* preferencesService = mitk::CoreServices::GetPreferencesService(); + return preferencesService->GetSystemPreferences()->Node("org.mitk.views.segmentation"); + } +} + +QmitkSegmentAnythingPreferencePage::QmitkSegmentAnythingPreferencePage() + : m_Ui(new Ui::QmitkSegmentAnythingPreferencePage), + m_Control(nullptr){} + +QmitkSegmentAnythingPreferencePage::~QmitkSegmentAnythingPreferencePage(){} + +void QmitkSegmentAnythingPreferencePage::Init(berry::IWorkbench::Pointer){} + +void QmitkSegmentAnythingPreferencePage::CreateQtControl(QWidget* parent) +{ + m_Control = new QWidget(parent); + m_Ui->setupUi(m_Control); +#ifndef _WIN32 + m_Ui->sysPythonComboBox->addItem("/usr/bin"); +#endif + this->AutoParsePythonPaths(); + m_Ui->timeoutEdit->setValidator(new QIntValidator(0, 1000, this)); + m_Ui->sysPythonComboBox->addItem("Select..."); + m_Ui->sysPythonComboBox->setCurrentIndex(0); + connect(m_Ui->installSAMButton, SIGNAL(clicked()), this, SLOT(OnInstallBtnClicked())); + connect(m_Ui->clearSAMButton, SIGNAL(clicked()), this, SLOT(OnClearInstall())); + connect(m_Ui->sysPythonComboBox, + QOverload<int>::of(&QComboBox::activated), + [=](int index) { OnSystemPythonChanged(m_Ui->sysPythonComboBox->itemText(index)); }); + QIcon deleteIcon = + QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/edit-delete.svg")); + m_Ui->clearSAMButton->setIcon(deleteIcon); + const QString storageDir = m_Installer.GetVirtualEnvPath(); + bool isInstalled = QmitkSegmentAnythingToolGUI::IsSAMInstalled(storageDir); + QString welcomeText; + if (isInstalled) + { + m_PythonPath = GetExactPythonPath(storageDir); + m_Installer.SetVirtualEnvPath(m_PythonPath); + welcomeText += " Segment Anything tool is already found installed."; + m_Ui->installSAMButton->setEnabled(false); + } + else + { + welcomeText += " Segment Anything tool not installed. Please click on \"Install SAM\" above. \ + The installation will create a new virtual environment using the System Python selected above."; + m_Ui->installSAMButton->setEnabled(true); + } + this->WriteStatusMessage(welcomeText); + m_Ui->samModelTypeComboBox->addItems(VALID_MODELS); + m_Ui->gpuComboBox->addItem(CPU_ID); + this->SetGPUInfo(); + this->Update(); +} + +QWidget* QmitkSegmentAnythingPreferencePage::GetQtControl() const +{ + return m_Control; +} + +bool QmitkSegmentAnythingPreferencePage::PerformOk() +{ + auto* prefs = GetPreferences(); + prefs->Put("sam parent path", m_Installer.STORAGE_DIR.toStdString()); + prefs->Put("sam python path", m_PythonPath.toStdString()); + prefs->Put("sam modeltype", m_Ui->samModelTypeComboBox->currentText().toStdString()); + prefs->PutInt("sam gpuid", FetchSelectedGPUFromUI()); + prefs->PutInt("sam timeout", std::stoi(m_Ui->timeoutEdit->text().toStdString())); + return true; +} + +void QmitkSegmentAnythingPreferencePage::PerformCancel(){} + +void QmitkSegmentAnythingPreferencePage::Update() +{ + auto* prefs = GetPreferences(); + m_Ui->samModelTypeComboBox->setCurrentText(QString::fromStdString(prefs->Get("sam modeltype", "vit_b"))); + m_Ui->timeoutEdit->setText(QString::number(prefs->GetInt("sam timeout", 300))); + int gpuId = prefs->GetInt("sam gpuid", -1); + if (gpuId == -1) + { + m_Ui->gpuComboBox->setCurrentText(CPU_ID); + } + else if (m_GpuLoader.GetGPUCount() == 0) + { + m_Ui->gpuComboBox->setCurrentText(QString::number(gpuId)); + } + else + { + std::vector<QmitkGPUSpec> specs = m_GpuLoader.GetAllGPUSpecs(); + QmitkGPUSpec gpuSpec = specs[gpuId]; + m_Ui->gpuComboBox->setCurrentText(QString::number(gpuSpec.id) + ": " + gpuSpec.name + " (" + gpuSpec.memory + ")"); + } +} + +QString QmitkSegmentAnythingPreferencePage::OnSystemPythonChanged(const QString &pyEnv) +{ + QString pyPath; + if (pyEnv == QString("Select...")) + { + QString path = QFileDialog::getExistingDirectory(m_Ui->sysPythonComboBox->parentWidget(), "Python Path", "dir"); + if (!path.isEmpty()) + { + this->OnSystemPythonChanged(path); // recall same function for new path validation + bool oldState = m_Ui->sysPythonComboBox->blockSignals(true); // block signal firing while inserting item + m_Ui->sysPythonComboBox->insertItem(0, path); + m_Ui->sysPythonComboBox->setCurrentIndex(0); + m_Ui->sysPythonComboBox->blockSignals(oldState); // unblock signal firing after inserting item. Remove this after Qt6 migration + } + } + else + { + QString uiPyPath = this->GetPythonPathFromUI(pyEnv); + pyPath = this->GetExactPythonPath(uiPyPath); + } + return pyPath; +} + +QString QmitkSegmentAnythingPreferencePage::GetPythonPathFromUI(const QString &pyUI) const +{ + QString fullPath = pyUI; + if (-1 != fullPath.indexOf(")")) + { + fullPath = fullPath.mid(fullPath.indexOf(")") + 2); + } + return fullPath.simplified(); +} + +QString QmitkSegmentAnythingPreferencePage::GetExactPythonPath(const QString &pyEnv) const +{ + QString fullPath = pyEnv; + bool isPythonExists = false; +#ifdef _WIN32 + isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python.exe")); + if (!isPythonExists && + !(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive))) + { + fullPath += QDir::separator() + QString("Scripts"); + isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python.exe")); + } +#else + isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python3")); + if (!isPythonExists && + !(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive))) + { + fullPath += QDir::separator() + QString("bin"); + isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python3")); + } +#endif + if (!isPythonExists) + { + fullPath.clear(); + } + return fullPath; +} + +void QmitkSegmentAnythingPreferencePage::AutoParsePythonPaths() +{ + QString homeDir = QDir::homePath(); + std::vector<QString> searchDirs; +#ifdef _WIN32 + searchDirs.push_back(QString("C:") + QDir::separator() + QString("ProgramData") + QDir::separator() + + QString("anaconda3")); +#else + // Add search locations for possible standard python paths here + searchDirs.push_back(homeDir + QDir::separator() + "anaconda3"); + searchDirs.push_back(homeDir + QDir::separator() + "miniconda3"); + searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "miniconda3"); + searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "anaconda3"); +#endif + for (QString searchDir : searchDirs) + { + if (searchDir.endsWith("anaconda3", Qt::CaseInsensitive)) + { + if (QDir(searchDir).exists()) + { + m_Ui->sysPythonComboBox->addItem("(base): " + searchDir); + searchDir.append((QDir::separator() + QString("envs"))); + } + } + for (QDirIterator subIt(searchDir, QDir::AllDirs, QDirIterator::NoIteratorFlags); subIt.hasNext();) + { + subIt.next(); + QString envName = subIt.fileName(); + if (!envName.startsWith('.')) // Filter out irrelevent hidden folders, if any. + { + m_Ui->sysPythonComboBox->addItem("(" + envName + "): " + subIt.filePath()); + } + } + } +} + +void QmitkSegmentAnythingPreferencePage::SetGPUInfo() +{ + std::vector<QmitkGPUSpec> specs = m_GpuLoader.GetAllGPUSpecs(); + for (const QmitkGPUSpec &gpuSpec : specs) + { + m_Ui->gpuComboBox->addItem(QString::number(gpuSpec.id) + ": " + gpuSpec.name + " (" + gpuSpec.memory + ")"); + } + if (specs.empty()) + { + m_Ui->gpuComboBox->setCurrentIndex(m_Ui->gpuComboBox->findText("cpu")); + } + else + { + m_Ui->gpuComboBox->setCurrentIndex(m_Ui->gpuComboBox->count()-1); + } +} + +int QmitkSegmentAnythingPreferencePage::FetchSelectedGPUFromUI() const +{ + QString gpuInfo = m_Ui->gpuComboBox->currentText(); + if ("cpu" == gpuInfo) + { + return -1; + } + else if(m_GpuLoader.GetGPUCount() == 0) + { + return static_cast<int>(gpuInfo.toInt()); + } + else + { + QString gpuId = gpuInfo.split(":", QString::SplitBehavior::SkipEmptyParts).first(); + return static_cast<int>(gpuId.toInt()); + } +} + +void QmitkSegmentAnythingPreferencePage::OnInstallBtnClicked() +{ + QString systemPython = OnSystemPythonChanged(m_Ui->sysPythonComboBox->currentText()); + if (!systemPython.isEmpty()) + { + this->WriteStatusMessage("STATUS: Installing SAM..."); + m_Ui->installSAMButton->setEnabled(false); + m_Installer.SetSystemPythonPath(systemPython); + bool isInstalled = false; + bool isFinished = m_Installer.SetupVirtualEnv(m_Installer.VENV_NAME); + if (isFinished) + { + isInstalled = QmitkSegmentAnythingToolGUI::IsSAMInstalled(m_Installer.GetVirtualEnvPath()); + } + if (isInstalled) + { + m_PythonPath = this->GetExactPythonPath(m_Installer.GetVirtualEnvPath()); + this->WriteStatusMessage("STATUS: Successfully installed SAM."); + } + else + { + this->WriteErrorMessage("ERROR: Couldn't install SAM."); + m_Ui->installSAMButton->setEnabled(true); + } + } +} + +void QmitkSegmentAnythingPreferencePage::OnClearInstall() +{ + QDir folderPath(m_Installer.GetVirtualEnvPath()); + bool isDeleted = folderPath.removeRecursively(); + if (isDeleted) + { + this->WriteStatusMessage("Deleted SAM installation."); + m_Ui->installSAMButton->setEnabled(true); + m_PythonPath.clear(); + } + else + { + MITK_ERROR << "The virtual environment couldn't be removed. Please check if you have the required access " + "privileges or, some other process is accessing the folders."; + } +} + +void QmitkSegmentAnythingPreferencePage::WriteStatusMessage(const QString &message) +{ + m_Ui->samInstallStatusLabel->setText(message); + m_Ui->samInstallStatusLabel->setStyleSheet("font-weight: bold; color: white"); + qApp->processEvents(); +} + +void QmitkSegmentAnythingPreferencePage::WriteErrorMessage(const QString &message) +{ + m_Ui->samInstallStatusLabel->setText(message); + m_Ui->samInstallStatusLabel->setStyleSheet("font-weight: bold; color: red"); + qApp->processEvents(); +} + +QString QmitkSAMInstaller::GetVirtualEnvPath() +{ + return STORAGE_DIR + VENV_NAME; +} + +bool QmitkSAMInstaller::SetupVirtualEnv(const QString &venvName) +{ + if (GetSystemPythonPath().isEmpty()) + { + return false; + } + QDir folderPath(GetBaseDir()); + folderPath.mkdir(venvName); + if (!folderPath.cd(venvName)) + { + return false; // Check if directory creation was successful. + } + mitk::ProcessExecutor::ArgumentListType args; + auto spExec = mitk::ProcessExecutor::New(); + auto spCommand = itk::CStyleCommand::New(); + spCommand->SetCallback(&PrintProcessEvent); + spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); + + args.push_back("-m"); + args.push_back("venv"); + args.push_back(venvName.toStdString()); +#ifdef _WIN32 + QString pythonFile = GetSystemPythonPath() + QDir::separator() + "python.exe"; + QString pythonExeFolder = "Scripts"; +#else + QString pythonFile = GetSystemPythonPath() + QDir::separator() + "python3"; + QString pythonExeFolder = "bin"; +#endif + spExec->Execute(GetBaseDir().toStdString(), pythonFile.toStdString(), args); // Setup local virtual environment + if (folderPath.cd(pythonExeFolder)) + { + this->SetPythonPath(folderPath.absolutePath()); + this->SetPipPath(folderPath.absolutePath()); + this->InstallPytorch(); + for (auto &package : PACKAGES) + { + this->PipInstall(package.toStdString(), &PrintProcessEvent); + } + std::string pythonCode; // python syntax to check if torch is installed with CUDA. + pythonCode.append("import torch;"); + pythonCode.append("print('Pytorch was installed with CUDA') if torch.cuda.is_available() else print('PyTorch was " + "installed WITHOUT CUDA');"); + this->ExecutePython(pythonCode, &PrintProcessEvent); + return true; + } + return false; +} diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.h b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.h new file mode 100644 index 0000000000..3a4118eaec --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.h @@ -0,0 +1,114 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef QmitkSegmentAnythingPreferencePage_h +#define QmitkSegmentAnythingPreferencePage_h + +#include <berryIQtPreferencePage.h> +#include <QmitknnUNetGPU.h> +#include <QString> +#include <QmitkSetupVirtualEnvUtil.h> +#include <QStandardPaths> +#include <ui_QmitkSegmentAnythingPreferencePage.h> + +class QWidget; + +namespace Ui +{ + class QmitkSegmentAnythingPreferencePage; +} + +class QmitkSAMInstaller : public QmitkSetupVirtualEnvUtil +{ +public: + const QString VENV_NAME = ".sam"; + const QString SAM_VERSION = "1.0"; // currently, unused + const std::vector<QString> PACKAGES = {QString("git+https://github.com/MIC-DKFZ/agent-sam.git@v0.1")}; + const QString STORAGE_DIR; + inline QmitkSAMInstaller( + const QString baseDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() + + qApp->organizationName() + QDir::separator()) + : QmitkSetupVirtualEnvUtil(baseDir), STORAGE_DIR(baseDir){}; + bool SetupVirtualEnv(const QString &) override; + QString GetVirtualEnvPath() override; +}; + +class QmitkSegmentAnythingPreferencePage : public QObject, public berry::IQtPreferencePage +{ + Q_OBJECT + Q_INTERFACES(berry::IPreferencePage) + +public: + QmitkSegmentAnythingPreferencePage(); + ~QmitkSegmentAnythingPreferencePage() override; + + void Init(berry::IWorkbench::Pointer workbench) override; + void CreateQtControl(QWidget* parent) override; + QWidget* GetQtControl() const override; + bool PerformOk() override; + void PerformCancel() override; + void Update() override; + +private slots: + void OnInstallBtnClicked(); + void OnClearInstall(); + QString OnSystemPythonChanged(const QString&); + +protected: + /** + * @brief Searches and parses paths of python virtual enviroments + * from predefined lookout locations + */ + void AutoParsePythonPaths(); + + /** + * @brief Get the virtual env path from UI combobox removing any + * extra special characters. + * + * @return QString + */ + QString GetPythonPathFromUI(const QString &) const; + + /** + * @brief Get the Exact Python Path for any OS + * from the virtual environment path. + * @return QString + */ + QString GetExactPythonPath(const QString &) const; + + /** + * @brief Adds GPU information to the gpu combo box. + * In case, there aren't any GPUs avaialble, the combo box will be + * rendered editable. + */ + void SetGPUInfo(); + + /** + * @brief Returns GPU id of the selected GPU from the Combo box. + * @return int + */ + int FetchSelectedGPUFromUI() const; + + void WriteStatusMessage(const QString &); + void WriteErrorMessage(const QString &); + +private: + Ui::QmitkSegmentAnythingPreferencePage* m_Ui; + QmitkSAMInstaller m_Installer; + QWidget* m_Control; + QmitkGPULoader m_GpuLoader; + QString m_PythonPath; + const QString CPU_ID = "cpu"; + const QStringList VALID_MODELS = {"vit_b", "vit_l", "vit_h"}; +}; + +#endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.ui b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.ui new file mode 100644 index 0000000000..b68da828a3 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.ui @@ -0,0 +1,153 @@ +<?xml version="1.0" encoding="UTF-8"?> +<ui version="4.0"> + <class>QmitkSegmentAnythingPreferencePage</class> + <widget class="QWidget" name="QmitkSegmentAnythingPreferencePage"> + <property name="geometry"> + <rect> + <x>0</x> + <y>0</y> + <width>656</width> + <height>779</height> + </rect> + </property> + <property name="windowTitle"> + <string>Form</string> + </property> + <layout class="QFormLayout" name="formLayout"> + <item row="0" column="0"> + <widget class="QLabel" name="invisibleLabel"/> + </item> + <item row="0" column="1"> + <layout class="QGridLayout" name="gridLayout"> + <item row="0" column="0" colspan="2"> + <widget class="QPushButton" name="installSAMButton"> + <property name="sizePolicy"> + <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> + <horstretch>0</horstretch> + <verstretch>0</verstretch> + </sizepolicy> + </property> + <property name="text"> + <string>Install Segment Anything</string> + </property> + </widget> + </item> + <item row="0" column="2" colspan="2"> + <widget class="QPushButton" name="clearSAMButton"> + <property name="sizePolicy"> + <sizepolicy hsizetype="Minimum" vsizetype="Fixed"> + <horstretch>0</horstretch> + <verstretch>0</verstretch> + </sizepolicy> + </property> + <property name="text"> + <string>Clear Install</string> + </property> + </widget> + </item> + <item row="1" column="0"> + <widget class="QLabel" name="pythonLabel"> + <property name="text"> + <string>System Python</string> + </property> + </widget> + </item> + <item row="1" column="1" colspan="3"> + <widget class="ctkComboBox" name="sysPythonComboBox" native="true"/> + </item> + <item row="2" column="0"> + <widget class="QLabel" name="samModelTypeLabel"> + <property name="text"> + <string>Model Type</string> + </property> + </widget> + </item> + <item row="2" column="1" colspan="3"> + <widget class="ctkComboBox" name="samModelTypeComboBox" native="true"/> + </item> + <item row="3" column="1" colspan="3"> + <widget class="QLabel" name="samModelTipLabel"> + <property name="text"> + <string><html><head/><body>Tip: Select vit_b for VRAM < 4GB, vit_l for VRAM < 6GB or vit_h for VRAM > 6GB.</body></html></string> + </property> + <property name="textFormat"> + <enum>Qt::RichText</enum> + </property> + <property name="wordWrap"> + <bool>true</bool> + </property> + </widget> + </item> + <item row="4" column="1" colspan="3"> + <widget class="ctkComboBox" name="gpuComboBox" native="true"/> + </item> + <item row="4" column="0"> + <widget class="QLabel" name="gpuSpinLabel"> + <property name="sizePolicy"> + <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> + <horstretch>0</horstretch> + <verstretch>0</verstretch> + </sizepolicy> + </property> + <property name="text"> + <string>Device Id:</string> + </property> + </widget> + </item> + <item row="5" column="1" colspan="3"> + <widget class="QLineEdit" name="timeoutEdit"> + <property name="text"> + <string>300</string> + </property> + </widget> + </item> + <item row="5" column="0"> + <widget class="QLabel" name="timeoutLabel"> + <property name="sizePolicy"> + <sizepolicy hsizetype="Preferred" vsizetype="Preferred"> + <horstretch>0</horstretch> + <verstretch>0</verstretch> + </sizepolicy> + </property> + <property name="text"> + <string>Time Out (s):</string> + </property> + </widget> + </item> + <item row="6" column="0" colspan="4"> + <widget class="QLabel" name="samInstallStatusLabel"> + <property name="textFormat"> + <enum>Qt::RichText</enum> + </property> + <property name="wordWrap"> + <bool>true</bool> + </property> + </widget> + </item> + </layout> + </item> + <item row="1" column="0"> + <spacer name="verticalSpacer"> + <property name="orientation"> + <enum>Qt::Vertical</enum> + </property> + <property name="sizeHint" stdset="0"> + <size> + <width>20</width> + <height>40</height> + </size> + </property> + </spacer> + </item> + </layout> + </widget> + <customwidgets> + <customwidget> + <class>ctkComboBox</class> + <extends>QWidget</extends> + <header>ctkComboBox.h</header> + </customwidget> + </customwidgets> + <resources/> + <connections/> +</ui> diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui index 578328a20f..419f143f68 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui @@ -1,233 +1,233 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkSegmentationPreferencePageControls</class> <widget class="QWidget" name="QmitkSegmentationPreferencePageControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>656</width> <height>779</height> </rect> </property> <property name="windowTitle"> <string>Form</string> </property> <layout class="QFormLayout" name="formLayout"> <item row="0" column="0"> <widget class="QLabel" name="compactViewLabel"> <property name="text"> <string>Compact view</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QCheckBox" name="compactViewCheckBox"> <property name="text"> <string>Hide tool button texts and increase icon size</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QLabel" name="displayLabel"> <property name="text"> <string>2D display</string> </property> </widget> </item> <item row="1" column="1"> <layout class="QVBoxLayout" name="displayOptionsLayout"> <item> <widget class="QRadioButton" name="outlineRadioButton"> <property name="text"> <string>Draw as outline</string> </property> <property name="checked"> <bool>true</bool> </property> <attribute name="buttonGroup"> <string notr="true">displayButtonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="overlayRadioButton"> <property name="text"> <string>Draw as transparent overlay</string> </property> <attribute name="buttonGroup"> <string notr="true">displayButtonGroup</string> </attribute> </widget> </item> </layout> </item> <item row="2" column="0"> <widget class="QLabel" name="selectionModeLabel"> <property name="text"> <string>Data node selection mode</string> </property> </widget> </item> <item row="2" column="1"> <widget class="QCheckBox" name="selectionModeCheckBox"> <property name="toolTip"> <string>If checked the segmentation plugin ensures that only the selected segmentation and the reference image are visible at one time.</string> </property> <property name="text"> <string>Show only selected nodes</string> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="labelSetPresetLabel"> <property name="text"> <string>Default label set preset</string> </property> </widget> </item> <item row="3" column="1"> <layout class="QGridLayout" name="gridLayout"> <item row="0" column="0"> <widget class="QLineEdit" name="labelSetPresetLineEdit"> <property name="clearButtonEnabled"> <bool>true</bool> </property> </widget> </item> <item row="0" column="1"> <widget class="QToolButton" name="labelSetPresetToolButton"> <property name="text"> <string>...</string> </property> </widget> </item> <item row="1" column="0" colspan="2"> <widget class="QLabel" name="labelSetPresetCmdLineArgLabel"> <property name="text"> - <string><html><head/><body>The default label set preset is currently overriden by the Segmentation.labelSetPreset command-line argument.</body></html></string> + <string><html><head/><body>The default label set preset is currently overridden by the Segmentation.labelSetPreset command-line argument.</body></html></string> </property> <property name="textFormat"> <enum>Qt::RichText</enum> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> </layout> </item> <item row="4" column="0"> <widget class="QLabel" name="labelCreationLabel"> <property name="text"> <string>Label creation</string> </property> </widget> </item> <item row="4" column="1"> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QRadioButton" name="defaultNameRadioButton"> <property name="text"> <string>Assign default name and color</string> </property> <property name="checked"> <bool>true</bool> </property> <attribute name="buttonGroup"> <string notr="true">labelCreationButtonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="askForNameRadioButton"> <property name="text"> <string>Ask for name and color</string> </property> <attribute name="buttonGroup"> <string notr="true">labelCreationButtonGroup</string> </attribute> </widget> </item> </layout> </item> <item row="5" column="0"> <widget class="QLabel" name="labelSuggestions"> <property name="text"> <string>Label suggestions</string> </property> </widget> </item> <item row="5" column="1"> <layout class="QGridLayout" name="gridLayout_2"> <item row="0" column="0"> <widget class="QLineEdit" name="suggestionsLineEdit"> <property name="clearButtonEnabled"> <bool>true</bool> </property> </widget> </item> <item row="0" column="1"> <widget class="QToolButton" name="suggestionsToolButton"> <property name="text"> <string>...</string> </property> </widget> </item> <item row="1" column="0" colspan="2"> <widget class="QLabel" name="suggestionsCmdLineArgLabel"> <property name="text"> <string><html><head/><body>Suggestions are currently enforced by the Segmentation.labelSuggestions command-line argument.</body></html></string> </property> <property name="textFormat"> <enum>Qt::RichText</enum> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> </layout> </item> <item row="6" column="1"> <widget class="QCheckBox" name="replaceStandardSuggestionsCheckBox"> <property name="text"> <string>Replace standard organ suggestions</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="7" column="1"> <widget class="QCheckBox" name="suggestOnceCheckBox"> <property name="text"> <string>Suggest once per segmentation</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="8" column="1"> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <resources/> <connections/> <buttongroups> <buttongroup name="labelCreationButtonGroup"/> <buttongroup name="displayButtonGroup"/> </buttongroups> </ui> diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp index d4db0bc770..3b518f8ba3 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,1083 +1,1083 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkSegmentationView.h" #include "mitkPluginActivator.h" // blueberry #include <berryIWorkbenchPage.h> // mitk #include <mitkApplicationCursor.h> #include <mitkBaseApplication.h> #include <mitkBaseRendererHelper.h> #include <mitkCameraController.h> #include <mitkLabelSetImage.h> #include <mitkLabelSetImageHelper.h> #include <mitkMultiLabelIOHelper.h> #include <mitkManualPlacementAnnotationRenderer.h> #include <mitkNodePredicateSubGeometry.h> #include <mitkSegmentationObjectFactory.h> #include <mitkSegTool2D.h> #include <mitkStatusBar.h> #include <mitkToolManagerProvider.h> #include <mitkVtkResliceInterpolationProperty.h> #include <mitkWorkbenchUtil.h> #include <mitkIPreferences.h> // Qmitk #include <QmitkRenderWindow.h> #include <QmitkStaticDynamicSegmentationDialog.h> #include <QmitkNewSegmentationDialog.h> #include <QmitkMultiLabelManager.h> // us #include <usModuleResource.h> #include <usModuleResourceStream.h> // Qt #include <QMessageBox> #include <QShortcut> #include <QDir> // vtk #include <vtkQImageToImageSource.h> #include <regex> namespace { QList<QmitkRenderWindow*> Get2DWindows(const QList<QmitkRenderWindow*> allWindows) { QList<QmitkRenderWindow*> all2DWindows; for (auto* window : allWindows) { if (window->GetRenderer()->GetMapperID() == mitk::BaseRenderer::Standard2D) { all2DWindows.append(window); } } return all2DWindows; } } const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; QmitkSegmentationView::QmitkSegmentationView() : m_Parent(nullptr) , m_Controls(nullptr) , m_RenderWindowPart(nullptr) , m_ToolManager(nullptr) , m_ReferenceNode(nullptr) , m_WorkingNode(nullptr) , m_DrawOutline(true) , m_SelectionMode(false) , m_MouseCursorSet(false) , m_DefaultLabelNaming(true) , m_SelectionChangeIsAlreadyBeingHandled(false) { auto isImage = mitk::TNodePredicateDataType<mitk::Image>::New(); auto isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); auto isDti = mitk::NodePredicateDataType::New("TensorImage"); auto isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); auto validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); m_SegmentationPredicate = mitk::NodePredicateAnd::New(); m_SegmentationPredicate->AddPredicate(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New()); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); m_ReferencePredicate = mitk::NodePredicateAnd::New(); m_ReferencePredicate->AddPredicate(validImages); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate)); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); } QmitkSegmentationView::~QmitkSegmentationView() { if (nullptr != m_Controls) { // deactivate all tools m_ToolManager->ActivateTool(-1); // removing all observers from working data for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_WorkingDataObserverTags.clear(); this->RemoveObserversFromWorkingImage(); // removing all observers from reference data for (NodeTagMapType::iterator dataIter = m_ReferenceDataObserverTags.begin(); dataIter != m_ReferenceDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_ReferenceDataObserverTags.clear(); mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>(); mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef); service->RemoveAllPlanePositions(); context->ungetService(ppmRef); m_ToolManager->SetReferenceData(nullptr); m_ToolManager->SetWorkingData(nullptr); } m_ToolManager->ActiveToolChanged -= mitk::MessageDelegate<Self>(this, &Self::ActiveToolChanged); delete m_Controls; } /**********************************************************************/ /* private Q_SLOTS */ /**********************************************************************/ void QmitkSegmentationView::OnReferenceSelectionChanged(QList<mitk::DataNode::Pointer>) { this->OnAnySelectionChanged(); } void QmitkSegmentationView::OnSegmentationSelectionChanged(QList<mitk::DataNode::Pointer>) { this->OnAnySelectionChanged(); } void QmitkSegmentationView::OnAnySelectionChanged() { // When only a segmentation has been selected and the method is then called by a reference image selection, // the already selected segmentation may not match the geometry predicate of the new reference image anymore. // This will trigger a recursive call of this method further below. While it would be resolved gracefully, we // can spare the extra call with an early-out. The original call of this method will handle the segmentation // selection change afterwards anyway. if (m_SelectionChangeIsAlreadyBeingHandled) return; auto selectedReferenceNode = m_Controls->referenceNodeSelector->GetSelectedNode(); bool referenceNodeChanged = false; m_ToolManager->ActivateTool(-1); if (m_ReferenceNode != selectedReferenceNode) { referenceNodeChanged = true; // Remove visibility observer for the current reference node if (m_ReferenceDataObserverTags.find(m_ReferenceNode) != m_ReferenceDataObserverTags.end()) { m_ReferenceNode->GetProperty("visible")->RemoveObserver(m_ReferenceDataObserverTags[m_ReferenceNode]); m_ReferenceDataObserverTags.erase(m_ReferenceNode); } // Set new reference node m_ReferenceNode = selectedReferenceNode; m_ToolManager->SetReferenceData(m_ReferenceNode); // Prepare for a potential recursive call when changing node predicates of the working node selector m_SelectionChangeIsAlreadyBeingHandled = true; if (m_ReferenceNode.IsNull()) { // Without a reference image, allow all segmentations to be selected m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_SelectionChangeIsAlreadyBeingHandled = false; } else { // With a reference image, only allow segmentations that fit the geometry of the reference image to be selected. m_Controls->workingNodeSelector->SetNodePredicate(mitk::NodePredicateAnd::New( mitk::NodePredicateSubGeometry::New(m_ReferenceNode->GetData()->GetGeometry()), m_SegmentationPredicate.GetPointer())); m_SelectionChangeIsAlreadyBeingHandled = false; this->ApplySelectionModeOnReferenceNode(); // Add visibility observer for the new reference node auto command = itk::SimpleMemberCommand<Self>::New(); command->SetCallbackFunction(this, &Self::ValidateSelectionInput); m_ReferenceDataObserverTags[m_ReferenceNode] = m_ReferenceNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command); } } auto selectedWorkingNode = m_Controls->workingNodeSelector->GetSelectedNode(); bool workingNodeChanged = false; if (m_WorkingNode != selectedWorkingNode) { workingNodeChanged = true; this->RemoveObserversFromWorkingImage(); // Remove visibility observer for the current working node if (m_WorkingDataObserverTags.find(m_WorkingNode) != m_WorkingDataObserverTags.end()) { m_WorkingNode->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[m_WorkingNode]); m_WorkingDataObserverTags.erase(m_WorkingNode); } // Set new working node m_WorkingNode = selectedWorkingNode; m_ToolManager->SetWorkingData(m_WorkingNode); if (m_WorkingNode.IsNotNull()) { this->ApplySelectionModeOnWorkingNode(); // Add visibility observer for the new segmentation node auto command = itk::SimpleMemberCommand<Self>::New(); command->SetCallbackFunction(this, &Self::ValidateSelectionInput); m_WorkingDataObserverTags[m_WorkingNode] = m_WorkingNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command); this->AddObserversToWorkingImage(); } } // Reset camera if any selection changed but only if both reference node and working node are set if ((referenceNodeChanged || workingNodeChanged) && (m_ReferenceNode.IsNotNull() && m_WorkingNode.IsNotNull())) { if (nullptr != m_RenderWindowPart) { m_RenderWindowPart->InitializeViews(m_ReferenceNode->GetData()->GetTimeGeometry(), false); } } this->UpdateGUI(); } void QmitkSegmentationView::OnLabelAdded(mitk::LabelSetImage::LabelValueType) { this->ValidateSelectionInput(); } void QmitkSegmentationView::OnLabelRemoved(mitk::LabelSetImage::LabelValueType) { this->ValidateSelectionInput(); } void QmitkSegmentationView::OnGroupRemoved(mitk::LabelSetImage::GroupIndexType) { this->ValidateSelectionInput(); } mitk::LabelSetImage* QmitkSegmentationView::GetWorkingImage() { if (m_WorkingNode.IsNull()) return nullptr; return dynamic_cast<mitk::LabelSetImage*>(m_WorkingNode->GetData()); } void QmitkSegmentationView::AddObserversToWorkingImage() { auto* workingImage = this->GetWorkingImage(); if (workingImage != nullptr) { workingImage->AddLabelAddedListener(mitk::MessageDelegate1<Self, mitk::LabelSetImage::LabelValueType>(this, &Self::OnLabelAdded)); workingImage->AddLabelRemovedListener(mitk::MessageDelegate1<Self, mitk::LabelSetImage::LabelValueType>(this, &Self::OnLabelRemoved)); workingImage->AddGroupRemovedListener(mitk::MessageDelegate1<Self, mitk::LabelSetImage::GroupIndexType>(this, &Self::OnGroupRemoved)); } } void QmitkSegmentationView::RemoveObserversFromWorkingImage() { auto* workingImage = this->GetWorkingImage(); if (workingImage != nullptr) { workingImage->RemoveLabelAddedListener(mitk::MessageDelegate1<Self, mitk::LabelSetImage::LabelValueType>(this, &Self::OnLabelAdded)); workingImage->RemoveLabelRemovedListener(mitk::MessageDelegate1<Self, mitk::LabelSetImage::LabelValueType>(this, &Self::OnLabelRemoved)); workingImage->RemoveGroupRemovedListener(mitk::MessageDelegate1<Self, mitk::LabelSetImage::GroupIndexType>(this, &Self::OnGroupRemoved)); } } void QmitkSegmentationView::OnVisibilityShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } bool isVisible = false; m_WorkingNode->GetBoolProperty("visible", isVisible); m_WorkingNode->SetVisibility(!isVisible); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnLabelToggleShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast<mitk::LabelSetImage*>(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } this->WaitCursorOn(); workingImage->GetActiveLabelSet()->SetNextActiveLabel(); workingImage->Modified(); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnNewSegmentation() { m_ToolManager->ActivateTool(-1); if (m_ReferenceNode.IsNull()) { MITK_ERROR << "'Create new segmentation' button should never be clickable unless a reference image is selected."; return; } mitk::Image::ConstPointer referenceImage = dynamic_cast<mitk::Image*>(m_ReferenceNode->GetData()); if (referenceImage.IsNull()) { QMessageBox::information( m_Parent, "New segmentation", "Please load and select an image before starting some action."); return; } if (referenceImage->GetDimension() <= 1) { QMessageBox::information( m_Parent, "New segmentation", "Segmentation is currently not supported for 2D images"); return; } auto segTemplateImage = referenceImage; if (referenceImage->GetDimension() > 3) { QmitkStaticDynamicSegmentationDialog dialog(m_Parent); dialog.SetReferenceImage(referenceImage.GetPointer()); dialog.exec(); segTemplateImage = dialog.GetSegmentationTemplate(); } mitk::DataNode::Pointer newSegmentationNode; try { this->WaitCursorOn(); newSegmentationNode = mitk::LabelSetImageHelper::CreateNewSegmentationNode(m_ReferenceNode, segTemplateImage); this->WaitCursorOff(); } catch (mitk::Exception& e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::warning(m_Parent, "New segmentation", "Could not create a new segmentation."); return; } auto newLabelSetImage = dynamic_cast<mitk::LabelSetImage*>(newSegmentationNode->GetData()); if (nullptr == newLabelSetImage) { // something went wrong return; } const auto labelSetPreset = this->GetDefaultLabelSetPreset(); if (labelSetPreset.empty() || !mitk::MultiLabelIOHelper::LoadLabelSetImagePreset(labelSetPreset, newLabelSetImage)) { auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage); if (!m_DefaultLabelNaming) QmitkNewSegmentationDialog::DoRenameLabel(newLabel, nullptr, m_Parent); newLabelSetImage->GetActiveLabelSet()->AddLabel(newLabel); } if (!this->GetDataStorage()->Exists(newSegmentationNode)) { this->GetDataStorage()->Add(newSegmentationNode, m_ReferenceNode); } if (m_ToolManager->GetWorkingData(0)) { m_ToolManager->GetWorkingData(0)->SetSelected(false); } newSegmentationNode->SetSelected(true); m_Controls->workingNodeSelector->SetCurrentSelectedNode(newSegmentationNode); } std::string QmitkSegmentationView::GetDefaultLabelSetPreset() const { auto labelSetPreset = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), ""); if (labelSetPreset.empty()) labelSetPreset = m_LabelSetPresetPreference.toStdString(); return labelSetPreset; } void QmitkSegmentationView::OnManualTool2DSelected(int id) { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); if (id >= 0) { std::string text = "Active Tool: \""; text += m_ToolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } } void QmitkSegmentationView::OnShowMarkerNodes(bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = m_ToolManager->GetTools().size(); for (unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast<mitk::SegTool2D*>(m_ToolManager->GetToolById(i)); if (nullptr == manualSegmentationTool) { continue; } manualSegmentationTool->SetShowMarkerNodes(state); } } void QmitkSegmentationView::OnCurrentLabelSelectionChanged(QmitkMultiLabelManager::LabelValueVectorType labels) { auto segmentation = this->GetCurrentSegmentation(); const auto labelValue = labels.front(); const auto groupID = segmentation->GetGroupIndexOfLabel(labelValue); if (groupID != segmentation->GetActiveLayer()) segmentation->SetActiveLayer(groupID); if (labelValue != segmentation->GetActiveLabelSet()->GetActiveLabel()->GetValue()) segmentation->GetActiveLabelSet()->SetActiveLabel(labelValue); segmentation->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnGoToLabel(mitk::LabelSetImage::LabelValueType /*label*/, const mitk::Point3D& pos) { if (m_RenderWindowPart) { m_RenderWindowPart->SetSelectedPosition(pos); } } void QmitkSegmentationView::OnLabelRenameRequested(mitk::Label* label, bool rename) const { auto segmentation = this->GetCurrentSegmentation(); if (rename) { QmitkNewSegmentationDialog::DoRenameLabel(label, segmentation, this->m_Parent, QmitkNewSegmentationDialog::Mode::RenameLabel); return; } QmitkNewSegmentationDialog::DoRenameLabel(label, nullptr, this->m_Parent, QmitkNewSegmentationDialog::Mode::NewLabel); } mitk::LabelSetImage* QmitkSegmentationView::GetCurrentSegmentation() const { auto workingNode = m_Controls->workingNodeSelector->GetSelectedNode(); if (workingNode.IsNull()) mitkThrow() << "Segmentation view is in an invalid state. Working node is null, but a label selection change has been triggered."; auto segmentation = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData()); if (nullptr == segmentation) mitkThrow() << "Segmentation view is in an invalid state. Working node contains no segmentation, but a label selection change has been triggered."; return segmentation; } /**********************************************************************/ /* private */ /**********************************************************************/ void QmitkSegmentationView::CreateQtPartControl(QWidget* parent) { m_Parent = parent; m_Controls = new Ui::QmitkSegmentationViewControls; m_Controls->setupUi(parent); // *------------------------ // * SHORTCUTS // *------------------------ QShortcut* visibilityShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_H), parent); connect(visibilityShortcut, &QShortcut::activated, this, &Self::OnVisibilityShortcutActivated); QShortcut* labelToggleShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_L, Qt::CTRL | Qt::Key::Key_I), parent); connect(labelToggleShortcut, &QShortcut::activated, this, &Self::OnLabelToggleShortcutActivated); // *------------------------ // * DATA SELECTION WIDGETS // *------------------------ m_Controls->referenceNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->referenceNodeSelector->SetNodePredicate(m_ReferencePredicate); m_Controls->referenceNodeSelector->SetInvalidInfo("Select an image"); m_Controls->referenceNodeSelector->SetPopUpTitel("Select an image"); m_Controls->referenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation."); m_Controls->workingNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_Controls->workingNodeSelector->SetInvalidInfo("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpTitel("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected."); connect(m_Controls->referenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &Self::OnReferenceSelectionChanged); connect(m_Controls->workingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &Self::OnSegmentationSelectionChanged); // *------------------------ // * TOOLMANAGER // *------------------------ m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_ToolManager->SetDataStorage(*(this->GetDataStorage())); m_ToolManager->InitializeTools(); - QString segTools2D = tr("Add Subtract Lasso Fill Erase Close Paint Wipe 'Region Growing' 'Live Wire' MonaiLabel2D"); + QString segTools2D = tr("Add Subtract Lasso Fill Erase Close Paint Wipe 'Region Growing' 'Live Wire' 'Segment Anything' MonaiLabel2D"); QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking GrowCut TotalSegmentator MonaiLabel3D"); #ifdef __linux__ segTools3D.append(" nnUNet"); // plugin not enabled for MacOS / Windows #endif std::regex extSegTool2DRegEx("SegTool2D$"); std::regex extSegTool3DRegEx("SegTool3D$"); auto tools = m_ToolManager->GetTools(); for (const auto &tool : tools) { if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx)) { segTools2D.append(QString(" '%1'").arg(tool->GetName())); } else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx)) { segTools3D.append(QString(" '%1'").arg(tool->GetName())); } } // setup 2D tools m_Controls->toolSelectionBox2D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox2D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox2D->SetToolGUIArea(m_Controls->toolGUIArea2D); m_Controls->toolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); connect(m_Controls->toolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected, this, &Self::OnManualTool2DSelected); // setup 3D Tools m_Controls->toolSelectionBox3D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox3D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox3D->SetToolGUIArea(m_Controls->toolGUIArea3D); m_Controls->toolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); m_Controls->slicesInterpolator->SetDataStorage(this->GetDataStorage()); // create general signal / slot connections connect(m_Controls->newSegmentationButton, &QToolButton::clicked, this, &Self::OnNewSegmentation); connect(m_Controls->slicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &Self::OnShowMarkerNodes); connect(m_Controls->multiLabelWidget, &QmitkMultiLabelManager::CurrentSelectionChanged, this, &Self::OnCurrentLabelSelectionChanged); connect(m_Controls->multiLabelWidget, &QmitkMultiLabelManager::GoToLabel, this, &Self::OnGoToLabel); connect(m_Controls->multiLabelWidget, &QmitkMultiLabelManager::LabelRenameRequested, this, &Self::OnLabelRenameRequested); auto command = itk::SimpleMemberCommand<Self>::New(); command->SetCallbackFunction(this, &Self::ValidateSelectionInput); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command); m_RenderWindowPart = this->GetRenderWindowPart(); if (nullptr != m_RenderWindowPart) { this->RenderWindowPartActivated(m_RenderWindowPart); } // Make sure the GUI notices if appropriate data is already present on creation. // Should be done last, if everything else is configured because it triggers the autoselection of data. m_Controls->referenceNodeSelector->SetAutoSelectNewNodes(true); m_Controls->workingNodeSelector->SetAutoSelectNewNodes(true); this->UpdateGUI(); } void QmitkSegmentationView::ActiveToolChanged() { if (nullptr == m_RenderWindowPart) { return; } mitk::TimeGeometry* interactionReferenceGeometry = nullptr; auto activeTool = m_ToolManager->GetActiveTool(); if (nullptr != activeTool && m_ReferenceNode.IsNotNull()) { mitk::Image::ConstPointer referenceImage = dynamic_cast<mitk::Image *>(m_ReferenceNode->GetData()); if (referenceImage.IsNotNull()) { // tool activated, reference image available: set reference geometry interactionReferenceGeometry = m_ReferenceNode->GetData()->GetTimeGeometry(); } } // set the interaction reference geometry for the render window part (might be nullptr) m_RenderWindowPart->SetInteractionReferenceGeometry(interactionReferenceGeometry); } void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_RenderWindowPart != renderWindowPart) { m_RenderWindowPart = renderWindowPart; } if (nullptr != m_Parent) { m_Parent->setEnabled(true); } if (nullptr == m_Controls) { return; } if (nullptr != m_RenderWindowPart) { auto all2DWindows = Get2DWindows(m_RenderWindowPart->GetQmitkRenderWindows().values()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, all2DWindows); if (!m_RenderWindowPart->HasCoupledRenderWindows()) { // react if the active tool changed, only if a render window part with decoupled render windows is used m_ToolManager->ActiveToolChanged += mitk::MessageDelegate<Self>(this, &Self::ActiveToolChanged); } } } void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_RenderWindowPart = nullptr; if (nullptr != m_Parent) { m_Parent->setEnabled(false); } // remove message-connection to make sure no message is processed if no render window part is available m_ToolManager->ActiveToolChanged -= mitk::MessageDelegate<Self>(this, &Self::ActiveToolChanged); m_Controls->slicesInterpolator->Uninitialize(); } void QmitkSegmentationView::RenderWindowPartInputChanged(mitk::IRenderWindowPart* /*renderWindowPart*/) { if (nullptr == m_RenderWindowPart) { return; } m_Controls->slicesInterpolator->Uninitialize(); auto all2DWindows = Get2DWindows(m_RenderWindowPart->GetQmitkRenderWindows().values()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, all2DWindows); } void QmitkSegmentationView::OnPreferencesChanged(const mitk::IPreferences* prefs) { auto labelSuggestions = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), ""); m_DefaultLabelNaming = labelSuggestions.empty() ? prefs->GetBool("default label naming", true) : false; // No default label naming when label suggestions are enforced via command-line argument if (nullptr != m_Controls) { m_Controls->multiLabelWidget->SetDefaultLabelNaming(m_DefaultLabelNaming); bool compactView = prefs->GetBool("compact view", false); int numberOfColumns = compactView ? 6 : 4; m_Controls->toolSelectionBox2D->SetLayoutColumns(numberOfColumns); m_Controls->toolSelectionBox2D->SetShowNames(!compactView); m_Controls->toolSelectionBox3D->SetLayoutColumns(numberOfColumns); m_Controls->toolSelectionBox3D->SetShowNames(!compactView); } m_DrawOutline = prefs->GetBool("draw outline", true); m_SelectionMode = prefs->GetBool("selection mode", false); m_LabelSetPresetPreference = QString::fromStdString(prefs->Get("label set preset", "")); this->ApplyDisplayOptions(); this->ApplySelectionMode(); } void QmitkSegmentationView::NodeAdded(const mitk::DataNode* node) { if (m_SegmentationPredicate->CheckNode(node)) this->ApplyDisplayOptions(const_cast<mitk::DataNode*>(node)); this->ApplySelectionMode(); } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { if (!m_SegmentationPredicate->CheckNode(node)) { return; } // remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations( node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>(); mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData()); mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image); } void QmitkSegmentationView::ApplyDisplayOptions() { if (nullptr == m_Parent) { return; } if (nullptr == m_Controls) { return; // might happen on initialization (preferences loaded) } mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { this->ApplyDisplayOptions(*iter); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (nullptr == node) { return; } auto labelSetImage = dynamic_cast<mitk::LabelSetImage*>(node->GetData()); if (nullptr == labelSetImage) { return; } // the outline property can be set in the segmentation preference page node->SetProperty("labelset.contour.active", mitk::BoolProperty::New(m_DrawOutline)); // force render window update to show outline mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplySelectionMode() { if (!m_SelectionMode) return; this->ApplySelectionModeOnReferenceNode(); this->ApplySelectionModeOnWorkingNode(); } void QmitkSegmentationView::ApplySelectionModeOnReferenceNode() { this->ApplySelectionMode(m_ReferenceNode, m_ReferencePredicate); } void QmitkSegmentationView::ApplySelectionModeOnWorkingNode() { this->ApplySelectionMode(m_WorkingNode, m_SegmentationPredicate); } void QmitkSegmentationView::ApplySelectionMode(mitk::DataNode* node, mitk::NodePredicateBase* predicate) { if (!m_SelectionMode || node == nullptr || predicate == nullptr) return; auto nodes = this->GetDataStorage()->GetSubset(predicate); for (auto iter = nodes->begin(); iter != nodes->end(); ++iter) (*iter)->SetVisibility(*iter == node); } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode* node) { QmitkRenderWindow* selectedRenderWindow = nullptr; auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* axialRenderWindow = renderWindowPart->GetQmitkRenderWindow("axial"); auto* sagittalRenderWindow = renderWindowPart->GetQmitkRenderWindow("sagittal"); auto* coronalRenderWindow = renderWindowPart->GetQmitkRenderWindow("coronal"); auto* threeDRenderWindow = renderWindowPart->GetQmitkRenderWindow("3d"); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, threeDRenderWindow->GetRenderer())) { selectedRenderWindow = threeDRenderWindow; } // make node visible if (nullptr != selectedRenderWindow) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>(); mitk::PlanePositionManagerService* service = context->getService<mitk::PlanePositionManagerService>(ppmRef); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); context->ungetService(ppmRef); selectedRenderWindow->GetRenderer()->GetCameraController()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes) { if (0 == nodes.size()) { return; } std::string markerName = "Position"; unsigned int numberOfNodes = nodes.size(); std::string nodeName = nodes.at(0)->GetName(); if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0)) { this->OnContourMarkerSelected(nodes.at(0)); return; } } void QmitkSegmentationView::ResetMouseCursor() { if (m_MouseCursorSet) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkSegmentationView::SetMouseCursor(const us::ModuleResource& resource, int hotspotX, int hotspotY) { // Remove previously set mouse cursor if (m_MouseCursorSet) { this->ResetMouseCursor(); } if (resource) { us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY); m_MouseCursorSet = true; } } void QmitkSegmentationView::UpdateGUI() { mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0); bool hasReferenceNode = referenceNode != nullptr; mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); bool hasWorkingNode = workingNode != nullptr; m_Controls->newSegmentationButton->setEnabled(false); if (hasReferenceNode) { m_Controls->newSegmentationButton->setEnabled(true); } if (hasWorkingNode && hasReferenceNode) { int layer = -1; referenceNode->GetIntProperty("layer", layer); workingNode->SetIntProperty("layer", layer + 1); } this->ValidateSelectionInput(); } void QmitkSegmentationView::ValidateSelectionInput() { auto referenceNode = m_Controls->referenceNodeSelector->GetSelectedNode(); auto workingNode = m_Controls->workingNodeSelector->GetSelectedNode(); bool hasReferenceNode = referenceNode.IsNotNull(); bool hasWorkingNode = workingNode.IsNotNull(); bool hasBothNodes = hasReferenceNode && hasWorkingNode; QString warning; bool toolSelectionBoxesEnabled = hasReferenceNode && hasWorkingNode; unsigned int numberOfLabels = 0; m_Controls->multiLabelWidget->setEnabled(hasWorkingNode); m_Controls->toolSelectionBox2D->setEnabled(hasBothNodes); m_Controls->toolSelectionBox3D->setEnabled(hasBothNodes); m_Controls->slicesInterpolator->setEnabled(false); m_Controls->interpolatorWarningLabel->hide(); if (hasReferenceNode) { if (nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows() && !referenceNode->IsVisible(nullptr)) { warning += tr("The selected reference image is currently not visible!"); toolSelectionBoxesEnabled = false; } } if (hasWorkingNode) { if (nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows() && !workingNode->IsVisible(nullptr)) { warning += (!warning.isEmpty() ? " " : "") + tr("The selected segmentation is currently not visible!"); toolSelectionBoxesEnabled = false; } m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(workingNode); m_Controls->multiLabelWidget->setEnabled(true); m_Controls->toolSelectionBox2D->setEnabled(true); m_Controls->toolSelectionBox3D->setEnabled(true); auto labelSetImage = dynamic_cast<mitk::LabelSetImage *>(workingNode->GetData()); numberOfLabels = labelSetImage->GetTotalNumberOfLabels(); if (numberOfLabels > 0) m_Controls->slicesInterpolator->setEnabled(true); m_Controls->multiLabelWidget->SetMultiLabelSegmentation(dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData())); } else { m_Controls->multiLabelWidget->SetMultiLabelSegmentation(nullptr); } toolSelectionBoxesEnabled &= numberOfLabels > 0; // Here we need to check whether the geometry of the selected segmentation image (working image geometry) // is aligned with the geometry of the 3D render window. // It is not allowed to use a geometry different from the working image geometry for segmenting. // We only need to this if the tool selection box would be enabled without this check. // Additionally this check only has to be performed for render window parts with coupled render windows. // For different render window parts the user is given the option to reinitialize each render window individually // (see QmitkRenderWindow::ShowOverlayMessage). if (toolSelectionBoxesEnabled && nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows()) { const mitk::BaseGeometry* workingNodeGeometry = workingNode->GetData()->GetGeometry(); const mitk::BaseGeometry* renderWindowGeometry = m_RenderWindowPart->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (nullptr != workingNodeGeometry && nullptr != renderWindowGeometry) { if (!mitk::Equal(*workingNodeGeometry->GetBoundingBox(), *renderWindowGeometry->GetBoundingBox(), mitk::eps, true)) { warning += (!warning.isEmpty() ? " " : "") + tr("Please reinitialize the selected segmentation image!"); toolSelectionBoxesEnabled = false; } } } m_Controls->toolSelectionBox2D->setEnabled(toolSelectionBoxesEnabled); m_Controls->toolSelectionBox3D->setEnabled(toolSelectionBoxesEnabled); this->UpdateWarningLabel(warning); m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(workingNode); } void QmitkSegmentationView::UpdateWarningLabel(QString text) { if (text.isEmpty()) { m_Controls->selectionWarningLabel->hide(); } else { m_Controls->selectionWarningLabel->setText("" + text + ""); m_Controls->selectionWarningLabel->show(); } } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h index 0d71e0274c..a4f3ea2571 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h @@ -1,175 +1,175 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSegmentationView_h #define QmitkSegmentationView_h #include "ui_QmitkSegmentationViewControls.h" #include <QmitkAbstractView.h> #include <mitkIRenderWindowPartListener.h> /** * @brief The segmentation view provides a set of tool to use different segmentation algorithms. * It provides two selection widgets to load an image node and a segmentation node * on which to perform the segmentation. Creating new segmentation nodes is also possible. * The available segmentation tools are grouped into "2D"- and "3D"-tools. * * Most segmentation tools / algorithms need some kind of user interaction, where the * user is asked to draw something in the image display or set some seed points / start values. -* The tools also often provide additional propeties so that a user can modify the +* The tools also often provide additional properties so that a user can modify the * algorithm's behavior. * * This class additionally provides options to work with different layers (create new layers, * switch between layers). * Moreover, a multilabel widget displays all the existing labels of a multilabel segmentation * for the currently active layer. -* The multilabel widget allows to control the labels by creatin new one, removing existing ones, +* The multilabel widget allows to control the labels by creating new ones, removing existing ones, * showing / hiding single labels, merging labels, (re-)naming them etc. * * Additionally the view provides an option to create "2D"- and "3D"-interpolations between * neighboring segmentation masks on unsegmented slices. * Interpolation for multilabel segmentations is currently not implemented. */ class QmitkSegmentationView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { Q_OBJECT public: static const std::string VIEW_ID; QmitkSegmentationView(); ~QmitkSegmentationView() override; private Q_SLOTS: // reaction to the selection of a new reference image in the selection widget void OnReferenceSelectionChanged(QList<mitk::DataNode::Pointer> nodes); // reaction to the selection of a new segmentation image in the selection widget void OnSegmentationSelectionChanged(QList<mitk::DataNode::Pointer> nodes); // reaction to the shortcut ("CTRL+H") for toggling the visibility of the working node void OnVisibilityShortcutActivated(); // reaction to the shortcut ("CTRL+L") for iterating over all labels void OnLabelToggleShortcutActivated(); // reaction to the button "New segmentation" void OnNewSegmentation(); void OnManualTool2DSelected(int id); void OnShowMarkerNodes(bool); void OnCurrentLabelSelectionChanged(QmitkMultiLabelManager::LabelValueVectorType labels); void OnGoToLabel(mitk::LabelSetImage::LabelValueType label, const mitk::Point3D&); void OnLabelRenameRequested(mitk::Label* label, bool rename) const; void OnLabelAdded(mitk::LabelSetImage::LabelValueType labelValue); void OnLabelRemoved(mitk::LabelSetImage::LabelValueType labelValue); void OnGroupRemoved(mitk::LabelSetImage::GroupIndexType groupIndex); private: using Self = QmitkSegmentationView; mitk::LabelSetImage* GetWorkingImage(); void AddObserversToWorkingImage(); void RemoveObserversFromWorkingImage(); void CreateQtPartControl(QWidget* parent) override; void SetFocus() override {} /** * @brief Enable or disable the SegmentationInteractor. * * The active tool is retrieved from the tool manager. * If the active tool is valid, the SegmentationInteractor is enabled * to listen to 'SegmentationInteractionEvent's. */ void ActiveToolChanged(); void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderWindowPart) override; void OnPreferencesChanged(const mitk::IPreferences* prefs) override; void NodeAdded(const mitk::DataNode* node) override; void NodeRemoved(const mitk::DataNode* node) override; void OnAnySelectionChanged(); // make sure all images / segmentations look according to the user preference settings void ApplyDisplayOptions(); // decorates a DataNode according to the user preference settings void ApplyDisplayOptions(mitk::DataNode* node); void ApplySelectionMode(); void ApplySelectionModeOnReferenceNode(); void ApplySelectionModeOnWorkingNode(); void ApplySelectionMode(mitk::DataNode* node, mitk::NodePredicateBase* predicate); // If a contourmarker is selected, the plane in the related widget will be reoriented according to the marker`s geometry void OnContourMarkerSelected(const mitk::DataNode* node); void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer> &nodes) override; void ResetMouseCursor(); void SetMouseCursor(const us::ModuleResource&, int hotspotX, int hotspotY); void UpdateGUI(); void ValidateSelectionInput(); void UpdateWarningLabel(QString text); std::string GetDefaultLabelSetPreset() const; mitk::LabelSetImage* GetCurrentSegmentation() const; QWidget* m_Parent; Ui::QmitkSegmentationViewControls* m_Controls; mitk::IRenderWindowPart* m_RenderWindowPart; mitk::ToolManager* m_ToolManager; mitk::DataNode::Pointer m_ReferenceNode; mitk::DataNode::Pointer m_WorkingNode; typedef std::map<mitk::DataNode*, unsigned long> NodeTagMapType; NodeTagMapType m_WorkingDataObserverTags; NodeTagMapType m_ReferenceDataObserverTags; unsigned int m_RenderingManagerObserverTag; mitk::NodePredicateAnd::Pointer m_ReferencePredicate; mitk::NodePredicateAnd::Pointer m_SegmentationPredicate; bool m_DrawOutline; bool m_SelectionMode; bool m_MouseCursorSet; QString m_LabelSetPresetPreference; bool m_DefaultLabelNaming; bool m_SelectionChangeIsAlreadyBeingHandled; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp index 70ab9cfbb3..8bbb2fd9f7 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp @@ -1,80 +1,82 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkPluginActivator.h" #include "QmitkSegmentationView.h" #include "QmitkSegmentationPreferencePage.h" +#include "QmitkSegmentAnythingPreferencePage.h" #include "QmitkSegmentationUtilitiesView.h" #include "QmitkSegmentationTaskListView.h" #include "QmitkAutocropAction.h" #include "QmitkAutocropLabelSetImageAction.h" #include "QmitkCreatePolygonModelAction.h" #include "QmitkLoadMultiLabelPresetAction.h" #include "QmitkSaveMultiLabelPresetAction.h" #include "QmitkConvertSurfaceToLabelAction.h" #include "QmitkConvertMaskToLabelAction.h" #include "QmitkConvertToMultiLabelSegmentationAction.h" #include "QmitkCreateMultiLabelSegmentationAction.h" #include <usModuleInitialization.h> US_INITIALIZE_MODULE using namespace mitk; ctkPluginContext* PluginActivator::m_context = nullptr; PluginActivator* PluginActivator::m_Instance = nullptr; PluginActivator::PluginActivator() { m_Instance = this; } PluginActivator::~PluginActivator() { m_Instance = nullptr; } void PluginActivator::start(ctkPluginContext *context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationPreferencePage, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentAnythingPreferencePage, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationUtilitiesView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationTaskListView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkAutocropAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkAutocropLabelSetImageAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkCreatePolygonModelAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkLoadMultiLabelPresetAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkSaveMultiLabelPresetAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConvertSurfaceToLabelAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConvertMaskToLabelAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConvertToMultiLabelSegmentationAction, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkCreateMultiLabelSegmentationAction, context) this->m_context = context; } void PluginActivator::stop(ctkPluginContext *) { this->m_context = nullptr; } PluginActivator* PluginActivator::getDefault() { return m_Instance; } ctkPluginContext*PluginActivator::getContext() { return m_context; } diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h index 4e41188322..9fbf842373 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h @@ -1,69 +1,69 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkDataNodeAddToSemanticRelationsAction_h #define QmitkDataNodeAddToSemanticRelationsAction_h #include <org_mitk_gui_qt_semanticrelations_Export.h> // mitk gui qt application plugin #include <QmitkAbstractDataNodeAction.h> // qt #include <QAction> namespace AddToSemanticRelationsAction { /** * @brief The function checks whether the given node is an image or a segmentation and calls the corresponding add function. * The corresponding add functions will add the data node to the semantic relations storage. * If an image is added, the 'AddImage' function will check if another image at the fitting control-point - information type cell * already exists. If so, the user is prompted to overwrite the existing image or abort the process. * If the user wants to overwrite the existing image, the image and it's corresponding segmentation nodes will be removed from the semantic relations storage. * If a segmentation is added, the parent image node will also be to the semantic relations storage. If the segmentation does not contain the required DICOM information, - * the DICOM information of the parent data will be transfered to the segmentation data. + * the DICOM information of the parent data will be transferred to the segmentation data. * * @pre The given dataStorage has to be valid (!nullptr). * @pre The given dataNode has to be valid (!nullptr). * The function simply returns if the preconditions are not met. * * @throw SemanticRelationException re-thrown. * * @param dataStorage The data storage to use for to remove the existing image and to check for the parent image node of a segmentation. * @param dataNode The data node to add. */ MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::DataStorage* dataStorage, const mitk::DataNode* image); void AddImage(mitk::DataStorage* dataStorage, const mitk::DataNode* image); void AddSegmentation(mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation); } class MITK_GUI_SEMANTICRELATIONS_EXPORT QmitkDataNodeAddToSemanticRelationsAction : public QAction, public QmitkAbstractDataNodeAction { Q_OBJECT public: QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite); QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite); private Q_SLOTS: void OnActionTriggered(bool); protected: void InitializeAction() override; }; #endif diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h index 8df9d19e23..639d04c265 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h @@ -1,106 +1,106 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSemanticRelationsView_h #define QmitkSemanticRelationsView_h // semantic relations plugin #include "ui_QmitkSemanticRelationsControls.h" #include "QmitkLesionInfoWidget.h" #include "QmitkSemanticRelationsContextMenu.h" // semantic relations module #include <mitkSemanticTypes.h> // semantic relations UI module #include <QmitkPatientTableInspector.h> // mitk gui common plugin #include <mitkIRenderWindowPartListener.h> // berry #include <berryISelectionListener.h> // mitk qt gui common plugin #include <QmitkAbstractView.h> class QmitkDnDDataNodeWidget; class QMenu; /* * @brief The QmitkSemanticRelationsView is an MITK view to combine and show the widgets of the 'SemanticRelationsUI'-module and this semantic relations plugin. * * It allows the MITK user to see and modify the content of the SemanticRelations-session. * A combo box is used to select and show the current patient. */ class QmitkSemanticRelationsView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { Q_OBJECT public: static const std::string VIEW_ID; void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderWindowPart) override; protected: void SetFocus() override; void CreateQtPartControl(QWidget* parent) override; private Q_SLOTS: void OnLesionSelectionChanged(const mitk::SemanticTypes::Lesion&); void OnDataNodeSelectionChanged(const QList<mitk::DataNode::Pointer>&); void OnDataNodeDoubleClicked(const mitk::DataNode*); void OnCaseIDSelectionChanged(const QString&); void OnNodesAdded(std::vector<mitk::DataNode*>); void OnNodeRemoved(const mitk::DataNode*); private: void SetUpConnections(); /** * @brief Provide a QItemSelectionModel, which supports the data role 'QmitkDataNodeRole' (\see QmitkRenderWindowDataModel). * * The provided QItemSelectionModel is used in the QmitkAbstractView-base class as the selection model of * the selection provider (\see QmitkAbstractView::SetSelectionProvider()). * The default selection provider is a QmitkDataNodeSelectionProvider. Each time a selection in the provided - * QItemSeletionModel is changed, a selection changed event is fired. All plugins (views), that subclass the + * QItemSelectionModel is changed, a selection changed event is fired. All plugins (views), that subclass the * QmitkAbstractView will be informed about the selection changed via the OnSelectionChanged-function. */ QItemSelectionModel* GetDataNodeSelectionModel() const override; void NodeRemoved(const mitk::DataNode* dataNode) override; void AddToComboBox(const mitk::SemanticTypes::CaseID& caseID); void RemoveFromComboBox(const mitk::SemanticTypes::CaseID& caseID); void OpenInEditor(const mitk::DataNode* dataNode); void SetControlledRenderer(); Ui::QmitkSemanticRelationsControls m_Controls; mitk::IRenderWindowPart* m_RenderWindowPart; QmitkLesionInfoWidget* m_LesionInfoWidget; QmitkPatientTableInspector* m_PatientTableInspector; QmitkDnDDataNodeWidget* m_DnDDataNodeWidget; QmitkSemanticRelationsContextMenu* m_ContextMenu; }; #endif diff --git a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/plugin.xml b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/plugin.xml index 596b89bd5c..20ad7f0e3b 100644 --- a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/plugin.xml +++ b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/plugin.xml @@ -1,29 +1,29 @@ <?xml version="1.0" encoding="UTF-8"?> <?eclipse version="3.0"?> <plugin> <extension point="org.blueberry.ui.editors"> <editor id="org.mitk.editors.stdmultiwidget" name="Standard Display" icon="resources/StdMultiWidgetEditor.svg" extensions="mitk" default="true" class="QmitkStdMultiWidgetEditor"> </editor> </extension> <extension point="org.blueberry.ui.preferencePages"> <page id="org.mitk.StdMultiWidgetEditorPreferencePage" name="Standard Multi Widget" class="QmitkStdMultiWidgetEditorPreferencePage" category="org.mitk.EditorsPreferencePage"> <keywordreference id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords"/> </page> </extension> <extension point="org.blueberry.ui.keywords"> - <keyword id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords" label="zooming panning contraint"/> + <keyword id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords" label="zooming panning constraint"/> <keyword id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords" label="show level window widget"/> <keyword id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords" label="pacs like mouse interaction select left mouse button action"/> <keyword id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords" label="rendering mode fxaa anti-aliasing"/> <keyword id="org.mitk.StdMultiWidgetEditorPreferencePageKeywords" label="crosshair gap size background decoration color corner annotation"/> </extension> </plugin> diff --git a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/src/internal/QmitkStdMultiWidgetEditorPreferencePage.ui b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/src/internal/QmitkStdMultiWidgetEditorPreferencePage.ui index 646add5dc0..82950ccf70 100644 --- a/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/src/internal/QmitkStdMultiWidgetEditorPreferencePage.ui +++ b/Plugins/org.mitk.gui.qt.stdmultiwidgeteditor/src/internal/QmitkStdMultiWidgetEditorPreferencePage.ui @@ -1,195 +1,195 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkStdMultiWidgetEditorPreferencePage</class> <widget class="QWidget" name="QmitkStdMultiWidgetEditorPreferencePage"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>518</width> <height>330</height> </rect> </property> <property name="windowTitle"> <string>External Programs</string> </property> <layout class="QGridLayout" name="gridLayout"> <item row="11" column="0"> <widget class="QLabel" name="label_8"> <property name="toolTip"> <string>The small text on the button left of each renderwindow.</string> </property> <property name="text"> <string>Corner annotation</string> </property> </widget> </item> <item row="2" column="0" colspan="3"> <widget class="QCheckBox" name="m_PACSLikeMouseMode"> <property name="layoutDirection"> <enum>Qt::LeftToRight</enum> </property> <property name="text"> <string>Use PACS like mouse interaction (select left mouse button action)</string> </property> <property name="tristate"> <bool>false</bool> </property> </widget> </item> <item row="0" column="0" colspan="3"> <widget class="QCheckBox" name="m_EnableFlexibleZooming"> <property name="toolTip"> - <string><html><head/><body>If activated, zooming and panning is limited to a certain space arround each image.</body></html></string> + <string><html><head/><body>If activated, zooming and panning is limited to a certain space around each image.</body></html></string> </property> <property name="layoutDirection"> <enum>Qt::LeftToRight</enum> </property> <property name="text"> <string>Use constraint zooming and panning</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="8" column="0"> <widget class="QLabel" name="label_2"> <property name="toolTip"> <string><html><head/><body>If two colors are set, a gradient background is generated.</body></html></string> </property> <property name="text"> <string>Background color</string> </property> </widget> </item> <item row="6" column="0"> <widget class="QLabel" name="label_9"> <property name="toolTip"> <string><html><head/><body>The gap in the middle of the crosshair in pixels.</body></html></string> </property> <property name="text"> <string>Crosshair gap size</string> </property> </widget> </item> <item row="8" column="2"> <widget class="QPushButton" name="m_ColorButton2"> <property name="text"> <string/> </property> </widget> </item> <item row="3" column="0" colspan="3"> <widget class="Line" name="line"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> </widget> </item> <item row="10" column="1"> <widget class="QPushButton" name="m_RenderWindowDecorationColor"> <property name="text"> <string/> </property> </widget> </item> <item row="6" column="1"> <widget class="QSpinBox" name="m_CrosshairGapSize"> <property name="value"> <number>32</number> </property> </widget> </item> <item row="10" column="0"> <widget class="QLabel" name="label_7"> <property name="toolTip"> <string><html><head/><body>The color is used for the following decorations (of each renderwindow):Rectangle borderCorner annotationCrosshairPlane geometry helper objects (3D Planes)Image navigator borders </body></html></string> </property> <property name="text"> <string>Decoration color</string> </property> </widget> </item> <item row="12" column="0"> <widget class="QPushButton" name="m_ResetButton"> <property name="text"> <string>Reset preferences</string> </property> </widget> </item> <item row="1" column="0" colspan="3"> <widget class="QCheckBox" name="m_ShowLevelWindowWidget"> <property name="layoutDirection"> <enum>Qt::LeftToRight</enum> </property> <property name="text"> <string>Show level/window widget</string> </property> <property name="checked"> <bool>true</bool> </property> </widget> </item> <item row="7" column="0"> <widget class="QLabel" name="label_6"> <property name="toolTip"> <string><html><head/><body>Choose the renderwindow from the multi widget.</body></html></string> </property> <property name="text"> <string>Render windows</string> </property> </widget> </item> <item row="8" column="1"> <widget class="QPushButton" name="m_ColorButton1"> <property name="text"> <string/> </property> </widget> </item> <item row="11" column="1" colspan="2"> <widget class="QLineEdit" name="m_RenderWindowDecorationText"/> </item> <item row="13" column="0"> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item row="7" column="1"> <widget class="QComboBox" name="m_RenderWindowChooser"> <item> <property name="text"> <string>stdmulti.widget0</string> </property> </item> <item> <property name="text"> <string>stdmulti.widget1</string> </property> </item> <item> <property name="text"> <string>stdmulti.widget2</string> </property> </item> <item> <property name="text"> <string>stdmulti.widget3</string> </property> </item> </widget> </item> </layout> </widget> <resources/> <connections/> </ui> diff --git a/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFScreenshotMaker.cpp b/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFScreenshotMaker.cpp index 4f4f60a21f..1675dfdcc5 100644 --- a/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFScreenshotMaker.cpp +++ b/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFScreenshotMaker.cpp @@ -1,144 +1,144 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Qmitk #include "QmitkToFScreenshotMaker.h" #include <QmitkServiceListWidget.h> // Mitk #include <mitkToFCameraDevice.h> #include <mitkIOUtil.h> // Qt #include <QString> #include <QStringList> #include <QMessageBox> const std::string QmitkToFScreenshotMaker::VIEW_ID = "org.mitk.views.tofscreenshotmaker"; QmitkToFScreenshotMaker::QmitkToFScreenshotMaker() : QmitkAbstractView(), m_SavingCounter(0) { } QmitkToFScreenshotMaker::~QmitkToFScreenshotMaker() { } void QmitkToFScreenshotMaker::SetFocus() { } void QmitkToFScreenshotMaker::CreateQtPartControl( QWidget *parent ) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi( parent ); connect( (QObject*)(m_Controls.m_MakeScreenshot), SIGNAL(clicked()), this, SLOT(OnMakeScreenshotClicked()) ); connect( m_Controls.m_ConnectedDeviceServiceListWidget, SIGNAL(ServiceSelectionChanged(us::ServiceReferenceU)), this, SLOT(OnSelectCamera())); std::string filter = ""; m_Controls.m_ConnectedDeviceServiceListWidget->Initialize<mitk::ToFImageSource>("ToFImageSourceName", filter); std::string defaultPath = "/tmp/"; #ifdef _WIN32 defaultPath = "C:/tmp/"; #endif m_Controls.m_PathToSaveFiles->setText(defaultPath.c_str()); } void QmitkToFScreenshotMaker::OnSelectCamera() { //Update gui according to device properties mitk::ToFImageGrabber* source = static_cast<mitk::ToFImageGrabber*>(m_Controls.m_ConnectedDeviceServiceListWidget->GetSelectedService<mitk::ToFImageSource>()); mitk::ToFCameraDevice* device = source->GetCameraDevice(); m_Controls.m_MakeScreenshot->setEnabled(device->IsCameraActive()); //todo: where do i get correct file extensions? std::vector<std::string> fileExtensions; fileExtensions.push_back(".png"); fileExtensions.push_back(".nrrd"); fileExtensions.push_back(".jpg"); QStringList extensions; for( unsigned int i = 0; i < fileExtensions.size(); ++i) { extensions.append(QString(fileExtensions.at(i).c_str())); } this->UpdateGUIElements(device, "no depth property available", m_Controls.m_SaveDepth, m_Controls.m_DepthFormat, extensions, ".nrrd"); //usually you want to save depth data, but there is no "HasDepthImage" property, because every depth - //camera should provide a depth iamge + //camera should provide a depth image m_Controls.m_SaveDepth->setChecked(true); m_Controls.m_SaveDepth->setEnabled(true); m_Controls.m_DepthFormat->setEnabled(true); this->UpdateGUIElements(device, "HasAmplitudeImage", m_Controls.m_SaveAmplitude , m_Controls.m_AmplitudeFormat, extensions, ".nrrd"); this->UpdateGUIElements(device, "HasIntensityImage", m_Controls.m_SaveIntensity, m_Controls.m_IntensityFormat, extensions, ".nrrd"); this->UpdateGUIElements(device, "HasRGBImage", m_Controls.m_SaveColor, m_Controls.m_ColorFormat, extensions, ".png"); //png is nice default for calibration this->UpdateGUIElements(device, "HasRawImage", m_Controls.m_SaveRaw, m_Controls.m_RawFormat, extensions, ".nrrd"); } void QmitkToFScreenshotMaker::UpdateGUIElements(mitk::ToFCameraDevice* device, const char* ToFImageType, QCheckBox* saveCheckBox, QComboBox* saveTypeComboBox, QStringList fileExentions, const char* preferredFormat) { bool isTypeProvidedByDevice = false; device->GetBoolProperty(ToFImageType, isTypeProvidedByDevice); saveCheckBox->setChecked(isTypeProvidedByDevice); saveCheckBox->setEnabled(isTypeProvidedByDevice); saveTypeComboBox->clear(); saveTypeComboBox->setEnabled(isTypeProvidedByDevice); saveTypeComboBox->addItems(fileExentions); int index = saveTypeComboBox->findText(preferredFormat); if ( index != -1 ) { // -1 for not found saveTypeComboBox->setCurrentIndex(index); } } void QmitkToFScreenshotMaker::OnMakeScreenshotClicked() { mitk::ToFImageGrabber* source = static_cast<mitk::ToFImageGrabber*>(m_Controls.m_ConnectedDeviceServiceListWidget->GetSelectedService<mitk::ToFImageSource>()); source->Update(); //### Save Images this->SaveImage(source->GetOutput(0), m_Controls.m_SaveDepth->isChecked(), m_Controls.m_PathToSaveFiles->text().toStdString(), std::string("Depth_"), m_Controls.m_DepthFormat->currentText().toStdString()); this->SaveImage(source->GetOutput(1), m_Controls.m_SaveAmplitude->isChecked(), m_Controls.m_PathToSaveFiles->text().toStdString(), std::string("Amplitude_"), m_Controls.m_AmplitudeFormat->currentText().toStdString()); this->SaveImage(source->GetOutput(2), m_Controls.m_SaveIntensity->isChecked(), m_Controls.m_PathToSaveFiles->text().toStdString(), std::string("Intensity_"), m_Controls.m_IntensityFormat->currentText().toStdString()); this->SaveImage(source->GetOutput(3), m_Controls.m_SaveColor->isChecked(), m_Controls.m_PathToSaveFiles->text().toStdString(), std::string("Color_"), m_Controls.m_ColorFormat->currentText().toStdString()); //todo, where is the raw data? //todo what about the surface or pre-processed data? m_SavingCounter++; } void QmitkToFScreenshotMaker::SaveImage(mitk::Image::Pointer image, bool saveImage, std::string path, std::string name, std::string extension) { if(saveImage) { std::stringstream outdepthimage; outdepthimage << path << name<< m_SavingCounter << extension; mitk::IOUtil::Save( image, outdepthimage.str() ); } } diff --git a/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFUtilView.cpp b/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFUtilView.cpp index 6395f6f164..f5148f105a 100644 --- a/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFUtilView.cpp +++ b/Plugins/org.mitk.gui.qt.tofutil/src/internal/QmitkToFUtilView.cpp @@ -1,536 +1,536 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include <mitkIRenderWindowPart.h> #include <mitkILinkedRenderWindowPart.h> // Qmitk #include "QmitkToFUtilView.h" // Qt #include <QMessageBox> #include <QString> #include <qmessagebox.h> #include <qfiledialog.h> #include <qcombobox.h> // MITK #include <mitkBaseRenderer.h> #include <mitkToFDistanceImageToPointSetFilter.h> #include <mitkTransferFunction.h> #include <mitkTransferFunctionProperty.h> #include <mitkToFDeviceFactoryManager.h> #include <mitkToFCameraDevice.h> #include <mitkCameraIntrinsicsProperty.h> #include <mitkSmartPointerProperty.h> #include <mitkRenderingModeProperty.h> #include <mitkVtkScalarModeProperty.h> // VTK #include <vtkCamera.h> #include <vtkPointData.h> #include <vtkPolyData.h> // ITK #include <itkCommand.h> #include <itksys/SystemTools.hxx> const std::string QmitkToFUtilView::VIEW_ID = "org.mitk.views.tofutil"; //Constructor QmitkToFUtilView::QmitkToFUtilView() : QmitkAbstractView() , m_Controls(nullptr) , m_Framerateoutput(false) , m_MitkDistanceImage(nullptr), m_MitkAmplitudeImage(nullptr), m_MitkIntensityImage(nullptr), m_Surface(nullptr) , m_DistanceImageNode(nullptr), m_AmplitudeImageNode(nullptr), m_IntensityImageNode(nullptr), m_RGBImageNode(nullptr), m_SurfaceNode(nullptr) , m_ToFImageRecorder(nullptr), m_ToFImageGrabber(nullptr), m_ToFDistanceImageToSurfaceFilter(nullptr), m_ToFCompositeFilter(nullptr) , m_2DDisplayCount(0) , m_RealTimeClock(nullptr) , m_StepsForFramerate(100) , m_2DTimeBefore(0.0) , m_2DTimeAfter(0.0) , m_CameraIntrinsics(nullptr) { this->m_Frametimer = new QTimer(this); this->m_ToFDistanceImageToSurfaceFilter = mitk::ToFDistanceImageToSurfaceFilter::New(); this->m_ToFCompositeFilter = mitk::ToFCompositeFilter::New(); this->m_ToFImageRecorder = mitk::ToFImageRecorder::New(); } //Destructor, specifically calling OnToFCameraStopped() and OnToFCammeraDiconnected() QmitkToFUtilView::~QmitkToFUtilView() { OnToFCameraStopped(); OnToFCameraDisconnected(); } -//Createing the PartControl Signal-Slot principal +//Creating the PartControl Signal-Slot principal void QmitkToFUtilView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkToFUtilViewControls; m_Controls->setupUi( parent ); //Looking for Input and Defining reaction connect(m_Frametimer, SIGNAL(timeout()), this, SLOT(OnUpdateCamera())); connect( (QObject*)(m_Controls->m_ToFConnectionWidget), SIGNAL(KinectAcquisitionModeChanged()), this, SLOT(OnKinectAcquisitionModeChanged()) ); // Todo in Widget2 connect( (QObject*)(m_Controls->m_ToFConnectionWidget), SIGNAL(ToFCameraConnected()), this, SLOT(OnToFCameraConnected()) ); connect( (QObject*)(m_Controls->m_ToFConnectionWidget), SIGNAL(ToFCameraDisconnected()), this, SLOT(OnToFCameraDisconnected()) ); connect( (QObject*)(m_Controls->m_ToFRecorderWidget), SIGNAL(ToFCameraStarted()), this, SLOT(OnToFCameraStarted()) ); connect( (QObject*)(m_Controls->m_ToFRecorderWidget), SIGNAL(ToFCameraStopped()), this, SLOT(OnToFCameraStopped()) ); connect( (QObject*)(m_Controls->m_ToFRecorderWidget), SIGNAL(RecordingStarted()), this, SLOT(OnToFCameraStopped()) ); connect( (QObject*)(m_Controls->m_ToFRecorderWidget), SIGNAL(RecordingStopped()), this, SLOT(OnToFCameraStarted()) ); } } -//SetFocus-Method -> actually seting Focus to the Recorder +//SetFocus-Method -> actually setting Focus to the Recorder void QmitkToFUtilView::SetFocus() { m_Controls->m_ToFRecorderWidget->setFocus(); } //Activated-Method->Generating RenderWindow void QmitkToFUtilView::Activated() { //get the current RenderWindowPart or open a new one if there is none auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); if (nullptr != renderWindowPart) { auto* linkedRenderWindowPart = dynamic_cast<mitk::ILinkedRenderWindowPart*>(renderWindowPart); if (linkedRenderWindowPart == nullptr) { - MITK_ERROR << "No linked render window part avaiable!!!"; + MITK_ERROR << "No linked render window part available!!!"; } else { linkedRenderWindowPart->EnableSlicingPlanes(false); } renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetDefaultViewDirection(mitk::AnatomicalPlane::Axial); renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SliceLockedOn(); renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SetDefaultViewDirection(mitk::AnatomicalPlane::Axial); renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SliceLockedOn(); renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SetDefaultViewDirection(mitk::AnatomicalPlane::Axial); renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SliceLockedOn(); mitk::RenderingManager::GetInstance()->InitializeViews(); this->UseToFVisibilitySettings(true); if (this->m_ToFCompositeFilter) { m_Controls->m_ToFCompositeFilterWidget->SetToFCompositeFilter(this->m_ToFCompositeFilter); } if (this->GetDataStorage()) { m_Controls->m_ToFCompositeFilterWidget->SetDataStorage(this->GetDataStorage()); } if (this->m_ToFImageGrabber.IsNull()) { m_Controls->m_ToFRecorderWidget->setEnabled(false); m_Controls->m_ToFVisualisationSettingsWidget->setEnabled(false); m_Controls->m_ToFCompositeFilterWidget->setEnabled(false); m_Controls->m_ToFMeasurementWidget->setEnabled(false); m_Controls->m_ToFSurfaceGenerationWidget->setEnabled(false); } } } //ZomnnieView-Method -> Resetting GUI to default. Why not just QmitkToFUtilView()?! void QmitkToFUtilView::ActivatedZombieView(berry::IWorkbenchPartReference::Pointer /*zombieView*/) { ResetGUIToDefault(); } void QmitkToFUtilView::Deactivated() { } void QmitkToFUtilView::Visible() { } //Reset of the ToFUtilView void QmitkToFUtilView::Hidden() { ResetGUIToDefault(); } void QmitkToFUtilView::OnToFCameraConnected() { MITK_DEBUG <<"OnToFCameraConnected"; this->m_2DDisplayCount = 0; this->m_ToFImageGrabber = m_Controls->m_ToFConnectionWidget->GetToFImageGrabber(); // initialize surface generation this->m_ToFDistanceImageToSurfaceFilter = mitk::ToFDistanceImageToSurfaceFilter::New(); // initialize ToFImageRecorder and ToFRecorderWidget this->m_ToFImageRecorder = mitk::ToFImageRecorder::New(); this->m_ToFImageRecorder->SetCameraDevice(this->m_ToFImageGrabber->GetCameraDevice()); m_Controls->m_ToFRecorderWidget->SetParameter(this->m_ToFImageGrabber, this->m_ToFImageRecorder); m_Controls->m_ToFRecorderWidget->setEnabled(true); m_Controls->m_ToFRecorderWidget->ResetGUIToInitial(); m_Controls->m_ToFVisualisationSettingsWidget->setEnabled(false); // initialize ToFCompositeFilterWidget this->m_ToFCompositeFilter = mitk::ToFCompositeFilter::New(); if (this->m_ToFCompositeFilter) { m_Controls->m_ToFCompositeFilterWidget->SetToFCompositeFilter(this->m_ToFCompositeFilter); } if (this->GetDataStorage()) { m_Controls->m_ToFCompositeFilterWidget->SetDataStorage(this->GetDataStorage()); } if ( this->GetRenderWindowPart() ) // initialize measurement widget m_Controls->m_ToFMeasurementWidget->InitializeWidget(this->GetRenderWindowPart()->GetQmitkRenderWindows(),this->GetDataStorage(), this->m_ToFDistanceImageToSurfaceFilter->GetCameraIntrinsics()); else MITK_WARN << "No render window part available!!! MeasurementWidget will not work."; this->m_RealTimeClock = mitk::RealTimeClock::New(); this->m_2DTimeBefore = this->m_RealTimeClock->GetCurrentStamp(); this->RequestRenderWindowUpdate(); } void QmitkToFUtilView::ResetGUIToDefault() { auto* renderWindowPart = this->GetRenderWindowPart(); if(nullptr != renderWindowPart) { auto* linkedRenderWindowPart = dynamic_cast<mitk::ILinkedRenderWindowPart*>(renderWindowPart); if(linkedRenderWindowPart == nullptr) { - MITK_ERROR << "No linked render window part avaiable!!!"; + MITK_ERROR << "No linked render window part available!!!"; } else { linkedRenderWindowPart->EnableSlicingPlanes(true); } renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetDefaultViewDirection(mitk::AnatomicalPlane::Axial); renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SliceLockedOff(); renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SetDefaultViewDirection(mitk::AnatomicalPlane::Sagittal); renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SliceLockedOff(); renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SetDefaultViewDirection(mitk::AnatomicalPlane::Coronal); renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SliceLockedOff(); this->UseToFVisibilitySettings(false); //global reinit mitk::RenderingManager::GetInstance()->InitializeViews(); this->RequestRenderWindowUpdate(); } } void QmitkToFUtilView::OnToFCameraDisconnected() { this->GetDataStorage()->Remove(m_DistanceImageNode); if(m_RGBImageNode) this->GetDataStorage()->Remove(m_RGBImageNode); if(m_AmplitudeImageNode) this->GetDataStorage()->Remove(m_AmplitudeImageNode); if(m_IntensityImageNode) this->GetDataStorage()->Remove(m_IntensityImageNode); if(m_SurfaceNode) this->GetDataStorage()->Remove(m_SurfaceNode); m_Controls->m_ToFRecorderWidget->OnStop(); m_Controls->m_ToFRecorderWidget->setEnabled(false); m_Controls->m_ToFVisualisationSettingsWidget->setEnabled(false); m_Controls->m_ToFMeasurementWidget->setEnabled(false); m_Controls->m_ToFSurfaceGenerationWidget->setEnabled(false); //clean up measurement widget m_Controls->m_ToFMeasurementWidget->CleanUpWidget(); } void QmitkToFUtilView::OnKinectAcquisitionModeChanged() { if (m_ToFCompositeFilter.IsNotNull()&&m_ToFImageGrabber.IsNotNull()) { if (m_SelectedCamera.contains("Kinect")) { if (m_ToFImageGrabber->GetBoolProperty("RGB")) { this->m_RGBImageNode = ReplaceNodeData("RGB image",this->m_ToFImageGrabber->GetOutput(3)); this->m_ToFDistanceImageToSurfaceFilter->SetInput(3,this->m_ToFImageGrabber->GetOutput(3)); } else if (m_ToFImageGrabber->GetBoolProperty("IR")) { this->m_MitkAmplitudeImage = m_ToFCompositeFilter->GetOutput(1); this->m_AmplitudeImageNode = ReplaceNodeData("Amplitude image",m_MitkAmplitudeImage); } } this->UseToFVisibilitySettings(true); } } void QmitkToFUtilView::OnToFCameraStarted() { if (m_ToFImageGrabber.IsNotNull()) { // initialize camera intrinsics if (this->m_ToFImageGrabber->GetProperty("CameraIntrinsics")) { m_CameraIntrinsics = dynamic_cast<mitk::CameraIntrinsicsProperty*>(this->m_ToFImageGrabber->GetProperty("CameraIntrinsics"))->GetValue(); MITK_INFO << m_CameraIntrinsics->ToString(); } else { m_CameraIntrinsics = nullptr; MITK_ERROR << "No camera intrinsics were found!"; } // set camera intrinsics if ( m_CameraIntrinsics.IsNotNull() ) { this->m_ToFDistanceImageToSurfaceFilter->SetCameraIntrinsics(m_CameraIntrinsics); } // initial update of image grabber this->m_ToFImageGrabber->Update(); bool hasRGBImage = false; m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("HasRGBImage",hasRGBImage); bool hasIntensityImage = false; m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("HasIntensityImage",hasIntensityImage); bool hasAmplitudeImage = false; m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("HasAmplitudeImage",hasAmplitudeImage); this->m_ToFCompositeFilter->SetInput(0,this->m_ToFImageGrabber->GetOutput(0)); if(hasAmplitudeImage) this->m_ToFCompositeFilter->SetInput(1,this->m_ToFImageGrabber->GetOutput(1)); if(hasIntensityImage) this->m_ToFCompositeFilter->SetInput(2,this->m_ToFImageGrabber->GetOutput(2)); // initial update of composite filter this->m_ToFCompositeFilter->Update(); this->m_MitkDistanceImage = m_ToFCompositeFilter->GetOutput(); this->m_DistanceImageNode = ReplaceNodeData("Distance image",m_MitkDistanceImage); std::string rgbFileName; m_ToFImageGrabber->GetCameraDevice()->GetStringProperty("RGBImageFileName",rgbFileName); if(hasRGBImage || (rgbFileName!="")) { if(m_ToFImageGrabber->GetBoolProperty("IR")) { this->m_MitkAmplitudeImage = m_ToFCompositeFilter->GetOutput(1); } else { this->m_RGBImageNode = ReplaceNodeData("RGB image",this->m_ToFImageGrabber->GetOutput(3)); } } else { this->m_RGBImageNode = nullptr; } if(hasAmplitudeImage) { this->m_MitkAmplitudeImage = m_ToFCompositeFilter->GetOutput(1); this->m_AmplitudeImageNode = ReplaceNodeData("Amplitude image",m_MitkAmplitudeImage); } if(hasIntensityImage) { this->m_MitkIntensityImage = m_ToFCompositeFilter->GetOutput(2); this->m_IntensityImageNode = ReplaceNodeData("Intensity image",m_MitkIntensityImage); } this->m_ToFDistanceImageToSurfaceFilter->SetInput(0,m_MitkDistanceImage); this->m_ToFDistanceImageToSurfaceFilter->SetInput(1,m_MitkAmplitudeImage); this->m_ToFDistanceImageToSurfaceFilter->SetInput(2,m_MitkIntensityImage); this->UseToFVisibilitySettings(true); this->m_SurfaceNode = ReplaceNodeData("Surface", nullptr); m_Controls->m_ToFCompositeFilterWidget->UpdateFilterParameter(); // initialize visualization widget m_Controls->m_ToFVisualisationSettingsWidget->Initialize(this->m_DistanceImageNode, this->m_AmplitudeImageNode, this->m_IntensityImageNode, this->m_SurfaceNode); m_Controls->m_ToFSurfaceGenerationWidget->Initialize(m_ToFDistanceImageToSurfaceFilter, m_ToFImageGrabber, m_CameraIntrinsics, m_SurfaceNode, GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("3d")->GetRenderer()->GetVtkRenderer()->GetActiveCamera()); // set distance image to measurement widget m_Controls->m_ToFMeasurementWidget->SetDistanceImage(m_MitkDistanceImage); this->m_Frametimer->start(50); m_Controls->m_ToFVisualisationSettingsWidget->setEnabled(true); m_Controls->m_ToFCompositeFilterWidget->setEnabled(true); m_Controls->m_ToFMeasurementWidget->setEnabled(true); m_Controls->m_ToFSurfaceGenerationWidget->setEnabled(true); } } void QmitkToFUtilView::OnToFCameraStopped() { m_Controls->m_ToFVisualisationSettingsWidget->setEnabled(false); m_Controls->m_ToFCompositeFilterWidget->setEnabled(false); this->m_Frametimer->stop(); } void QmitkToFUtilView::OnUpdateCamera() { if(!m_Controls->m_ToFSurfaceGenerationWidget->UpdateSurface()) { // update pipeline this->m_MitkDistanceImage->Update(); } this->RequestRenderWindowUpdate(); if (m_Framerateoutput) { this->m_2DDisplayCount++; if ((this->m_2DDisplayCount % this->m_StepsForFramerate) == 0) { this->m_2DTimeAfter = this->m_RealTimeClock->GetCurrentStamp() - this->m_2DTimeBefore; MITK_INFO << " 2D-Display-framerate (fps): " << this->m_StepsForFramerate / (this->m_2DTimeAfter / 1000); this->m_2DTimeBefore = this->m_RealTimeClock->GetCurrentStamp(); } } } void QmitkToFUtilView::OnChangeCoronalWindowOutput(int index) { this->OnToFCameraStopped(); if(index == 0) { if(this->m_IntensityImageNode.IsNotNull()) this->m_IntensityImageNode->SetVisibility(false); if(this->m_RGBImageNode.IsNotNull()) this->m_RGBImageNode->SetVisibility(true); } else if(index == 1) { if(this->m_IntensityImageNode.IsNotNull()) this->m_IntensityImageNode->SetVisibility(true); if(this->m_RGBImageNode.IsNotNull()) this->m_RGBImageNode->SetVisibility(false); } this->RequestRenderWindowUpdate(); this->OnToFCameraStarted(); } mitk::DataNode::Pointer QmitkToFUtilView::ReplaceNodeData( std::string nodeName, mitk::BaseData* data ) { mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode(nodeName); if (node.IsNull()) { node = mitk::DataNode::New(); node->SetName(nodeName); node->SetBoolProperty("binary",false); node->SetData(data); this->GetDataStorage()->Add(node); } else { node->SetData(data); } return node; } void QmitkToFUtilView::UseToFVisibilitySettings(bool useToF) { //We need this property for every node. auto renderingModePropertyForTransferFunction = mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::COLORTRANSFERFUNCTION_COLOR); auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* axialRenderer = mitk::BaseRenderer::GetInstance(renderWindowPart->GetQmitkRenderWindow("axial")->renderWindow()); auto* sagittalRenderer = mitk::BaseRenderer::GetInstance(renderWindowPart->GetQmitkRenderWindow("sagittal")->renderWindow()); auto* coronalRenderer = mitk::BaseRenderer::GetInstance(renderWindowPart->GetQmitkRenderWindow("coronal")->renderWindow()); auto* threeDimRenderer = mitk::BaseRenderer::GetInstance(renderWindowPart->GetQmitkRenderWindow("3d")->renderWindow()); // set node properties if (m_DistanceImageNode.IsNotNull()) { this->m_DistanceImageNode->SetProperty( "visible" , mitk::BoolProperty::New( true )); this->m_DistanceImageNode->SetVisibility( !useToF, sagittalRenderer ); this->m_DistanceImageNode->SetVisibility( !useToF, coronalRenderer ); this->m_DistanceImageNode->SetVisibility( !useToF, threeDimRenderer ); this->m_DistanceImageNode->SetProperty("Image Rendering.Mode", renderingModePropertyForTransferFunction); } if (m_AmplitudeImageNode.IsNotNull()) { this->m_AmplitudeImageNode->SetVisibility( !useToF, axialRenderer ); this->m_AmplitudeImageNode->SetVisibility( !useToF, coronalRenderer ); this->m_AmplitudeImageNode->SetVisibility( !useToF, threeDimRenderer ); this->m_AmplitudeImageNode->SetProperty("Image Rendering.Mode", renderingModePropertyForTransferFunction); } if (m_IntensityImageNode.IsNotNull()) { this->m_IntensityImageNode->SetProperty( "visible" , mitk::BoolProperty::New( true )); this->m_IntensityImageNode->SetVisibility( !useToF, axialRenderer ); this->m_IntensityImageNode->SetVisibility( !useToF, sagittalRenderer ); this->m_IntensityImageNode->SetVisibility( !useToF, threeDimRenderer ); this->m_IntensityImageNode->SetProperty("Image Rendering.Mode", renderingModePropertyForTransferFunction); } if ((m_RGBImageNode.IsNotNull())) { this->m_RGBImageNode->SetProperty( "visible" , mitk::BoolProperty::New( true )); this->m_RGBImageNode->SetVisibility( !useToF, axialRenderer ); this->m_RGBImageNode->SetVisibility( !useToF, sagittalRenderer ); this->m_RGBImageNode->SetVisibility( !useToF, threeDimRenderer ); } // initialize images if (m_MitkDistanceImage.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( this->m_MitkDistanceImage->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_2DWINDOWS); } if(this->m_SurfaceNode.IsNotNull()) { QHash<QString, QmitkRenderWindow*> renderWindowHashMap = renderWindowPart->GetQmitkRenderWindows(); QHashIterator<QString, QmitkRenderWindow*> i(renderWindowHashMap); while (i.hasNext()){ i.next(); this->m_SurfaceNode->SetVisibility( false, mitk::BaseRenderer::GetInstance(i.value()->renderWindow()) ); } this->m_SurfaceNode->SetVisibility( true, mitk::BaseRenderer::GetInstance(renderWindowPart->GetQmitkRenderWindow("3d")->renderWindow() ) ); } //disable/enable gradient background renderWindowPart->EnableDecorations(!useToF, QStringList(QString("background"))); if((this->m_RGBImageNode.IsNotNull())) { bool RGBImageHasDifferentResolution = false; m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("RGBImageHasDifferentResolution",RGBImageHasDifferentResolution); if(RGBImageHasDifferentResolution) { //update the display geometry by using the RBG image node. Only for renderwindow coronal mitk::RenderingManager::GetInstance()->InitializeView(renderWindowPart->GetQmitkRenderWindow("coronal")->renderWindow(), this->m_RGBImageNode->GetData()->GetGeometry()); } } } diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp index c8271b953b..9e3665c522 100644 --- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp +++ b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp @@ -1,89 +1,89 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkTubeGraphDeleteLabelGroupDialog.h" #include <QAbstractItemView> #include <QPushButton> #include <QLayout> #include <QLabel> #include <QListWidget> QmitkTubeGraphDeleteLabelGroupDialog::QmitkTubeGraphDeleteLabelGroupDialog(QWidget* parent) :QDialog(parent) { QDialog::setFixedSize(400, 400); auto layout = new QVBoxLayout(this); layout->setMargin(5); layout->setSpacing(5); descriptionLabel = new QLabel("Which Label Group should be removed?", this); layout->addWidget(descriptionLabel); labelGroupListWidget = new QListWidget(this); labelGroupListWidget->setSelectionMode(QAbstractItemView::MultiSelection); layout->addWidget(labelGroupListWidget); auto buttonLayout = new QHBoxLayout(); deleteButton = new QPushButton("Delete", this); buttonLayout->addWidget(deleteButton); connect( deleteButton, SIGNAL(clicked()), this, SLOT(OnDeleteLabelGroupClicked()) ); - cancleButton = new QPushButton("Cancle", this); + cancleButton = new QPushButton("Cancel", this); buttonLayout->addWidget(cancleButton); connect( cancleButton, SIGNAL(clicked()), this, SLOT(reject()) ); layout->addLayout(buttonLayout); deleteButton->setFocus(); } QmitkTubeGraphDeleteLabelGroupDialog::~QmitkTubeGraphDeleteLabelGroupDialog() { delete descriptionLabel; delete labelGroupListWidget; delete deleteButton; delete cancleButton; } void QmitkTubeGraphDeleteLabelGroupDialog::OnDeleteLabelGroupClicked() { //get selected items and save it in vector m_LabelGroupList.clear(); for (int i =0; i < labelGroupListWidget->count(); i++) { QListWidgetItem* newItem= labelGroupListWidget->item(i); if(newItem->isSelected()) //For all checked items { m_LabelGroupList.push_back(newItem->text()); } } this->accept(); } QStringList QmitkTubeGraphDeleteLabelGroupDialog::GetSelectedLabelGroups() { return m_LabelGroupList; } void QmitkTubeGraphDeleteLabelGroupDialog::SetLabelGroups(const QStringList &labelGroups) { for (const auto &labelGroup : labelGroups) labelGroupListWidget->addItem(labelGroup); } diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp index 8f27f53700..42242f42f1 100644 --- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp +++ b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp @@ -1,95 +1,95 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkTubeGraphNewAnnotationDialog.h" #include <qpushbutton.h> #include <qlayout.h> #include <qlineedit.h> #include <qlabel.h> #include <qlistwidget.h> QmitkTubeGraphNewAnnotationDialog::QmitkTubeGraphNewAnnotationDialog(QWidget* parent) :QDialog(parent) { QDialog::setFixedSize(200, 200); layout = new QVBoxLayout(this); layout->setMargin(5); layout->setSpacing(5); annotationNameLabel = new QLabel("Enter the name of the annotation!", this); layout->addWidget(annotationNameLabel); annotationNameLineEdit = new QLineEdit(this); layout->addWidget(annotationNameLineEdit); annotationDescriptionLabel = new QLabel("Enter a description!", this); layout->addWidget(annotationDescriptionLabel); annotationDescriptionLineEdit = new QLineEdit(this); layout->addWidget(annotationDescriptionLineEdit); buttonLayout = new QHBoxLayout(); okButton = new QPushButton("Ok", this); buttonLayout->addWidget(okButton, 0, Qt::AlignRight); connect( okButton, SIGNAL(clicked()), this, SLOT(OnAddingAnnotation()) ); - cancleButton = new QPushButton("Cancle", this); + cancleButton = new QPushButton("Cancel", this); buttonLayout->addWidget(cancleButton, 0, Qt::AlignRight); connect( cancleButton, SIGNAL(clicked()), this, SLOT(reject()) ); layout->addLayout(buttonLayout); annotationNameLineEdit->setFocus(); } void QmitkTubeGraphNewAnnotationDialog::OnAddingAnnotation() { if (annotationNameLineEdit->text().isEmpty()) { annotationNameLineEdit->setStyleSheet("border: 1px solid red"); return; } m_NewAnnotationName = annotationNameLineEdit->text(); m_NewAnnotationDescription = annotationDescriptionLineEdit->text(); this->accept(); } QmitkTubeGraphNewAnnotationDialog::~QmitkTubeGraphNewAnnotationDialog() { delete layout; delete okButton; delete cancleButton; // delete buttonLayout; delete annotationNameLabel; delete annotationNameLineEdit; delete annotationDescriptionLabel; delete annotationDescriptionLineEdit; } QString QmitkTubeGraphNewAnnotationDialog::GetAnnotationName() { return m_NewAnnotationName; } QString QmitkTubeGraphNewAnnotationDialog::GetAnnotationDescription() { return m_NewAnnotationDescription; } diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp index 16a9ccc49b..d3559fc168 100644 --- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp +++ b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp @@ -1,270 +1,270 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkTubeGraphNewLabelGroupDialog.h" #include <qpushbutton.h> #include <qlayout.h> #include <qlineedit.h> #include <qlabel.h> #include <qlistwidget.h> #include <qtreewidget.h> #include <qheaderview.h> #include "mitkTubeGraphDefaultLabelGroups.h" QmitkTubeGraphNewLabelGroupDialog::QmitkTubeGraphNewLabelGroupDialog(QWidget* parent) :QDialog(parent) ,m_NewLabelGroup() { QDialog::setFixedSize(200, 200); layout = new QVBoxLayout(this); layout->setMargin(5); layout->setSpacing(5); newLabelGroupButton = new QPushButton("Create new label group", this); layout->addWidget(newLabelGroupButton, 0, Qt::AlignHCenter); connect( newLabelGroupButton, SIGNAL(clicked()), this, SLOT(OnCreateNewLabelGroup()) ); standardLabelGroupButton = new QPushButton("Add standard label group", this); layout->addWidget(standardLabelGroupButton, 0, Qt::AlignHCenter); connect( standardLabelGroupButton, SIGNAL(clicked()), this, SLOT(OnAddStandardLabelGroup()) ); spacer = new QSpacerItem( 20, 40, QSizePolicy::Minimum, QSizePolicy::Minimum ); layout->addSpacerItem(spacer); buttonLayout = new QHBoxLayout(); okButton = new QPushButton("Ok", this); buttonLayout->addWidget(okButton, 0, Qt::AlignRight); okButton->setVisible(false); - cancleButton = new QPushButton("Cancle", this); + cancleButton = new QPushButton("Cancel", this); buttonLayout->addWidget(cancleButton, 0, Qt::AlignRight); connect( cancleButton, SIGNAL(clicked()), this, SLOT(reject()) ); layout->addLayout(buttonLayout); newLabelGroupButton->setFocus(); } QmitkTubeGraphNewLabelGroupDialog::~QmitkTubeGraphNewLabelGroupDialog() { //delete layout; ////delete buttonLayout; //delete spacer; //delete okButton; //delete cancleButton; //delete labelGroupDescriptionLabel; /* delete labelGroupLineEdit; delete labelDescriptionLabel; delete labelLineEdit; delete addLabelButton; delete labelListWidget; */ //delete labelGroupTreeWidget; } void QmitkTubeGraphNewLabelGroupDialog::OnCreateNewLabelGroup() { QDialog::setFixedSize(400, 200); layout->removeWidget(newLabelGroupButton); delete newLabelGroupButton; layout->removeWidget(standardLabelGroupButton); delete standardLabelGroupButton; layout->removeWidget(okButton); layout->removeWidget(cancleButton); layout->removeItem(spacer); layout->removeItem(buttonLayout); labelGroupDescriptionLabel = new QLabel("Enter the label group name!", this); layout->addWidget(labelGroupDescriptionLabel); labelGroupLineEdit = new QLineEdit(this); layout->addWidget(labelGroupLineEdit); labelDescriptionLabel = new QLabel("Enter a label name!", this); layout->addWidget(labelDescriptionLabel); auto labelLayout = new QHBoxLayout(); labelLineEdit = new QLineEdit(this); labelLayout->addWidget(labelLineEdit); addLabelButton = new QPushButton("+", this); labelLayout->addWidget(addLabelButton); connect( addLabelButton, SIGNAL(clicked()), this, SLOT(OnAddingLabel()) ); layout->addLayout(labelLayout); labelListWidget = new QListWidget(this); labelListWidget->setDragDropMode(QAbstractItemView::InternalMove); labelListWidget->addItem("Undefined"); layout->addWidget(labelListWidget); layout->addLayout(buttonLayout); connect( okButton, SIGNAL(clicked()), this, SLOT(OnAddingNewLabelGroup()) ); okButton->setVisible(true); } void QmitkTubeGraphNewLabelGroupDialog::OnAddStandardLabelGroup() { QDialog::setFixedSize(400, 200); layout->removeWidget(newLabelGroupButton); delete newLabelGroupButton; layout->removeWidget(standardLabelGroupButton); delete standardLabelGroupButton; layout->removeWidget(okButton); layout->removeWidget(cancleButton); layout->removeItem(spacer); layout->removeItem(buttonLayout); labelGroupDescriptionLabel = new QLabel("Choose one of the standard label group!", this); layout->addWidget(labelGroupDescriptionLabel); labelGroupTreeWidget = new QTreeWidget(this); labelGroupTreeWidget->header()->close(); auto defaultLabelGroups = new mitk::TubeGraphDefaultLabelGroups(); m_LabelGroupsLiver = defaultLabelGroups->GetLabelGroupForLiver(); m_LabelGroupsLung = defaultLabelGroups->GetLabelGroupForLung(); auto liverItem = new QTreeWidgetItem(labelGroupTreeWidget); liverItem->setText(0, tr("Liver")); QTreeWidgetItem* liverChildItem; for (unsigned int k = 0; k < m_LabelGroupsLiver.size(); k++) { liverChildItem = new QTreeWidgetItem(liverItem); liverChildItem->setText(0, QString::fromStdString(m_LabelGroupsLiver.at(k)->labelGroupName)); } liverItem->setExpanded(true); auto lungItem = new QTreeWidgetItem(labelGroupTreeWidget); lungItem->setText(0, tr("Lung")); QTreeWidgetItem* lungChildItem; for (unsigned int k = 0; k < m_LabelGroupsLung.size(); k++) { lungChildItem = new QTreeWidgetItem(lungItem); lungChildItem->setText(0, QString::fromStdString(m_LabelGroupsLung.at(k)->labelGroupName)); } lungItem->setExpanded(true); labelGroupTreeWidget->insertTopLevelItem(1,lungItem); delete defaultLabelGroups; layout->addWidget(labelGroupTreeWidget); layout->addLayout(buttonLayout); connect( okButton, SIGNAL(clicked()), this, SLOT(OnAddingStandardLabelGroup()) ); okButton->setVisible(true); } void QmitkTubeGraphNewLabelGroupDialog::OnAddingLabel() { if (labelLineEdit->text().isEmpty()) { labelLineEdit->setStyleSheet("border: 1px solid red"); return; } labelListWidget->addItem(labelLineEdit->text()); labelLineEdit->clear(); } void QmitkTubeGraphNewLabelGroupDialog::OnAddingNewLabelGroup() { if (labelGroupLineEdit->text().isEmpty()) { labelGroupLineEdit->setStyleSheet("border: 1px solid red"); return; } m_NewLabelGroup = new LabelGroupType(); m_NewLabelGroup->labelGroupName = (labelGroupLineEdit->text()).toStdString(); for (int i =0; i < labelListWidget->count(); i++) { auto label = new LabelType(); label->labelName = (labelListWidget->item(i)->text()).toStdString(); mitk::Color color; if(label->labelName.compare("Undefined") == 0) { color[0] = 170; color[1] = 170; color[2] = 169; } else { color[0] = rand() % 255; color[1] = rand() % 255; color[2] = rand() % 255; } label->labelColor = color; label->isVisible = true; m_NewLabelGroup->labels.push_back(label); } this->accept(); } void QmitkTubeGraphNewLabelGroupDialog::OnAddingStandardLabelGroup() { if (labelGroupTreeWidget->selectedItems().isEmpty()) { labelGroupDescriptionLabel->setStyleSheet("border: 1px solid red"); return; } if(labelGroupTreeWidget->selectedItems().at(0)->parent()->text(0) == "Lung") { for (unsigned int k = 0; k < m_LabelGroupsLung.size(); k++) { if(m_LabelGroupsLung.at(k)->labelGroupName == (labelGroupTreeWidget->selectedItems().at(0)->text(0)).toStdString()) m_NewLabelGroup = m_LabelGroupsLung.at(k); } } else { for (unsigned int k = 0; k < m_LabelGroupsLiver.size(); k++) { if(m_LabelGroupsLiver.at(k)->labelGroupName == (labelGroupTreeWidget->selectedItems().at(0)->text(0)).toStdString()) m_NewLabelGroup = m_LabelGroupsLiver.at(k); } } if (m_NewLabelGroup == nullptr) return; this->accept(); } QmitkTubeGraphNewLabelGroupDialog::LabelGroupType* QmitkTubeGraphNewLabelGroupDialog::GetLabelGroup() { return m_NewLabelGroup; } diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui index 96ba85fee2..c1b48b36a4 100644 --- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui +++ b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui @@ -1,559 +1,559 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkTubeGraphViewControls</class> <widget class="QWidget" name="QmitkTubeGraphViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>385</width> <height>739</height> </rect> </property> <property name="windowTitle"> <string/> </property> <layout class="QVBoxLayout" name="verticalLayout_5"> <item> <widget class="QGroupBox" name="activeNodeGroupBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>75</weight> <bold>true</bold> </property> <property name="title"> <string>Active Tube Graph</string> </property> <property name="flat"> <bool>false</bool> </property> <property name="checkable"> <bool>false</bool> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <property name="sizeConstraint"> <enum>QLayout::SetDefaultConstraint</enum> </property> <item> <widget class="QmitkDataStorageComboBox" name="activeGraphComboBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> </widget> </item> </layout> </widget> </item> <item> <widget class="QGroupBox" name="activationGroupBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>75</weight> <bold>true</bold> </property> <property name="title"> <string>Activation Mode</string> </property> <layout class="QHBoxLayout" name="horizontalLayout_3"> <item> <layout class="QVBoxLayout" name="verticalLayout_4"> <item> <widget class="QGroupBox" name="activationModeGroupBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Expanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>50</weight> <bold>false</bold> </property> <property name="title"> <string/> </property> <property name="checkable"> <bool>false</bool> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <widget class="QRadioButton" name="noneModeRadioButton"> <property name="text"> <string>None</string> </property> <property name="checked"> <bool>true</bool> </property> <attribute name="buttonGroup"> <string>buttonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="singleModeRadioButton"> <property name="text"> <string>Single</string> </property> <attribute name="buttonGroup"> <string>buttonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="multipleModeRadioButton"> <property name="text"> <string>Multiple</string> </property> <attribute name="buttonGroup"> <string>buttonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="peripheryModeRadioButton"> <property name="text"> <string>Periphery</string> </property> <attribute name="buttonGroup"> <string>buttonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="rootModeRadioButton"> <property name="text"> <string>Path to Root</string> </property> <attribute name="buttonGroup"> <string>buttonGroup</string> </attribute> </widget> </item> <item> <widget class="QRadioButton" name="pointModeRadioButton"> <property name="text"> <string>Point to Point</string> </property> <attribute name="buttonGroup"> <string>buttonGroup</string> </attribute> </widget> </item> </layout> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QPushButton" name="setRootButton"> <property name="sizePolicy"> <sizepolicy hsizetype="Minimum" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="toolTip"> <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Enable to select a new root with left mouse click in the image.</body></html></string> </property> <property name="text"> <string/> </property> <property name="icon"> <iconset> <normaloff>:/QmitkExt/icon_seedpoint.png</normaloff>:/QmitkExt/icon_seedpoint.png</iconset> </property> <property name="checkable"> <bool>true</bool> </property> <property name="flat"> <bool>false</bool> </property> </widget> </item> <item> <widget class="QPushButton" name="deselectAllButton"> <property name="font"> <weight>50</weight> <bold>false</bold> </property> <property name="text"> <string>Deselect All</string> </property> </widget> </item> </layout> </item> </layout> </item> <item> <widget class="QGroupBox" name="shortInformationGroupBox"> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Expanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>50</weight> <italic>true</italic> <bold>false</bold> </property> <property name="title"> <string>Short Information about Selection</string> </property> <layout class="QVBoxLayout" name="verticalLayout_9"> <item> <widget class="QLabel" name="shortInformationLabel"> <property name="font"> <italic>false</italic> </property> <property name="text"> <string/> </property> <property name="alignment"> <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set> </property> </widget> </item> </layout> </widget> </item> </layout> </widget> </item> <item> <widget class="QTabWidget" name="tubeGraphTabWidget"> <property name="enabled"> <bool>true</bool> </property> <property name="sizePolicy"> <sizepolicy hsizetype="Expanding" vsizetype="Expanding"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="font"> <weight>75</weight> <bold>true</bold> </property> <property name="contextMenuPolicy"> <enum>Qt::DefaultContextMenu</enum> </property> <property name="autoFillBackground"> <bool>true</bool> </property> <property name="locale"> <locale language="English" country="UnitedStates"/> </property> <property name="tabShape"> <enum>QTabWidget::Rounded</enum> </property> <property name="currentIndex"> <number>3</number> </property> <widget class="QWidget" name="attributationTab"> <attribute name="title"> <string>Attributation</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QToolBox" name="toolBox"> <widget class="QWidget" name="page"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>343</width> <height>282</height> </rect> </property> <attribute name="label"> <string/> </attribute> </widget> <widget class="QWidget" name="page_2"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>98</width> <height>28</height> </rect> </property> <attribute name="label"> <string/> </attribute> </widget> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_2"> <item> <widget class="QPushButton" name="addLabelGroupButton"> <property name="sizePolicy"> <sizepolicy hsizetype="Fixed" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>+</string> </property> </widget> </item> <item> <widget class="QPushButton" name="removeLabelGroupButton"> <property name="sizePolicy"> <sizepolicy hsizetype="Fixed" vsizetype="Fixed"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="text"> <string>-</string> </property> </widget> </item> </layout> </item> </layout> </widget> <widget class="QWidget" name="annotationTab"> <attribute name="title"> <string>Annotation</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_6"> <item> <widget class="QTableWidget" name="annotationsTableWidget"> <property name="enabled"> <bool>true</bool> </property> <property name="font"> <family>MS Shell Dlg 2</family> <kerning>true</kerning> </property> <property name="frameShape"> <enum>QFrame::WinPanel</enum> </property> <property name="dragEnabled"> <bool>false</bool> </property> <property name="selectionBehavior"> <enum>QAbstractItemView::SelectRows</enum> </property> <property name="showGrid"> <bool>true</bool> </property> <column> <property name="text"> <string>Name</string> </property> </column> <column> <property name="text"> <string>Description</string> </property> </column> <column> <property name="text"> <string>Tube</string> </property> </column> </widget> </item> <item> <layout class="QHBoxLayout" name="horizontalLayout_4"> <item> <widget class="QPushButton" name="addAnnotationButton"> <property name="text"> <string>+</string> </property> </widget> </item> <item> <widget class="QPushButton" name="deleteAnnotationButton"> <property name="text"> <string>--</string> </property> </widget> </item> </layout> </item> </layout> </widget> <widget class="QWidget" name="editTab"> <attribute name="title"> <string>Edit</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_7"> <item> <widget class="QLabel" name="editDescriptionLabel"> <property name="text"> <string>Please select the region you want to interact with!</string> </property> </widget> </item> <item> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>20</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="editSelectionNewButton"> <property name="text"> <string>Connect</string> </property> </widget> </item> <item> <spacer name="verticalSpacer_5"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item> <widget class="QPushButton" name="editSelectionSeperateButton"> <property name="text"> - <string>Seperate</string> + <string>Separate</string> </property> </widget> </item> <item> <widget class="QPushButton" name="editSelectionDeleteButton"> <property name="text"> <string>Delete</string> </property> </widget> </item> <item> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <widget class="QWidget" name="informationTab"> <attribute name="title"> <string>Information</string> </attribute> <layout class="QVBoxLayout" name="verticalLayout_8"> <item> <widget class="QLabel" name="informationLabel"> <property name="text"> <string/> </property> </widget> </item> <item> <spacer name="verticalSpacer_4"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>345</height> </size> </property> </spacer> </item> </layout> </widget> </widget> </item> <item> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Preferred</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>20</height> </size> </property> </spacer> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkDataStorageComboBox</class> <extends>QComboBox</extends> <header location="global">QmitkDataStorageComboBox.h</header> </customwidget> </customwidgets> <resources/> <connections/> <slots> <slot>OnActivationModeChanged()</slot> </slots> <buttongroups> <buttongroup name="buttonGroup"/> </buttongroups> </ui> diff --git a/Plugins/org.mitk.gui.qt.ultrasound/src/internal/QmitkUltrasoundSupport.h b/Plugins/org.mitk.gui.qt.ultrasound/src/internal/QmitkUltrasoundSupport.h index bf7ee4f2fc..cfc051fc7a 100644 --- a/Plugins/org.mitk.gui.qt.ultrasound/src/internal/QmitkUltrasoundSupport.h +++ b/Plugins/org.mitk.gui.qt.ultrasound/src/internal/QmitkUltrasoundSupport.h @@ -1,181 +1,181 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkUltrasoundSupport_h #define QmitkUltrasoundSupport_h #include <mitkLookupTable.h> #include <mitkLookupTableProperty.h> #include <berryISelectionListener.h> #include <QmitkAbstractView.h> #include "ui_QmitkUltrasoundSupportControls.h" #include "QmitkUSAbstractCustomWidget.h" #include "QmitkUSControlsBModeWidget.h" #include "QmitkUSControlsDopplerWidget.h" #include "QmitkUSControlsProbesWidget.h" #include <mitkBaseRenderer.h> #include "QmitkRenderWindow.h" #include <mitkStandaloneDataStorage.h> #include <QmitkLevelWindowWidget.h> #include <QmitkSliceWidget.h> #include <QTime> #include <ctkServiceEvent.h> /*! \brief UltrasoundSupport This plugin provides functionality to manage Ultrasound devices, create video devices and to view device images. \ingroup ${plugin_target}_internal */ class QmitkUltrasoundSupport : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: void SetFocus() override; static const std::string VIEW_ID; void CreateQtPartControl(QWidget *parent) override; QmitkUltrasoundSupport(); ~QmitkUltrasoundSupport() override; public slots: /* * \brief This is called when the newDeviceWidget is closed */ void OnNewDeviceWidgetDone(); protected slots: void OnClickedAddNewDevice(); void OnChangedFramerateLimit(); void OnClickedEditDevice(); /* *\brief Called, when the selection in the list of the active devices changes. */ void OnChangedActiveDevice(); void OnClickedFreezeButton(); void OnDeviceServiceEvent(const ctkServiceEvent event); /* - * \brief This is the main imaging loop that updates the image and is called regularily during the imaging process + * \brief This is the main imaging loop that updates the image and is called regularly during the imaging process */ void UpdateImage(); void RenderImage2d(); void RenderImage3d(); void StartTimers(); void StopTimers(); protected: void CreateControlWidgets(); void RemoveControlWidgets(); Ui::UltrasoundSupportControls* m_Controls; QmitkUSAbstractCustomWidget* m_ControlCustomWidget; QmitkUSControlsBModeWidget* m_ControlBModeWidget; QmitkUSControlsDopplerWidget* m_ControlDopplerWidget; QmitkUSControlsProbesWidget* m_ControlProbesWidget; bool m_ImageAlreadySetToNode; unsigned int m_CurrentImageWidth; unsigned int m_CurrentImageHeight; /** Keeps track of the amount of output Nodes*/ unsigned int m_AmountOfOutputs; - /** The device that is currently used to aquire images */ + /** The device that is currently used to acquire images */ mitk::USDevice::Pointer m_Device; void SetTimerIntervals(int intervalPipeline, int interval2D, int interval3D); /** This timer triggers periodic updates to the pipeline */ QTimer* m_UpdateTimer; QTimer* m_RenderingTimer2d; QTimer* m_RenderingTimer3d; /** These clocks are used to compute the framerate in the methods DisplayImage(),RenderImage2d() and RenderImage3d(). */ QTime m_Clock; QTime m_Clock2d; QTime m_Clock3d; - /** A counter to comute the framerate. */ + /** A counter to compute the framerate. */ int m_FrameCounterPipeline; int m_FrameCounter2d; int m_FrameCounter3d; int m_FPSPipeline, m_FPS2d, m_FPS3d; /** Stores the properties of some QWidgets (and the tool storage file name) to QSettings.*/ void StoreUISettings(); /** Loads the properties of some QWidgets (and the tool storage file name) from QSettings.*/ void LoadUISettings(); /** The nodes that we feed images into.*/ std::vector<mitk::DataNode::Pointer> m_Node; /** Adds a new node to the m_Nodes vector*/ void InitNewNode(); /** Destroys the last node in the m_Nodes vector */ void DestroyLastNode(); /** Checks the amount of slices in the image from the USDevice and creates as many Nodes as there are slices */ void UpdateAmountOfOutputs(); /** This function just checks how many nodes there are currently and sets the laser image to a jet transparent colormap. */ void UpdateLevelWindows(); bool m_ForceRequestUpdateAll; void SetColormap(mitk::DataNode::Pointer node, mitk::LookupTable::LookupTableType type); - /** The seperated slices from m_Image */ + /** The separated slices from m_Image */ std::vector<mitk::Image::Pointer> m_curOutput; /** The old geometry of m_Image. It is needed to check if the geometry changed (e.g. because * the zoom factor was modified) and the image needs to be reinitialized. */ mitk::SlicedGeometry3D::Pointer m_OldGeometry; QList<ctkServiceReference> m_CustomWidgetServiceReference; double m_CurrentDynamicRange; /* Spacing calibration variables and methods */ mitk::Point3D m_Xpoint1,m_Xpoint2,m_Ypoint1,m_Ypoint2; double m_XSpacing, m_YSpacing; double ComputeSpacing(mitk::Point3D p1, mitk::Point3D p2, double distance); protected slots: void SetXPoint1(); void SetXPoint2(); void SetYPoint1(); void SetYPoint2(); void WriteSpacingToDevice(); }; #endif diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox index 4414f06d79..5c4024fe23 100644 --- a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox +++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox @@ -1,130 +1,130 @@ /** \page org_mitk_views_volumevisualization The Volume Visualization Plugin \imageMacro{volume_visualization-dox.svg,"Icon of the Volume Visualization Plugin",2.00} \tableofcontents \section QVV_Overview Overview The Volume Visualization Plugin is a basic tool for volume rendering of three dimensional medical images. MITK provides generic transfer function presets for medical CT and MRT data. These functions that map the gray-value to color and opacity can be interactively edited. Additionally, there are controls to quickly generate commonly used transfer function shapes like the threshold and bell curve to help identify a range of grey-values. \imageMacro{QmitkVolumeVisualization_Overview.png,"",16.00} \section QVV_EnableVRPage Volume Rendering \subsection QVV_LoadingImage Select an image and enable volume rendering Select an image on top of the view and click on the checkbox left of 'Volume rendering'. \note Volume Visualization imposes following restrictions on images: <ul> <li> It has to be a 3D scalar image, that means e.g. a CT or MRT image. <li> 3D+t images are supported for rendering, but the histograms are not computed. <li> Also be aware that volume visualization requires a huge amount of memory. Very large images may not work unless you use the 64bit version. </ul> \subsection QVV_LODGPU Dropdown menu for the blend modes -Two dropdown menu is located right next to the 'Volume rendering' checkbox. It allows you to select a blend mode (Composite, Maximim intensity, Minimum intensity, Average intensity, and Additive intensity). +Two dropdown menu is located right next to the 'Volume rendering' checkbox. It allows you to select a blend mode (Composite, Maximum intensity, Minimum intensity, Average intensity, and Additive intensity). Blend modes define how the volume voxels, intersected by the rendering rays, are pooled. The 'Composite' mode specifies standard volume rendering, for which each voxel contributes equally with opacity and color. Other 'blend' modes visualize the voxel of the maximum or minimum intensity or average or add the intensities along the rendering ray. \section QVV_PresetPage Applying premade presets \subsection QVV_Preset Internal presets There are some internal presets given that can be used with normal CT data (given in Houndsfield units). A large set of medical data has been tested with those presets, but they may not suit some special cases. Click on the 'Preset' tab for using internal or custom presets. \imageMacro{QmitkVolumeVisualization_InternalPresets.png,"",8.30} <ul> <li> 'CT Generic' is the default transfer function that is first applied. <li> 'CT Black&White' does not use any colors for the volume visualization as it may be distracting on some data. <li> 'CT Cardiac' is well-suited for CT images containing the heart. <li> 'CT Bone' emphasizes bones and shows other areas more transparent. <li> 'CT Bone (Gradient)' is like 'CT Bone' but shows only the surface from other organs by using the gradient. <li> 'MR Generic' is the default transfer function that can be used on MRT data (which is not normalized like CT data). <li> 'CT Thorax small' is useful if only a proportion of the thorax is selected to emphasize details. <li> 'CT Thorax large' is useful if a large proportion or the entire thorax is selected to emphasize details. </ul> \subsection QVV_CustomPreset Saving and loading custom presets After creating or editing a transfer function (see \ref QVV_Editing or \ref QVV_ThresholdBell), the custom transfer function can be stored and later retrieved on the filesystem. Click 'Save' (respectively 'Load') button below the preset selection to save (load) the threshold-, color- and gradient function combined in a single .xml file. \section QVV_ThresholdBell Interactively create transfer functions Besides the possibility to directly edit the transfer functions (\ref QVV_Editing), the plugin provides two commonly known shapes to quickly generate transfer functions with a few clicks. Both generators have two parameters that can be modified by first clicking on the cross and then moving the mouse up/down and left/right. The first parameter 'center' (controlled by horizontal movement of the mouse) specifies the gray value where the center of the shape will be located. The second parameter 'width' (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape. \subsection Threshold Click on the 'Threshold' tab to activate the threshold function generator. \imageMacro{QmitkVolumeVisualization_Threshold.png,"",8.21} A threshold shape begins with zero and raises to one across the 'center' parameter. Lower widths result in steeper threshold functions. \subsection Bell Click on the 'Bell' tab to activate the bell-shaped threshold function generator. \imageMacro{QmitkVolumeVisualization_Bell.png,"",8.23} A threshold shape begins with zero and raises to one at the 'center' parameter and then lowers again to zero. The 'width' parameter corresponds to the width of the bell. \section QVV_Editing Customize transfer functions in detail \subsection QVV_Navigate Choosing gray value interval to edit \imageMacro{QmitkVolumeVisualization_Slider.png,"",8.23} To navigate across the gray value range or to zoom in some ranges use the 'range'-slider. All three function editors have in common following: <ul> <li> By left-clicking a new point is added. <li> By right-clicking a point is deleted. -<li> By left-clicking and holding, an exisiting point can be dragged. +<li> By left-clicking and holding, an existing point can be dragged. <li> By pressing arrow keys, the currently selected point is moved. <li> By pressing the 'DELETE' key, the currently selected point is deleted. <li> Between points the transferfunctions are linear interpolated. </ul> There are three transfer functions to customize: \subsection QVV_GO Grayvalue -> Opacity \imageMacro{QmitkVolumeVisualization_Opacity.png,"Gray values will be mapped to opacity.",8.04} An opacity of 0 means total transparent, an opacity of 1 means total opaque. The opacity editor allows changing the opacity for all gray values independently. You can alter the position of control points using your mouse. You can add control points by left-clicking on the graph. To remove a control point again you can right-click on the respective point. \subsection QVV_GC Grayvalue -> Color \imageMacro{QmitkVolumeVisualization_Color.png,"Gray values will be mapped to color.",8.81} The color transfer function editor also allows you to change its color by double-clicking a point. You can add color control points by left-clicking on the color bar. To remove a control point again right-click on the respective point. \subsection QVV_GGO Grayvalue and Gradient -> Opacity \imageMacro{QmitkVolumeVisualization_Gradient.png,"",8.85} The gradient editor allows you to change the gradient influence for all gray values independently. You can move the existing control points using your mouse. Additionally, you can add control points by left-clicking on the graph. To remove a control point again, right-click on the respective point. */ diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp b/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp index cba95f5cf5..53662af647 100755 --- a/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp +++ b/Plugins/org.mitk.gui.qt.volumevisualization/src/internal/QmitkVolumeVisualizationView.cpp @@ -1,245 +1,245 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkVolumeVisualizationView.h" #include <vtkSmartVolumeMapper.h> #include <mitkImage.h> #include <mitkTimeNavigationController.h> #include <mitkTransferFunction.h> #include <mitkTransferFunctionInitializer.h> #include <mitkTransferFunctionProperty.h> #include <mitkNodePredicateDataType.h> #include <mitkNodePredicateDimension.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateOr.h> #include <mitkNodePredicateProperty.h> #include <mitkProperties.h> const std::string QmitkVolumeVisualizationView::VIEW_ID = "org.mitk.views.volumevisualization"; enum { DEFAULT_RENDERMODE = 0, RAYCAST_RENDERMODE = 1, GPU_RENDERMODE = 2 }; QmitkVolumeVisualizationView::QmitkVolumeVisualizationView() : QmitkAbstractView() , m_Controls(nullptr) { } void QmitkVolumeVisualizationView::SetFocus() { } void QmitkVolumeVisualizationView::CreateQtPartControl(QWidget* parent) { m_Controls = new Ui::QmitkVolumeVisualizationViewControls; m_Controls->setupUi(parent); m_Controls->volumeSelectionWidget->SetDataStorage(GetDataStorage()); m_Controls->volumeSelectionWidget->SetNodePredicate(mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType<mitk::Image>::New(), mitk::NodePredicateOr::New(mitk::NodePredicateDimension::New(3), mitk::NodePredicateDimension::New(4)), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")))); m_Controls->volumeSelectionWidget->SetSelectionIsOptional(true); m_Controls->volumeSelectionWidget->SetEmptyInfo(QString("Please select a 3D / 4D image volume")); m_Controls->volumeSelectionWidget->SetPopUpTitel(QString("Select image volume")); // Fill the transfer function presets in the generator widget std::vector<std::string> names; mitk::TransferFunctionInitializer::GetPresetNames(names); for (const auto& name : names) { m_Controls->transferFunctionGeneratorWidget->AddPreset(QString::fromStdString(name)); } // see vtkVolumeMapper::BlendModes m_Controls->blendMode->addItem("Composite", vtkVolumeMapper::COMPOSITE_BLEND); m_Controls->blendMode->addItem("Maximum intensity", vtkVolumeMapper::MAXIMUM_INTENSITY_BLEND); m_Controls->blendMode->addItem("Minimum intensity", vtkVolumeMapper::MINIMUM_INTENSITY_BLEND); m_Controls->blendMode->addItem("Average intensity", vtkVolumeMapper::AVERAGE_INTENSITY_BLEND); m_Controls->blendMode->addItem("Additive", vtkVolumeMapper::ADDITIVE_BLEND); connect(m_Controls->volumeSelectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkVolumeVisualizationView::OnCurrentSelectionChanged); connect(m_Controls->enableRenderingCB, SIGNAL(toggled(bool)), this, SLOT(OnEnableRendering(bool))); connect(m_Controls->blendMode, SIGNAL(activated(int)), this, SLOT(OnBlendMode(int))); connect(m_Controls->transferFunctionGeneratorWidget, SIGNAL(SignalUpdateCanvas()), m_Controls->transferFunctionWidget, SLOT(OnUpdateCanvas())); connect(m_Controls->transferFunctionGeneratorWidget, SIGNAL(SignalTransferFunctionModeChanged(int)), SLOT(OnMitkInternalPreset(int))); m_Controls->enableRenderingCB->setEnabled(false); m_Controls->blendMode->setEnabled(false); m_Controls->transferFunctionWidget->setEnabled(false); m_Controls->transferFunctionGeneratorWidget->setEnabled(false); m_Controls->volumeSelectionWidget->SetAutoSelectNewNodes(true); this->m_TimePointChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_TimePointChangeListener, &QmitkSliceNavigationListener::SelectedTimePointChanged, this, &QmitkVolumeVisualizationView::OnSelectedTimePointChanged); } void QmitkVolumeVisualizationView::RenderWindowPartActivated(mitk::IRenderWindowPart *renderWindowPart) { this->m_TimePointChangeListener.RenderWindowPartActivated(renderWindowPart); } void QmitkVolumeVisualizationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart *renderWindowPart) { this->m_TimePointChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void QmitkVolumeVisualizationView::OnMitkInternalPreset(int mode) { auto node = m_SelectedNode.Lock(); if (node.IsNull()) { return; } mitk::TransferFunctionProperty::Pointer transferFuncProp; if (node->GetProperty(transferFuncProp, "TransferFunction")) { // first item is only information if (--mode == -1) return; - // -- Creat new TransferFunction + // -- Create new TransferFunction mitk::TransferFunctionInitializer::Pointer tfInit = mitk::TransferFunctionInitializer::New(transferFuncProp->GetValue()); tfInit->SetTransferFunctionMode(mode); RequestRenderWindowUpdate(); m_Controls->transferFunctionWidget->OnUpdateCanvas(); } } void QmitkVolumeVisualizationView::OnCurrentSelectionChanged(QList<mitk::DataNode::Pointer> nodes) { m_SelectedNode = nullptr; if (nodes.empty() || nodes.front().IsNull()) { UpdateInterface(); return; } auto selectedNode = nodes.front(); auto image = dynamic_cast<mitk::Image*>(selectedNode->GetData()); if (nullptr != image) { m_SelectedNode = selectedNode; } UpdateInterface(); } void QmitkVolumeVisualizationView::OnEnableRendering(bool state) { auto selectedNode = m_SelectedNode.Lock(); if (selectedNode.IsNull()) { return; } selectedNode->SetProperty("volumerendering", mitk::BoolProperty::New(state)); UpdateInterface(); RequestRenderWindowUpdate(); } void QmitkVolumeVisualizationView::OnBlendMode(int index) { auto selectedNode = m_SelectedNode.Lock(); if (selectedNode.IsNull()) return; int mode = m_Controls->blendMode->itemData(index).toInt(); selectedNode->SetProperty("volumerendering.blendmode", mitk::IntProperty::New(mode)); this->RequestRenderWindowUpdate(); } void QmitkVolumeVisualizationView::OnSelectedTimePointChanged(const mitk::TimePointType & /*newTimePoint*/) { this->UpdateInterface(); } void QmitkVolumeVisualizationView::UpdateInterface() { if (m_SelectedNode.IsExpired()) { // turnoff all m_Controls->enableRenderingCB->setChecked(false); m_Controls->enableRenderingCB->setEnabled(false); m_Controls->blendMode->setCurrentIndex(0); m_Controls->blendMode->setEnabled(false); m_Controls->transferFunctionWidget->SetDataNode(nullptr); m_Controls->transferFunctionWidget->setEnabled(false); m_Controls->transferFunctionGeneratorWidget->SetDataNode(nullptr); m_Controls->transferFunctionGeneratorWidget->setEnabled(false); return; } bool enabled = false; auto selectedNode = m_SelectedNode.Lock(); selectedNode->GetBoolProperty("volumerendering", enabled); m_Controls->enableRenderingCB->setEnabled(true); m_Controls->enableRenderingCB->setChecked(enabled); if (!enabled) { // turnoff all except volumerendering checkbox m_Controls->blendMode->setCurrentIndex(0); m_Controls->blendMode->setEnabled(false); m_Controls->transferFunctionWidget->SetDataNode(nullptr); m_Controls->transferFunctionWidget->setEnabled(false); m_Controls->transferFunctionGeneratorWidget->SetDataNode(nullptr); m_Controls->transferFunctionGeneratorWidget->setEnabled(false); return; } // otherwise we can activate em all m_Controls->blendMode->setEnabled(true); // Determine Combo Box mode int blendMode; if (selectedNode->GetIntProperty("volumerendering.blendmode", blendMode)) m_Controls->blendMode->setCurrentIndex(blendMode); const auto timeStep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimeStep(); m_Controls->transferFunctionWidget->SetDataNode(selectedNode, timeStep); m_Controls->transferFunctionWidget->setEnabled(true); m_Controls->transferFunctionGeneratorWidget->SetDataNode(selectedNode, timeStep); m_Controls->transferFunctionGeneratorWidget->setEnabled(true); } diff --git a/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox b/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox index d25bb1c70d..d7d2d1025e 100644 --- a/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox +++ b/Plugins/org.mitk.gui.qt.xnat/documentation/UserManual/QmitkXnatPluginManual.dox @@ -1,113 +1,113 @@ /** \page org_mitk_gui_qt_xnat The XNAT Plugin \imageMacro{xnat-docu-icon.png,"Icon of XNAT Plugin",1.00} \tableofcontents \section org_mitk_gui_qt_xnatOverview Overview This plug-in is allows the communication with a XNAT server from within MITK. The benefits of this plug-in are: <ul> <li>Browsing through the XNAT data hierarchy <li>Downloading data and visualize/process it in the MITK Workbench <li>Uploading data from within the MITK Workbench </ul> \imageMacro{QmitkXnat_IMGTreeBrowser.png,"The XNAT tree-browser plugin", 6.00} \section org_mitk_gui_qt_xnatConnection Connect to XNAT For communicating with XNAT you have to connect to your XNAT instance. \subsection org_mitk_gui_qt_xnatPreferences XNAT preferences In order to establish the connection to XNAT you have to specify the XNAT server address, username and password in the XNAT preference page. It is also possible to specify a network proxy if you are behind one (this could lead to connection errors). Via the download path you can tell MITK where to save the data that is uploaded or downloaded. A screenshot of the preference page can be seen below. \imageMacro{QmitkXnat_IMGPreferences.png,"The XNAT preference page", 10.00} \subsection org_mitk_gui_qt_xnatSessionHandling Session time-out handling Once you are connected to XNAT, MITK takes care about the session handling. A existing XNAT session times out after a certain period of inactivity, usually after 15 minutes. One minute before session time-out MITK asks you to renew the session: \imageMacro{QmitkXnat_IMGSessionAboutToTimeOut.png,"Notification that the session will time-out in a minute", 6.00} If you do not renew the session MITK notifies you if the session has expired: \imageMacro{QmitkXnat_IMGSessionExpired.png,"Notification that the session has expired", 6.00} \section org_mitk_gui_qt_xnatBrowsing Browse data -Once you are connected to XNAT, MITK displays the XNAT data hierachy as a tree within the XNAT tree browser. -You can browse through the data by expanding the tree items ( which ist also possible via double click). +Once you are connected to XNAT, MITK displays the XNAT data hierarchy as a tree within the XNAT tree browser. +You can browse through the data by expanding the tree items (which is also possible via double click). If you hover the mouse cursor over an item you will see a tool tip with detailed information. The following table gives an overview about the icons of the treeview and the related XNAT objects <table> <caption id="multi_row">XNAT Icon Overview</caption> <tr><th>Icon <th>XNAT object <tr><td>\image html xnat-server.png <td>XNAT Server <tr><td>\image html xnat-project.png <td>XNAT Project <tr><td>\image html xnat-subject.png <td>XNAT Subject <tr><td>\image html xnat-experiment.png <td>XNAT Experiment <tr><td>\image html xnat-folder-icon.png <td>XNAT Scan top-level folder <tr><td>\image html xnat-scan.png <td>XNAT Scan <tr><td>\image html xnat-folder-icon.png <td>XNAT Resource top-level folder <tr><td>\image html xnat-resource.png <td>XNAT Resource folder <tr><td>\image html xnat-file.png <td>XNAT File </table> If you have selected a XNAT project, subject or experiment, MITK displays detailed information in a separate info area below the tree browser \section org_mitk_gui_qt_xnatDownload Download data MITK allows you to download your data from XNAT. You can either simply download the data to your file system or your can download it and open it immediately in the workbench. \subsection org_mitk_gui_qt_xnatDownload_file_system Download data to file system -If you just want to download data, simply right-click on a XNAT file or scan on the tree brower and select "Download". The data will be stored in the specified download location. +If you just want to download data, simply right-click on a XNAT file or scan on the tree browser and select "Download". The data will be stored in the specified download location. \subsection org_mitk_gui_qt_xnatDownload_in_MITK Download data and open it in MITK You can download and open data in three ways: <ul> <li>One is via right-click on a file or scan and selecting "Download and open". <li>You can also double-click on a file or scan. MITK will then ask you if you want to download and open the data. <li>The other one is via selecting a file or scan with left-click and then click on the download button above the tree view </ul> -\imageMacro{QmitkXnat_IMGDownloadButton.png,"The XNAT dowload button", 16.00} +\imageMacro{QmitkXnat_IMGDownloadButton.png,"The XNAT download button", 16.00} \section org_mitk_gui_qt_xnatUpload Upload data You can also upload data to XNAT from within the workbench. Please note that it is currently only possible to upload files as resources. Uploading DICOMs is not yet available. \subsection org_mitk_gui_qt_xnatUpload1 Upload from file system If you just want to upload a local file, right-click on a resource and select "Upload". A file dialog will open, which allows you to select a file for upload. \subsection org_mitk_gui_qt_xnatUpload2 Upload via data manager If you want to upload data from within the MITK Workbench you can simply right-click on the data node in the data manager and select "Upload to XNAT". An "XNAT Upload dialog" will appear: \imageMacro{QmitkXnat_IMGUploadDialog.png,"The XNAT upload dialog", 16.00} You can then either select a existing resource folder if MITK is able to find ones or you can select the upload destination in a tree view. \subsection org_mitk_gui_qt_xnatUpload3 Upload via drag and drop Another way to upload the data is to drag the data node on the XNAT resource where you want to upload it to. \subsection org_mitk_gui_qt_xnatUpload4 Upload via XNAT Plugin Finally, if you select a data node and you select a XNAT resource, the upload button of the XNAT plugin will be enabled. If you click on that, the data will be uploaded. \imageMacro{QmitkXnat_IMGUploadButton.png,"The XNAT upload button", 16.00} \section org_mitk_gui_qt_xnatAddResourceFolder Create a resource folder You can also create new resources (i.e. folders to group your files in XNAT). Therefor you can either right-click on a project, subject, experiment or scan and enter the name of the folder in the appearing dialog. Or you simply select one of these items and click on the "Add folder button" above the tree browser. \imageMacro{QmitkXnat_IMGAddFolderButton.png,"The XNAT add folder button", 16.00} \subsection org_mitk_gui_qt_xnatCreateSubject Create a subject You can create subjects by right-clicking on a project and selecting "Create new subject". A dialog will appear where you have to enter the subject information. \subsection org_mitk_gui_qt_xnatCreateExperiment Create a experiment You can create experiments by right-clicking on a subject and selecting "Create new experiment". A dialog will appear where you have to enter the experiment information. */ diff --git a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatConnectionPreferencePage.cpp b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatConnectionPreferencePage.cpp index 30d9b3f565..5eaf8a507d 100644 --- a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatConnectionPreferencePage.cpp +++ b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatConnectionPreferencePage.cpp @@ -1,296 +1,296 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkXnatConnectionPreferencePage.h" #include "QmitkXnatTreeBrowserView.h" #include "org_mitk_gui_qt_xnatinterface_Activator.h" #include <QFileDialog> #include <QLabel> #include <QPushButton> #include <QLineEdit> #include <QGridLayout> #include <QMessageBox> #include <QApplication> #include <QMap> #include "ctkXnatSession.h" #include "ctkXnatLoginProfile.h" #include "ctkXnatException.h" #include <mitkIOUtil.h> #include <mitkCoreServices.h> #include <mitkIPreferencesService.h> #include <mitkIPreferences.h> using namespace berry; namespace { mitk::IPreferences* GetPreferences() { auto* preferencesService = mitk::CoreServices::GetPreferencesService(); return preferencesService->GetSystemPreferences()->Node(QmitkXnatTreeBrowserView::VIEW_ID.toStdString()); } } QmitkXnatConnectionPreferencePage::QmitkXnatConnectionPreferencePage() : m_Control(nullptr) { } void QmitkXnatConnectionPreferencePage::Init(berry::IWorkbench::Pointer) { } void QmitkXnatConnectionPreferencePage::CreateQtControl(QWidget* parent) { m_Controls.setupUi(parent); m_Control = new QWidget(parent); m_Control->setLayout(m_Controls.gridLayout); ctkXnatSession* session; try { session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); } catch (std::invalid_argument&) { session = nullptr; } if (session != nullptr && session->isOpen()) { m_Controls.xnatTestConnectionLabel->setStyleSheet("color: green"); m_Controls.xnatTestConnectionLabel->setText("Already connected."); m_Controls.xnatTestConnectionButton->setEnabled(false); } const QIntValidator *portV = new QIntValidator(0, 65535, parent); m_Controls.inXnatPort->setValidator(portV); const QRegExp hostRx("^(https?)://[^ /](\\S)+$"); const QRegExpValidator *hostV = new QRegExpValidator(hostRx, parent); m_Controls.inXnatHostAddress->setValidator(hostV); connect(m_Controls.xnatTestConnectionButton, SIGNAL(clicked()), this, SLOT(TestConnection())); connect(m_Controls.inXnatHostAddress, SIGNAL(editingFinished()), this, SLOT(UrlChanged())); connect(m_Controls.inXnatDownloadPath, SIGNAL(editingFinished()), this, SLOT(DownloadPathChanged())); connect(m_Controls.cbUseNetworkProxy, SIGNAL(toggled(bool)), this, SLOT(onUseNetworkProxy(bool))); connect(m_Controls.btnDownloadPath, SIGNAL(clicked()), this, SLOT(OnDownloadPathButtonClicked())); m_Controls.groupBoxProxySettings->setVisible(m_Controls.cbUseNetworkProxy->isChecked()); this->Update(); } QWidget* QmitkXnatConnectionPreferencePage::GetQtControl() const { return m_Control; } bool QmitkXnatConnectionPreferencePage::PerformOk() { auto* prefs = GetPreferences(); if (prefs != nullptr) { prefs->Put(m_Controls.xnatHostAddressLabel->text().toStdString(), m_Controls.inXnatHostAddress->text().toStdString()); prefs->Put(m_Controls.xnatPortLabel->text().toStdString(), m_Controls.inXnatPort->text().toStdString()); prefs->Put(m_Controls.xnatUsernameLabel->text().toStdString(), m_Controls.inXnatUsername->text().toStdString()); prefs->Put(m_Controls.xnatPasswortLabel->text().toStdString(), m_Controls.inXnatPassword->text().toStdString()); prefs->Put(m_Controls.xnatDownloadPathLabel->text().toStdString(), m_Controls.inXnatDownloadPath->text().toStdString()); // Network proxy settings prefs->PutBool(m_Controls.cbUseNetworkProxy->text().toStdString(), m_Controls.cbUseNetworkProxy->isChecked()); prefs->Put(m_Controls.proxyAddressLabel->text().toStdString(), m_Controls.inProxyAddress->text().toStdString()); prefs->Put(m_Controls.proxyPortLabel->text().toStdString(), m_Controls.inProxyPort->text().toStdString()); prefs->Put(m_Controls.proxyUsernameLabel->text().toStdString(), m_Controls.inProxyUsername->text().toStdString()); prefs->Put(m_Controls.proxyPasswordLabel->text().toStdString(), m_Controls.inProxyPassword->text().toStdString()); // Silent Mode prefs->PutBool(m_Controls.cbUseSilentMode->text().toStdString(), m_Controls.cbUseSilentMode->isChecked()); //Write prefs->Flush(); return true; } return false; } void QmitkXnatConnectionPreferencePage::PerformCancel() { } bool QmitkXnatConnectionPreferencePage::UserInformationEmpty() { // To check empty QLineEdits in the following QString errString; if (m_Controls.inXnatHostAddress->text().isEmpty()) { errString += "Server Address is empty.\n"; } if (m_Controls.inXnatUsername->text().isEmpty()) { errString += "Username is empty.\n"; } if (m_Controls.inXnatPassword->text().isEmpty()) { errString += "Password is empty.\n"; } // if something is empty if (!errString.isEmpty()) { m_Controls.xnatTestConnectionLabel->setStyleSheet("color: red"); m_Controls.xnatTestConnectionLabel->setText("Connecting failed.\n" + errString); return true; } else { return false; } } void QmitkXnatConnectionPreferencePage::Update() { auto* prefs = GetPreferences(); if (prefs != nullptr) { m_Controls.inXnatHostAddress->setText(QString::fromStdString(prefs->Get(m_Controls.xnatHostAddressLabel->text().toStdString(), m_Controls.inXnatHostAddress->text().toStdString()))); m_Controls.inXnatPort->setText(QString::fromStdString(prefs->Get(m_Controls.xnatPortLabel->text().toStdString(), m_Controls.inXnatPort->text().toStdString()))); m_Controls.inXnatUsername->setText(QString::fromStdString(prefs->Get(m_Controls.xnatUsernameLabel->text().toStdString(), m_Controls.inXnatUsername->text().toStdString()))); m_Controls.inXnatPassword->setText(QString::fromStdString(prefs->Get(m_Controls.xnatPasswortLabel->text().toStdString(), m_Controls.inXnatPassword->text().toStdString()))); m_Controls.inXnatDownloadPath->setText(QString::fromStdString(prefs->Get(m_Controls.xnatDownloadPathLabel->text().toStdString(), m_Controls.inXnatDownloadPath->text().toStdString()))); // Network proxy settings m_Controls.cbUseNetworkProxy->setChecked(prefs->GetBool(m_Controls.cbUseNetworkProxy->text().toStdString(), false)); m_Controls.inProxyAddress->setText(QString::fromStdString(prefs->Get(m_Controls.proxyAddressLabel->text().toStdString(), m_Controls.inProxyAddress->text().toStdString()))); m_Controls.inProxyPort->setText(QString::fromStdString(prefs->Get(m_Controls.proxyPortLabel->text().toStdString(), m_Controls.inProxyPort->text().toStdString()))); m_Controls.inProxyUsername->setText(QString::fromStdString(prefs->Get(m_Controls.proxyUsernameLabel->text().toStdString(), m_Controls.inProxyUsername->text().toStdString()))); m_Controls.inProxyPassword->setText(QString::fromStdString(prefs->Get(m_Controls.proxyPasswordLabel->text().toStdString(), m_Controls.inProxyPassword->text().toStdString()))); // Silent Mode m_Controls.cbUseSilentMode->setChecked(prefs->GetBool(m_Controls.cbUseSilentMode->text().toStdString(), false)); } } void QmitkXnatConnectionPreferencePage::UrlChanged() { m_Controls.inXnatHostAddress->setStyleSheet(""); QString str = m_Controls.inXnatHostAddress->text(); while (str.endsWith("/")) { str = str.left(str.length() - 1); } m_Controls.inXnatHostAddress->setText(str); QUrl url(m_Controls.inXnatHostAddress->text()); if (!url.isValid()) { m_Controls.inXnatHostAddress->setStyleSheet("background-color: red"); } } void QmitkXnatConnectionPreferencePage::DownloadPathChanged() { m_Controls.inXnatDownloadPath->setStyleSheet(""); QString downloadPath = m_Controls.inXnatDownloadPath->text(); if (!downloadPath.isEmpty()) { if (downloadPath.lastIndexOf("/") != downloadPath.size() - 1) { downloadPath.append("/"); m_Controls.inXnatDownloadPath->setText(downloadPath); } QFileInfo path(m_Controls.inXnatDownloadPath->text()); if (!path.isDir()) { m_Controls.inXnatDownloadPath->setStyleSheet("background-color: red"); } } } void QmitkXnatConnectionPreferencePage::onUseNetworkProxy(bool status) { m_Controls.groupBoxProxySettings->setVisible(status); } void QmitkXnatConnectionPreferencePage::OnDownloadPathButtonClicked() { QString dir = QFileDialog::getExistingDirectory(); if (!dir.endsWith("/") || !dir.endsWith("\\")) dir.append("/"); m_Controls.inXnatDownloadPath->setText(dir); } void QmitkXnatConnectionPreferencePage::TestConnection() { if(UserInformationEmpty()) { return; } try { mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); } catch (const std::invalid_argument &) { if (!UserInformationEmpty()) { PerformOk(); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CreateXnatSession(); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); } } try { mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->OpenXnatSession(); m_Controls.xnatTestConnectionLabel->setStyleSheet("color: green"); m_Controls.xnatTestConnectionLabel->setText("Connecting successful."); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CloseXnatSession(); } catch (const ctkXnatAuthenticationException& auth) { m_Controls.xnatTestConnectionLabel->setStyleSheet("color: red"); m_Controls.xnatTestConnectionLabel->setText("Connecting failed:\nAuthentication error."); MITK_INFO << auth.message().toStdString(); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CloseXnatSession(); } catch (const ctkException& e) { m_Controls.xnatTestConnectionLabel->setStyleSheet("color: red"); - m_Controls.xnatTestConnectionLabel->setText("Connecting failed:\nInvalid Server Adress\nPossibly due to missing OpenSSL for HTTPS connections"); + m_Controls.xnatTestConnectionLabel->setText("Connecting failed:\nInvalid Server Address\nPossibly due to missing OpenSSL for HTTPS connections"); MITK_INFO << e.message().toStdString(); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CloseXnatSession(); } } diff --git a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserView.cpp b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserView.cpp index b30b0f326a..0df20f10f2 100644 --- a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserView.cpp +++ b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserView.cpp @@ -1,1338 +1,1338 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkXnatTreeBrowserView.h" #include <mitkCoreServices.h> #include <mitkIPreferencesService.h> #include <mitkIPreferences.h> // Qmitk #include "org_mitk_gui_qt_xnatinterface_Activator.h" // CTK XNAT Core #include <ctkXnatAssessor.h> #include <ctkXnatAssessorFolder.h> #include <ctkXnatDataModel.h> #include <ctkXnatException.h> #include <ctkXnatExperiment.h> #include "ctkXnatFile.h" #include <ctkXnatProject.h> #include <ctkXnatReconstruction.h> #include <ctkXnatReconstructionFolder.h> #include <ctkXnatResource.h> #include <ctkXnatResourceFolder.h> #include <ctkXnatScan.h> #include <ctkXnatScanFolder.h> #include <ctkXnatSubject.h> // MITK XNAT #include <mitkDataStorage.h> #include <QmitkIOUtil.h> #include <QmitkXnatProjectWidget.h> #include <QmitkXnatSubjectWidget.h> #include <QmitkXnatExperimentWidget.h> #include <QmitkXnatCreateObjectDialog.h> #include <QmitkXnatUploadFromDataStorageDialog.h> // Qt #include <QAction> #include <QClipboard> #include <QDateTime> #include <QDialog> #include <QDir> #include <QDirIterator> #include <QFileDialog> #include <QInputDialog> #include <QMenu> #include <QMessageBox> #include <QTimer> #include <QFileInfoList> #include <QmitkPreferencesDialog.h> // Poco #include <Poco/Zip/Decompress.h> const QString QmitkXnatTreeBrowserView::VIEW_ID = "org.mitk.views.xnat.treebrowser"; static bool isDirWriteable(QDir myDir) { const QFileInfoList tmpInfo = myDir.entryInfoList(); foreach (QFileInfo f, tmpInfo) { if(f.fileName() == ".") return f.isWritable(); } return true; } static bool doesDirExist(QDir myDir) { if (!myDir.exists()) { if(!myDir.mkpath(".")) { MITK_INFO << "Path Creation Failed."; return false; } } return true; } QmitkXnatTreeBrowserView::QmitkXnatTreeBrowserView() : m_DataStorageServiceTracker(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetContext()), m_TreeModel(new QmitkXnatTreeModel()), m_Tracker(nullptr), m_DownloadPath(QString::fromStdString(mitk::CoreServices::GetPreferencesService()->GetSystemPreferences()->Node(VIEW_ID.toStdString())->Get("Download Path", ""))), m_SilentMode(false) { m_DataStorageServiceTracker.open(); // Set DownloadPath if (m_DownloadPath.isEmpty()) { QString xnatFolder = "XNAT_DOWNLOADS"; QDir dir(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetContext()->getDataFile("").absoluteFilePath()); dir.mkdir(xnatFolder); dir.setPath(dir.path() + "/" + xnatFolder); m_DownloadPath = dir.path() + "/"; } } QmitkXnatTreeBrowserView::~QmitkXnatTreeBrowserView() { m_DataStorageServiceTracker.close(); delete m_TreeModel; delete m_Tracker; } void QmitkXnatTreeBrowserView::SetFocus() { } void QmitkXnatTreeBrowserView::FilePathNotAvailableWarning(QString file) { MITK_INFO << "Download of " << file.toStdString() << " failed! Download Path not available!"; QMessageBox::critical(m_Controls.treeView, "Download failed!", "Download of " + file + " failed!\nDownload Path " + m_DownloadPath + " not available. \n\nChange Download Path in Settings!"); QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.SetSelectedPage("org.mitk.gui.qt.application.XnatConnectionPreferencePage"); _PreferencesDialog.exec(); m_Controls.groupBox->hide(); } void QmitkXnatTreeBrowserView::ToggleConnection() { ctkXnatSession* session = nullptr; try { session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); } catch (std::invalid_argument&) { mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CreateXnatSession(); session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); } if (session != nullptr && session->isOpen()) { mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CloseXnatSession(); m_Controls.btnXnatConnect->setToolTip("Connect"); m_Controls.btnXnatConnect->setIcon(QIcon(":/xnat-plugin/xnat-connect.png")); CleanUp(); } else if (session != nullptr && !session->isOpen()) { try { mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->OpenXnatSession(); m_Controls.btnXnatConnect->setToolTip("Disconnect"); m_Controls.btnXnatConnect->setIcon(QIcon(":/xnat-plugin/xnat-disconnect.png")); m_Controls.searchField->setEnabled(true); m_Controls.searchModeBox->setEnabled(true); } catch (const ctkXnatAuthenticationException& auth) { MITK_INFO << auth.message().toStdString(); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CloseXnatSession(); QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.SetSelectedPage("org.mitk.gui.qt.application.XnatConnectionPreferencePage"); _PreferencesDialog.exec(); } catch (const ctkException& e) { MITK_INFO << e.message().toStdString(); mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatSessionManager()->CloseXnatSession(); QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.SetSelectedPage("org.mitk.gui.qt.application.XnatConnectionPreferencePage"); _PreferencesDialog.exec(); } catch (...) { QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.SetSelectedPage("org.mitk.gui.qt.application.XnatConnectionPreferencePage"); _PreferencesDialog.exec(); } } } void QmitkXnatTreeBrowserView::CreateQtPartControl(QWidget *parent) { // Create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.treeView->setModel(m_TreeModel); m_Controls.treeView->header()->hide(); m_Controls.treeView->setSelectionMode(QAbstractItemView::ExtendedSelection); m_Controls.treeView->setAcceptDrops(true); m_Controls.treeView->setDropIndicatorShown(true); m_Controls.treeView->setSelectionMode(QAbstractItemView::SingleSelection); m_Controls.treeView->setContextMenuPolicy(Qt::CustomContextMenu); m_Controls.groupBox->hide(); m_Controls.wgtExperimentInfo->hide(); m_Controls.wgtSubjectInfo->hide(); m_Controls.wgtProjectInfo->hide(); m_Tracker = new mitk::XnatSessionTracker(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()); m_ContextMenu = new QMenu(m_Controls.treeView); connect(m_Controls.treeView, SIGNAL(clicked(const QModelIndex&)), SLOT(ItemSelected(const QModelIndex&))); connect(m_Controls.treeView, SIGNAL(customContextMenuRequested(const QPoint&)), this, SLOT(OnContextMenuRequested(const QPoint&))); connect(m_Tracker, SIGNAL(AboutToBeClosed(ctkXnatSession*)), this, SLOT(CleanTreeModel(ctkXnatSession*))); connect(m_Tracker, SIGNAL(Opened(ctkXnatSession*)), this, SLOT(UpdateSession(ctkXnatSession*))); m_Tracker->Open(); connect(m_Controls.treeView, SIGNAL(doubleClicked(const QModelIndex&)), this, SLOT(OnActivatedNode(const QModelIndex&))); connect(m_Controls.treeView, SIGNAL(clicked(const QModelIndex&)), this, SLOT(OnXnatNodeSelected(const QModelIndex&))); connect(m_TreeModel, SIGNAL(ResourceDropped(const QList<mitk::DataNode*>&, ctkXnatObject*, const QModelIndex&)), this, SLOT(OnUploadResource(const QList<mitk::DataNode*>&, ctkXnatObject*, const QModelIndex&))); connect(m_Controls.btnXnatConnect, SIGNAL(clicked()), SLOT(ToggleConnection())); connect(m_Controls.btnXnatUpload, SIGNAL(clicked()), this, SLOT(OnUploadFromDataStorage())); connect(m_Controls.btnXnatDownload, SIGNAL(clicked()), this, SLOT(OnDownloadSelectedXnatFile())); connect(m_Controls.btnCreateXnatFolder, SIGNAL(clicked()), this, SLOT(OnCreateResourceFolder())); connect(m_Controls.searchField, SIGNAL(textChanged(const QString&)), this, SLOT(Search(const QString&))); } void QmitkXnatTreeBrowserView::OnCreateResourceFolder() { QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); if(!index.isValid()) return; ctkXnatObject* parent = index.data(Qt::UserRole).value<ctkXnatObject*>(); this->InternalAddResourceFolder(parent); OnContextMenuRefreshItem(); } void QmitkXnatTreeBrowserView::Search(const QString &toSearch) { if(m_AlreadyInSearch) return; m_AlreadyInSearch = true; m_Controls.treeView->collapseAll(); m_Controls.treeView->expandToDepth(m_Controls.searchModeBox->currentIndex()); m_Controls.treeView->clearSelection(); foreach (const QModelIndex &hidden, m_hiddenItems) { m_Controls.treeView->setRowHidden(hidden.row(),hidden.parent(),false); } m_hiddenItems.clear(); if(toSearch.isEmpty()) { m_Controls.treeView->collapseAll(); m_Controls.treeView->expandToDepth(0); m_AlreadyInSearch = false; return; } QModelIndexList items = m_Controls.treeView->model()->match( m_Controls.treeView->model()->index(0,0), Qt::DisplayRole, QVariant::fromValue(toSearch), -1, Qt::MatchContains|Qt::MatchRecursive); if(!items.isEmpty()) { foreach (const QModelIndex &match, items) { int depth = 0; QModelIndex tparent = match; while ( tparent.parent().isValid() ) { tparent = tparent.parent(); depth++; } switch (depth) { case 1: //Project Level if(m_Controls.searchModeBox->currentIndex() == ProjectLevel) { m_hiddenItems.append(match); m_Controls.treeView->setRowHidden(match.row(),match.parent(),true); } break; case 2: //Patient level if(m_Controls.searchModeBox->currentIndex() == SubjectLevel) { m_hiddenItems.append(match); m_Controls.treeView->setRowHidden(match.row(),match.parent(),true); } break; default: break; } } } m_AlreadyInSearch = false; } void QmitkXnatTreeBrowserView::OnDownloadSelectedXnatFile() { QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); if(!index.isValid()) return; ctkXnatObject* selectedXnatObject = index.data(Qt::UserRole).value<ctkXnatObject*>(); bool enableDownload = dynamic_cast<ctkXnatFile*>(selectedXnatObject) != nullptr; enableDownload |= dynamic_cast<ctkXnatScan*>(selectedXnatObject) != nullptr; if (enableDownload) { this->InternalFileDownload(index, true); } } void QmitkXnatTreeBrowserView::OnUploadFromDataStorage() { QmitkXnatUploadFromDataStorageDialog dialog; dialog.SetDataStorage(this->GetDataStorage()); int result = dialog.exec(); if (result == QDialog::Accepted) { QList<mitk::DataNode*> nodes; nodes << dialog.GetSelectedNode().GetPointer(); QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); if (!index.isValid()) return; ctkXnatObject* parent = m_TreeModel->xnatObject(index); this->OnUploadResource(nodes, parent, index); } } void QmitkXnatTreeBrowserView::OnXnatNodeSelected(const QModelIndex& index) { if (!index.isValid()) return; ctkXnatObject* selectedXnatObject = index.data(Qt::UserRole).value<ctkXnatObject*>(); // enable download button bool enableDownload = dynamic_cast<ctkXnatFile*>(selectedXnatObject) != nullptr; enableDownload |= dynamic_cast<ctkXnatScan*>(selectedXnatObject) != nullptr; m_Controls.btnXnatDownload->setEnabled(enableDownload); // enable folder creation bool enableCreateFolder = dynamic_cast<ctkXnatProject*>(selectedXnatObject) != nullptr; enableCreateFolder |= dynamic_cast<ctkXnatSubject*>(selectedXnatObject) != nullptr; enableCreateFolder |= dynamic_cast<ctkXnatExperiment*>(selectedXnatObject) != nullptr; enableCreateFolder |= dynamic_cast<ctkXnatResourceFolder*>(selectedXnatObject) != nullptr; m_Controls.btnCreateXnatFolder->setEnabled(enableCreateFolder); // enable upload bool enableUpload = dynamic_cast<ctkXnatResource*>(selectedXnatObject) != nullptr; m_Controls.btnXnatUpload->setEnabled(enableUpload); } void QmitkXnatTreeBrowserView::OnActivatedNode(const QModelIndex& index) { if (!index.isValid()) return; ctkXnatObject* selectedXnatObject = index.data(Qt::UserRole).value<ctkXnatObject*>(); bool enableDownload = dynamic_cast<ctkXnatFile*>(selectedXnatObject) != nullptr; enableDownload |= dynamic_cast<ctkXnatScan*>(selectedXnatObject) != nullptr; if (enableDownload) { if(!m_SilentMode) { QMessageBox msgBox; QString fname = selectedXnatObject->name() != "" ? selectedXnatObject->name() : index.data(Qt::DisplayRole).toString(); QString msg ("Do you want to download "+ fname +"?"); msgBox.setWindowTitle("MITK XNAT download"); msgBox.setText(msg); msgBox.setIcon(QMessageBox::Question); msgBox.setStandardButtons(QMessageBox::Ok | QMessageBox::Cancel); int result = msgBox.exec(); if (result == QMessageBox::Ok) { InternalFileDownload(index, true); } } else { InternalFileDownload(index, true); } } } void QmitkXnatTreeBrowserView::UpdateSession(ctkXnatSession* session) { if (session != nullptr && session->isOpen()) { // Fill model and show in the GUI m_TreeModel->addDataModel(session->dataModel()); m_Controls.treeView->reset(); connect(session, SIGNAL(progress(QUuid,double)), this, SLOT(OnProgress(QUuid,double))); connect(session, SIGNAL(timedOut()), this, SLOT(SessionTimedOutMsg())); connect(session, SIGNAL(aboutToTimeOut()), this, SLOT(SessionTimesOutSoonMsg())); } } void QmitkXnatTreeBrowserView::CleanTreeModel(ctkXnatSession* session) { if (session != nullptr) { m_TreeModel->removeDataModel(session->dataModel()); m_Controls.treeView->reset(); } } void QmitkXnatTreeBrowserView::OnProgress(QUuid /*queryID*/, double progress) { if (progress > 0) { unsigned int currentProgress = progress*100; if (m_Controls.groupBox->isHidden()) { m_Controls.groupBox->show(); m_Controls.progressBar->setValue(0); } m_Controls.progressBar->setValue(currentProgress); } } void QmitkXnatTreeBrowserView::OnPreferencesChanged(const mitk::IPreferences* prefs) { QString downloadPath = QString::fromStdString(prefs->Get("Download Path", "")); QDir downloadDir (downloadPath); if (downloadPath.length() != 0 && downloadDir.exists()) m_DownloadPath = downloadPath; m_SilentMode = prefs->GetBool("Silent Mode", false); } void QmitkXnatTreeBrowserView::InternalFileDownload(const QModelIndex& index, bool loadData) { if (!index.isValid()) return; QDir rootDownloadDir(m_DownloadPath); if(isDirWriteable(rootDownloadDir) == false) { - MITK_INFO << "Download directory access permission unsufficient! " << m_DownloadPath; - QMessageBox::critical(nullptr,"Download directory access permission unsufficient!", + MITK_INFO << "Download directory access permission insufficient! " << m_DownloadPath; + QMessageBox::critical(nullptr,"Download directory access permission insufficient!", "You have no permission to write to selected download directory " + m_DownloadPath +"!\n\nChange Download Path in Settings!"); QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.SetSelectedPage("org.mitk.gui.qt.application.XnatConnectionPreferencePage"); _PreferencesDialog.exec(); return; } ctkXnatObject* xnatObject = m_TreeModel->xnatObject(index); if (xnatObject != nullptr) { m_Controls.progressBar->setMinimum(0); m_Controls.progressBar->setMaximum(100); // The path to the downloaded file QString filePath; QDir downloadPath (m_DownloadPath); auto serverURL = QString::fromStdString(mitk::CoreServices::GetPreferencesService()->GetSystemPreferences()->Node(VIEW_ID.toStdString())->Get("Server Address", "")); bool isDICOM (false); bool filePathExists (true); // If a scan was selected, downloading the contained DICOM folder as ZIP ctkXnatScan* scan = dynamic_cast<ctkXnatScan*>(xnatObject); if (scan != nullptr) { isDICOM = true; if (!scan->isFetched()) scan->fetch(); QList<ctkXnatObject*> children = scan->children(); foreach (ctkXnatObject* obj, children) { if (obj->name() == "DICOM") { QString uriId = obj->resourceUri(); uriId.replace("/data/archive/projects/", ""); QString folderName = m_DownloadPath + uriId + "/"; downloadPath = folderName; filePathExists = doesDirExist(downloadPath); if(filePathExists) { try { this->InternalDICOMDownload(obj, downloadPath); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); return; } serverURL = obj->resourceUri(); } else { FilePathNotAvailableWarning("DICOM folder"); return; } } } } else { ctkXnatFile* file = dynamic_cast<ctkXnatFile*>(xnatObject); if (file == nullptr) { MITK_ERROR << "Selected XNAT object not downloadable!"; return; } QString uriId = file->parent()->resourceUri(); uriId.replace("/data/archive/projects/", ""); QString folderName = m_DownloadPath + uriId + "/"; downloadPath = folderName; filePathExists = doesDirExist(downloadPath); filePath = folderName + file->name(); // Checking if the file exists already if (downloadPath.exists(file->name())) { MITK_INFO << "File '" << file->name().toStdString() << "' already exists!"; serverURL = file->parent()->resourceUri(); } else { if (file->property("collection") == QString("DICOM")) { isDICOM = true; ctkXnatObject* parent = file->parent(); QString uriId = parent->resourceUri(); uriId.replace("/data/archive/projects/", ""); QString folderName = m_DownloadPath + uriId + "/"; downloadPath = folderName; filePathExists = doesDirExist(downloadPath); if(filePathExists) { try { this->InternalDICOMDownload(parent, downloadPath); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); return; } } else { FilePathNotAvailableWarning(parent->name()); return; } serverURL = parent->resourceUri(); } //Normal file download, no DICOM download else { if(filePathExists) { this->SetStatusInformation("Downloading file " + file->name()); file->download(filePath); } else { MITK_INFO << "File Download Failed."; } serverURL = file->parent()->resourceUri(); // Checking if the file exists now if (downloadPath.exists(file->name())) { MITK_INFO << "Download of " << file->name().toStdString() << " completed!"; if(!m_SilentMode) { QMessageBox msgBox; msgBox.setText("Download of " + file->name() + " completed!"); msgBox.setIcon(QMessageBox::Information); msgBox.exec(); } m_Controls.groupBox->hide(); } else { if(filePathExists) { MITK_INFO << "Download of " << file->name().toStdString() << " failed!"; QMessageBox::critical(m_Controls.treeView, "Download failed!", "Download of " + file->name() + " failed!"); m_Controls.groupBox->hide(); return; } else { FilePathNotAvailableWarning(file->name()); return; } } } } } if (loadData) { QFileInfoList fileList; if (isDICOM) { fileList = downloadPath.entryInfoList(QDir::Files); } else { QFileInfo fileInfo(filePath); fileList << fileInfo; } mitk::StringProperty::Pointer xnatURL = mitk::StringProperty::New(serverURL.toStdString()); try { this->InternalOpenFiles(fileList, xnatURL); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); return; } } } } void QmitkXnatTreeBrowserView::InternalDICOMDownload(ctkXnatObject *obj, QDir &DICOMDirPath) { QString filePath = m_DownloadPath + obj->property("label") + ".zip"; this->SetStatusInformation("Downloading DICOM series " + obj->parent()->name()); // In case of DICOM zip download we do not know the total file size - // Because of that the dowload progres cannot be calculated + // Because of that the download progress cannot be calculated // Because of that we use the busy indicator of the progress bar by setting min and max to 0 m_Controls.progressBar->setMinimum(0); m_Controls.progressBar->setMaximum(0); m_Controls.progressBar->show(); obj->download(filePath); std::ifstream in(filePath.toStdString().c_str(), std::ios::binary); poco_assert(in); // decompress to XNAT_DOWNLOAD dir Poco::Zip::Decompress dec(in, Poco::Path(DICOMDirPath.path().toStdString()), true); dec.decompressAllFiles(); in.close(); QFile::remove(filePath); // Checking if the file exists now if (DICOMDirPath.exists()) { if(!m_SilentMode) { MITK_INFO << "Download of DICOM series completed!"; QMessageBox msgBox; msgBox.setText("Download of DICOM series completed!"); msgBox.setIcon(QMessageBox::Information); msgBox.exec(); m_Controls.groupBox->hide(); } } else { MITK_INFO << "Download of DICOM series failed!"; QMessageBox msgBox; msgBox.setText("Download of DICOM series failed!"); msgBox.setIcon(QMessageBox::Critical); msgBox.exec(); m_Controls.groupBox->hide(); } } void QmitkXnatTreeBrowserView::InternalOpenFiles(const QFileInfoList & fileList, mitk::StringProperty::Pointer xnatURL) { if (fileList.isEmpty()) { MITK_WARN << "No files available for loading!"; return; } mitk::IDataStorageService* dsService = m_DataStorageServiceTracker.getService(); mitk::DataStorage::Pointer dataStorage = dsService->GetDataStorage()->GetDataStorage(); QStringList list; list << fileList.at(0).absoluteFilePath(); try { mitk::DataStorage::SetOfObjects::Pointer nodes = QmitkIOUtil::Load(list, *dataStorage); if (nodes->size() == 1) { mitk::DataNode* node = nodes->at(0); node->SetProperty("xnat.url", xnatURL); } } catch (const mitk::Exception& e) { MITK_INFO << e; return; } mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects( dsService->GetDataStorage()->GetDataStorage()); } void QmitkXnatTreeBrowserView::OnContextMenuDownloadFile() { QModelIndex index = m_Controls.treeView->currentIndex(); InternalFileDownload(index, false); } void QmitkXnatTreeBrowserView::OnContextMenuDownloadAndOpenFile() { QModelIndex index = m_Controls.treeView->currentIndex(); InternalFileDownload(index, true); } void QmitkXnatTreeBrowserView::OnContextMenuCreateResourceFolder() { const QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); ctkXnatObject* parentObject = m_TreeModel->xnatObject(index); if (parentObject != nullptr) { this->InternalAddResourceFolder(parentObject); } } ctkXnatResource* QmitkXnatTreeBrowserView::InternalAddResourceFolder(ctkXnatObject *parent) { bool ok; QString folderName = QInputDialog::getText(m_Controls.treeView, tr("Create XNAT resource folder"), tr("Folder name:"), QLineEdit::Normal, tr("data"), &ok); if (ok) { if (folderName.isEmpty()) folderName = "NO LABEL"; // if called on the resource-folder level we need to provide he corresponding // parent instead of the folder ctkXnatResourceFolder* resourceFolder = dynamic_cast<ctkXnatResourceFolder*>(parent); if (resourceFolder != nullptr) { parent = parent->parent(); } try { return parent->addResourceFolder(folderName); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); return nullptr; } } else { return nullptr; } } void QmitkXnatTreeBrowserView::InternalFileUpload(ctkXnatFile* file) { m_Controls.groupBox->setTitle("Uploading file..."); m_Controls.groupBox->show(); try { file->save(); MITK_INFO << "Upload of " << file->name().toStdString() << " completed!"; if(!m_SilentMode) { QMessageBox msgBox; msgBox.setText("Upload of " + file->name() + " completed!"); msgBox.setIcon(QMessageBox::Information); msgBox.show(); msgBox.exec(); } } catch (ctkXnatException &e) { QMessageBox msgbox; msgbox.setText(e.what()); msgbox.setIcon(QMessageBox::Critical); msgbox.exec(); m_Controls.progressBar->setValue(0); } m_Controls.groupBox->hide(); } void QmitkXnatTreeBrowserView::OnContextMenuUploadFile() { QString filename = QFileDialog::getOpenFileName(m_Controls.treeView, tr("Open File"), QDir::homePath()); const QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); ctkXnatResource* resource = dynamic_cast<ctkXnatResource*>(m_TreeModel->xnatObject(index)); if (resource != nullptr && filename.length() != 0) { ctkXnatFile* file = new ctkXnatFile(resource); file->setLocalFilePath(filename); QFileInfo fileInfo (filename); file->setName(fileInfo.fileName()); try { this->InternalFileUpload(file); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); return; } m_TreeModel->addChildNode(index, file); } } void QmitkXnatTreeBrowserView::OnContextMenuCopyXNATUrlToClipboard() { const QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); ctkXnatObject* currentXnatObject = m_TreeModel->xnatObject(index); if (currentXnatObject != nullptr) { auto serverURL = QString::fromStdString(mitk::CoreServices::GetPreferencesService()->GetSystemPreferences()->Node(VIEW_ID.toStdString())->Get("Server Address", "")); serverURL.append(currentXnatObject->resourceUri()); QClipboard *clipboard = QApplication::clipboard(); clipboard->setText(serverURL); } } void QmitkXnatTreeBrowserView::OnContextMenuRefreshItem() { const QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); if (index.isValid()) { this->m_TreeModel->refresh(index); } } void QmitkXnatTreeBrowserView::OnUploadResource(const QList<mitk::DataNode*>& droppedNodes, ctkXnatObject* parentObject, const QModelIndex& parentIndex) { if (parentObject == nullptr) return; //1. If not dropped on a resource, create a new folder //temporarily remove the annoying message box that upload was successful.. ctkXnatResource* resource = dynamic_cast<ctkXnatResource*>(parentObject); // store original resource folder object for later use ctkXnatResourceFolder* originalResourceFolder = dynamic_cast<ctkXnatResourceFolder*>(parentObject); if (resource == nullptr) { resource = this->InternalAddResourceFolder(parentObject); } if (resource == nullptr) { MITK_WARN << "Resource folder could not be created!"; return; } //2. Save files locally //3. Upload file mitk::DataNode* node = nullptr; foreach (node, droppedNodes) { mitk::BaseData* data = node->GetData(); if (!data) return; //We have to replace special characters due to XNAT inability to get along with them (" " is replaced by "%20", what leads to nasty behaviour!) QString fileName(QString::fromStdString(ReplaceSpecialChars(node->GetName()))); ctkXnatFile* xnatFile = new ctkXnatFile(resource); if (dynamic_cast<mitk::Image*>(data)) { fileName.append(".nrrd"); } else if (dynamic_cast<mitk::Surface*>(data)) { fileName.append(".vtk"); } else if (dynamic_cast<mitk::PointSet*>(data)) { fileName.append(".mps"); } else { MITK_WARN << "Could not upload file! File-type not supported"; QMessageBox msgbox; msgbox.setText("Could not upload file! File-type not supported"); msgbox.setIcon(QMessageBox::Critical); msgbox.exec(); return; } xnatFile->setName(fileName); QString xnatFolder = "XNAT_UPLOADS"; QDir dir(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetContext()->getDataFile("").absoluteFilePath()); dir.mkdir(xnatFolder); fileName = dir.path().append("/" + fileName); mitk::IOUtil::Save (data, fileName.toStdString()); // TODO Check if file exists // AbstractFileReader::SetDefaultDataNodeProperties // und in die andere SetDefaultDataNodeProperties // PropertyName klein: mtime.initial + Kommentar mitk::StringProperty::Pointer orignalFilePath = mitk::StringProperty::New(); node->GetProperty(orignalFilePath, "path"); xnatFile->setLocalFilePath(fileName); try { this->InternalFileUpload(xnatFile); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); return; } QFile::remove(fileName); if (originalResourceFolder == nullptr) { m_TreeModel->refresh(parentIndex); } else { m_TreeModel->refresh(parentIndex.parent()); } // The filename for uploading // QFileInfo fileInfo; // if (surface) // { // // Save surface // fileName.append(".stl"); // xnatFile->setName(fileName); // dir.setPath(dir.path().append("/" + fileName)); // QString origFile = QString::fromStdString(orignalFilePath->GetValueAsString()); // origFile.append("/" + fileName); // origFile.append(".stl"); // fileInfo.setFile(origFile); // if (!fileInfo.exists()) // mitk::IOUtil::Save(surface, dir.path().toStdString()); // } // this->uploadFileToXnat(xnatFile, dir.path()); } } void QmitkXnatTreeBrowserView::OnContextMenuRequested(const QPoint & pos) { if(m_TreeModel==nullptr) { return; } QModelIndex index = m_Controls.treeView->indexAt(pos); if(index.isValid() == false) { return; } m_ContextMenu->clear(); QAction* actRefreshItem = new QAction("Refresh", m_ContextMenu); m_ContextMenu->addAction(actRefreshItem); connect(actRefreshItem, SIGNAL(triggered()), this, SLOT(OnContextMenuRefreshItem())); QAction* actGetXNATURL = new QAction("Copy XNAT URL to clipboard", m_ContextMenu); m_ContextMenu->addAction(actGetXNATURL); connect(actGetXNATURL, SIGNAL(triggered()), this, SLOT(OnContextMenuCopyXNATUrlToClipboard())); m_ContextMenu->addSeparator(); ctkXnatObject* xnatObject = m_TreeModel->xnatObject(index); bool downloadable = false; downloadable |= dynamic_cast<ctkXnatFile*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatScan*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatScanFolder*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatAssessor*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatAssessorFolder*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatResource*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatReconstruction*>(xnatObject)!=nullptr; downloadable |= dynamic_cast<ctkXnatReconstructionFolder*>(xnatObject)!=nullptr; bool canHaveResourceFolder = false; canHaveResourceFolder |= dynamic_cast<ctkXnatProject*>(xnatObject) != nullptr; canHaveResourceFolder |= dynamic_cast<ctkXnatSubject*>(xnatObject) != nullptr; canHaveResourceFolder |= dynamic_cast<ctkXnatExperiment*>(xnatObject) != nullptr; canHaveResourceFolder |= dynamic_cast<ctkXnatResourceFolder*>(xnatObject) != nullptr; bool uploadFilePossible = false; uploadFilePossible |= dynamic_cast<ctkXnatResource*>(xnatObject) != nullptr; uploadFilePossible |= dynamic_cast<ctkXnatScan*>(xnatObject) != nullptr; uploadFilePossible |= dynamic_cast<ctkXnatAssessor*>(xnatObject) != nullptr; if (downloadable) { QAction* actDownload = new QAction("Download", m_ContextMenu); connect(actDownload, SIGNAL(triggered()), this, SLOT(OnContextMenuDownloadFile())); m_ContextMenu->addAction(actDownload); ctkXnatFile* file = dynamic_cast<ctkXnatFile*>(xnatObject); if (file) { QAction* actView = new QAction("Download and Open", m_ContextMenu); connect(actView, SIGNAL(triggered()), this, SLOT(OnContextMenuDownloadAndOpenFile())); m_ContextMenu->addAction(actView); } } if (canHaveResourceFolder) { QAction* actCreateResource = new QAction("Add resource folder", m_ContextMenu); connect(actCreateResource, SIGNAL(triggered()), this, SLOT(OnContextMenuCreateResourceFolder())); m_ContextMenu->addAction(actCreateResource); } if (uploadFilePossible) { QAction* actUploadFile = new QAction("Upload File", m_ContextMenu); connect(actUploadFile, SIGNAL(triggered()), this, SLOT(OnContextMenuUploadFile())); m_ContextMenu->addAction(actUploadFile); } ctkXnatProject* project = dynamic_cast<ctkXnatProject*>(xnatObject); if (project != nullptr) { QAction* actCreateSubject = new QAction("Create new subject", m_ContextMenu); m_ContextMenu->addAction(actCreateSubject); connect(actCreateSubject, SIGNAL(triggered()), this, SLOT(OnContextMenuCreateNewSubject())); } ctkXnatSubject* subject = dynamic_cast<ctkXnatSubject*>(xnatObject); if (subject != nullptr) { QAction* actCreateExperiment = new QAction("Create new experiment", m_ContextMenu); m_ContextMenu->addAction(actCreateExperiment); connect(actCreateExperiment, SIGNAL(triggered()), this, SLOT(OnContextMenuCreateNewExperiment())); } m_ContextMenu->popup(QCursor::pos()); } void QmitkXnatTreeBrowserView::CleanUp() { m_Controls.wgtExperimentInfo->hide(); m_Controls.wgtSubjectInfo->hide(); m_Controls.wgtProjectInfo->hide(); m_Controls.btnCreateXnatFolder->setEnabled(false); m_Controls.btnXnatDownload->setEnabled(false); m_Controls.btnXnatUpload->setEnabled(false); m_Controls.searchField->setEnabled(false); m_Controls.searchField->setText(""); m_Controls.searchModeBox->setEnabled(false); } std::string QmitkXnatTreeBrowserView::ReplaceSpecialChars(const std::string& input) const { QString convertedString = QString(QUrl::toPercentEncoding(QString::fromStdString(input))); return convertedString.toStdString(); } void QmitkXnatTreeBrowserView::ItemSelected(const QModelIndex& index) { //TODO: CTK seems to ignore spaces while creating the http request. This will lead to corrupted http request that will fail. QVariant variant = m_TreeModel->data(index, Qt::UserRole); if (variant.isValid()) { ctkXnatSession *session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); ctkXnatObject* object = variant.value<ctkXnatObject*>(); ctkXnatProject* project = dynamic_cast<ctkXnatProject*>(object); ctkXnatSubject* subject = dynamic_cast<ctkXnatSubject*>(object); ctkXnatExperiment* experiment = dynamic_cast<ctkXnatExperiment*>(object); if (project != nullptr) { m_Controls.wgtExperimentInfo->hide(); m_Controls.wgtSubjectInfo->hide(); m_Controls.wgtProjectInfo->SetProject(project); m_Controls.wgtProjectInfo->show(); } else if (subject != nullptr) { QMap<QString, QString> paramMap; paramMap.insert("columns", "dob,gender,handedness,weight,height"); QUuid requestID = session->httpGet(QString("%1/subjects").arg(subject->parent()->resourceUri()), paramMap); QList<QVariantMap> results = session->httpSync(requestID); foreach(const QVariantMap& propertyMap, results) { QMapIterator<QString, QVariant> it(propertyMap); bool isConcretSubject = false; if (it.hasNext()) { it.next(); QVariant var = it.value(); // After CTK Change (subjectID = name) to (subjectID = ID) // CHANGE TO: if (var == subject->property("ID")) if (var == subject->property("URI").right(11)) { isConcretSubject = true; } else { isConcretSubject = false; } it.toFront(); } while (it.hasNext() && isConcretSubject) { it.next(); QString str = it.key().toLatin1().data(); QVariant var = it.value(); subject->setProperty(str, var); } } m_Controls.wgtExperimentInfo->hide(); m_Controls.wgtProjectInfo->hide(); m_Controls.wgtSubjectInfo->SetSubject(subject); m_Controls.wgtSubjectInfo->show(); } else if (experiment != nullptr) { QMap<QString, QString> paramMap; paramMap.insert("columns", "date,time,scanner,modality"); QUuid requestID = session->httpGet(QString("%1/experiments").arg(experiment->parent()->resourceUri()), paramMap); QList<QVariantMap> results = session->httpSync(requestID); foreach(const QVariantMap& propertyMap, results) { QMapIterator<QString, QVariant> it(propertyMap); bool isConcretExperiment = false; if (it.hasNext()) { it.next(); QVariant var = it.value(); if (var == experiment->property("URI")) { isConcretExperiment = true; } else { isConcretExperiment = false; } it.toFront(); } while (it.hasNext() && isConcretExperiment) { it.next(); QString str = it.key().toLatin1().data(); QVariant var = it.value(); experiment->setProperty(str, var); } } m_Controls.wgtSubjectInfo->hide(); m_Controls.wgtProjectInfo->hide(); m_Controls.wgtExperimentInfo->SetExperiment(experiment); m_Controls.wgtExperimentInfo->show(); } } } void QmitkXnatTreeBrowserView::OnContextMenuCreateNewSubject() { QModelIndex index = m_Controls.treeView->currentIndex(); QVariant variant = m_TreeModel->data(index, Qt::UserRole); if (variant.isValid()) { QmitkXnatCreateObjectDialog* dialog = new QmitkXnatCreateObjectDialog(QmitkXnatCreateObjectDialog::SpecificType::SUBJECT); if (dialog->exec() == QDialog::Accepted) { ctkXnatProject* project = dynamic_cast<ctkXnatProject*>(variant.value<ctkXnatObject*>()); ctkXnatSubject* subject = dynamic_cast<ctkXnatSubject*>(dialog->GetXnatObject()); subject->setParent(project); try { subject->save(); } catch(const ctkRuntimeException& exc) { //TODO: Implement isValid-flag to check if ctkRuntimeExceptio is valid http-exception. QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); project->remove(subject); delete subject; return; } // Get xnat session from micro service ctkXnatSession* session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); // Update View m_TreeModel->removeDataModel(session->dataModel()); UpdateSession(session); } } } void QmitkXnatTreeBrowserView::OnContextMenuCreateNewExperiment() { QModelIndex index = m_Controls.treeView->currentIndex(); QVariant variant = m_TreeModel->data(index, Qt::UserRole); if (variant.isValid()) { QmitkXnatCreateObjectDialog* dialog = new QmitkXnatCreateObjectDialog(QmitkXnatCreateObjectDialog::SpecificType::EXPERIMENT); if (dialog->exec() == QDialog::Accepted) { ctkXnatSubject* subject = dynamic_cast<ctkXnatSubject*>(variant.value<ctkXnatObject*>()); ctkXnatExperiment* experiment = dynamic_cast<ctkXnatExperiment*>(dialog->GetXnatObject()); experiment->setParent(subject); experiment->setProperty("xsiType", experiment->imageModality()); try { experiment->save(); } catch(const ctkRuntimeException& exc) { QmitkHttpStatusCodeHandler::HandleErrorMessage(exc.what()); subject->remove(experiment); delete experiment; return; } // Get xnat session from micro service ctkXnatSession* session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference<ctkXnatSession>()); // Update View m_TreeModel->removeDataModel(session->dataModel()); UpdateSession(session); } } } void QmitkXnatTreeBrowserView::SetStatusInformation(const QString& text) { m_Controls.groupBox->setTitle(text); m_Controls.progressBar->setValue(0); m_Controls.groupBox->show(); } void QmitkXnatTreeBrowserView::SessionTimedOutMsg() { ctkXnatSession* session = qobject_cast<ctkXnatSession*>(QObject::sender()); if (session == nullptr) return; ctkXnatDataModel* dataModel = session->dataModel(); m_TreeModel->removeDataModel(dataModel); m_Controls.treeView->reset(); session->close(); QMessageBox::warning(m_Controls.treeView, "Session Timeout", "The session timed out."); m_Controls.btnXnatConnect->setToolTip("Connect"); m_Controls.btnXnatConnect->setIcon(QIcon(":/xnat-plugin/xnat-connect.png")); CleanUp(); } void QmitkXnatTreeBrowserView::SessionTimesOutSoonMsg() { ctkXnatSession* session = qobject_cast<ctkXnatSession*>(QObject::sender()); if (session == nullptr) return; QMessageBox msgBox; msgBox.setIcon(QMessageBox::Warning); msgBox.setWindowTitle("Session Timeout Soon"); msgBox.setText("The session will time out in 1 minute.\nDo you want to renew the session?"); msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::No); msgBox.setDefaultButton(QMessageBox::No); msgBox.show(); QTimer* timer = new QTimer(this); timer->start(60000); this->connect(timer, SIGNAL(timeout()), &msgBox, SLOT(reject())); if (msgBox.exec() == QMessageBox::Yes){ session->renew(); } timer->stop(); } diff --git a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserViewControls.ui b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserViewControls.ui index f2f67f3aea..86c8ea8747 100644 --- a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserViewControls.ui +++ b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatTreeBrowserViewControls.ui @@ -1,245 +1,245 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkXnatTreeBrowserViewControls</class> <widget class="QWidget" name="QmitkXnatTreeBrowserViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>455</width> <height>332</height> </rect> </property> <property name="minimumSize"> <size> <width>0</width> <height>0</height> </size> </property> <property name="windowTitle"> <string>QmitkTemplate</string> </property> <layout class="QVBoxLayout" name="verticalLayout"> <item> <layout class="QHBoxLayout" name="horizontalLayout"> <item> <widget class="QPushButton" name="btnXnatUpload"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> <string>Upload to XNAT</string> </property> <property name="styleSheet"> <string notr="true"/> </property> <property name="text"> <string/> </property> <property name="icon"> <iconset resource="../../resources/xnat.qrc"> <normaloff>:/xnat-plugin/xnat-upload.png</normaloff>:/xnat-plugin/xnat-upload.png</iconset> </property> <property name="iconSize"> <size> <width>32</width> <height>32</height> </size> </property> </widget> </item> <item> <widget class="QPushButton" name="btnXnatDownload"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> <string>Download File</string> </property> <property name="text"> <string/> </property> <property name="icon"> <iconset resource="../../resources/xnat.qrc"> <normaloff>:/xnat-plugin/xnat-download.png</normaloff>:/xnat-plugin/xnat-download.png</iconset> </property> <property name="iconSize"> <size> <width>32</width> <height>32</height> </size> </property> </widget> </item> <item> <widget class="QPushButton" name="btnCreateXnatFolder"> <property name="enabled"> <bool>false</bool> </property> <property name="toolTip"> <string>Create Folder</string> </property> <property name="text"> <string/> </property> <property name="icon"> <iconset resource="../../resources/xnat.qrc"> <normaloff>:/xnat-plugin/xnat-folder.png</normaloff>:/xnat-plugin/xnat-folder.png</iconset> </property> <property name="iconSize"> <size> <width>32</width> <height>32</height> </size> </property> </widget> </item> <item> <widget class="QPushButton" name="btnXnatConnect"> <property name="enabled"> <bool>true</bool> </property> <property name="toolTip"> <string>Connect</string> </property> <property name="text"> <string/> </property> <property name="icon"> <iconset resource="../../resources/xnat.qrc"> <normaloff>:/xnat-plugin/xnat-connect.png</normaloff>:/xnat-plugin/xnat-connect.png</iconset> </property> <property name="iconSize"> <size> <width>32</width> <height>32</height> </size> </property> <property name="checkable"> <bool>false</bool> </property> </widget> </item> <item> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> </layout> </item> <item> <layout class="QHBoxLayout" name="searchLayout"> <item> <widget class="QLineEdit" name="searchField"> <property name="enabled"> <bool>false</bool> </property> </widget> </item> <item> <widget class="QComboBox" name="searchModeBox"> <property name="enabled"> <bool>false</bool> </property> <property name="currentIndex"> <number>1</number> </property> <item> <property name="text"> <string>Projects</string> </property> </item> <item> <property name="text"> <string>Patients</string> </property> </item> </widget> </item> </layout> </item> <item> <layout class="QVBoxLayout" name="verticalLayout_2"> <item> <widget class="QTreeView" name="treeView"> <property name="uniformRowHeights"> <bool>false</bool> </property> <property name="sortingEnabled"> <bool>false</bool> </property> <property name="animated"> <bool>false</bool> </property> <property name="expandsOnDoubleClick"> <bool>true</bool> </property> </widget> </item> </layout> </item> <item> <widget class="QGroupBox" name="groupBox"> <property name="title"> - <string>Dowloading file ...</string> + <string>Downloading file ...</string> </property> <layout class="QVBoxLayout" name="verticalLayout_3"> <item> <widget class="QProgressBar" name="progressBar"> <property name="value"> <number>0</number> </property> </widget> </item> </layout> </widget> </item> <item> <layout class="QVBoxLayout" name="infoVerticalLayout"> <item> <widget class="QmitkXnatProjectWidget" name="wgtProjectInfo" native="true"/> </item> <item> <widget class="QmitkXnatExperimentWidget" name="wgtExperimentInfo" native="true"/> </item> <item> <widget class="QmitkXnatSubjectWidget" name="wgtSubjectInfo" native="true"/> </item> </layout> </item> </layout> </widget> <layoutdefault spacing="6" margin="11"/> <customwidgets> <customwidget> <class>QmitkXnatProjectWidget</class> <extends>QWidget</extends> <header>QmitkXnatProjectWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkXnatSubjectWidget</class> <extends>QWidget</extends> <header>QmitkXnatSubjectWidget.h</header> <container>1</container> </customwidget> <customwidget> <class>QmitkXnatExperimentWidget</class> <extends>QWidget</extends> <header>QmitkXnatExperimentWidget.h</header> <container>1</container> </customwidget> </customwidgets> <resources> <include location="../../resources/xnat.qrc"/> </resources> <connections/> </ui> diff --git a/Plugins/org.mitk.planarfigure/src/internal/mitkPlanarFigureActivator.h b/Plugins/org.mitk.planarfigure/src/internal/mitkPlanarFigureActivator.h index f2774a3133..d2c6c05575 100644 --- a/Plugins/org.mitk.planarfigure/src/internal/mitkPlanarFigureActivator.h +++ b/Plugins/org.mitk.planarfigure/src/internal/mitkPlanarFigureActivator.h @@ -1,49 +1,49 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkPlanarFigureActivator_h #define mitkPlanarFigureActivator_h #include <ctkPluginActivator.h> namespace mitk { /** * \ingroup org_mitk_planarfigure_internal * * \brief The plug-in activator for the planar figure module * - * When the plug-in is started by the framework, it initialzes planar figure specific things. + * When the plug-in is started by the framework, it initializes planar figure specific things. */ class PlanarFigureActivator : public QObject, public ctkPluginActivator { Q_OBJECT Q_PLUGIN_METADATA(IID "org_mitk_planarfigure") Q_INTERFACES(ctkPluginActivator) public: /** * Registers sandbox core object factories. */ void start(ctkPluginContext* context) override; void stop(ctkPluginContext* context) override; }; } #endif diff --git a/SuperBuild.cmake b/SuperBuild.cmake index 1ab1ad5f59..c02d3fc7b3 100644 --- a/SuperBuild.cmake +++ b/SuperBuild.cmake @@ -1,502 +1,502 @@ #----------------------------------------------------------------------------- # Convenient macro allowing to download a file #----------------------------------------------------------------------------- if(NOT MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL) set(MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL https://www.mitk.org/download/thirdparty) endif() macro(downloadFile url dest) file(DOWNLOAD ${url} ${dest} STATUS status) list(GET status 0 error_code) list(GET status 1 error_msg) if(error_code) message(FATAL_ERROR "error: Failed to download ${url} - ${error_msg}") endif() endmacro() #----------------------------------------------------------------------------- # MITK Prerequisites #----------------------------------------------------------------------------- if(UNIX AND NOT APPLE) include(mitkFunctionCheckPackageHeader) # Check for libxt-dev mitkFunctionCheckPackageHeader(StringDefs.h libxt-dev /usr/include/X11/) # Check for libtiff4-dev mitkFunctionCheckPackageHeader(tiff.h libtiff4-dev) endif() # We need a proper patch program. On Linux and MacOS, we assume # that "patch" is available. On Windows, we download patch.exe # if not patch program is found. find_program(PATCH_COMMAND patch) if((NOT PATCH_COMMAND OR NOT EXISTS ${PATCH_COMMAND}) AND WIN32) downloadFile(${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/patch.exe ${CMAKE_CURRENT_BINARY_DIR}/patch.exe) find_program(PATCH_COMMAND patch ${CMAKE_CURRENT_BINARY_DIR}) endif() if(NOT PATCH_COMMAND) message(FATAL_ERROR "No patch program found.") endif() #----------------------------------------------------------------------------- # ExternalProjects #----------------------------------------------------------------------------- get_property(external_projects GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS) if(MITK_CTEST_SCRIPT_MODE) # Write a file containing the list of enabled external project targets. # This file can be read by a ctest script to separately build projects. set(SUPERBUILD_TARGETS ) foreach(proj ${external_projects}) if(MITK_USE_${proj}) list(APPEND SUPERBUILD_TARGETS ${proj}) endif() endforeach() file(WRITE "${CMAKE_BINARY_DIR}/SuperBuildTargets.cmake" "set(SUPERBUILD_TARGETS ${SUPERBUILD_TARGETS})") endif() # A list of "nice" external projects, playing well together with CMake set(nice_external_projects ${external_projects}) list(REMOVE_ITEM nice_external_projects Boost) foreach(proj ${nice_external_projects}) if(MITK_USE_${proj}) set(EXTERNAL_${proj}_DIR "${${proj}_DIR}" CACHE PATH "Path to ${proj} build directory") mark_as_advanced(EXTERNAL_${proj}_DIR) if(EXTERNAL_${proj}_DIR) set(${proj}_DIR ${EXTERNAL_${proj}_DIR}) endif() endif() endforeach() -set(EXTERNAL_BOOST_ROOT "${BOOST_ROOT}" CACHE PATH "Path to Boost directory") -mark_as_advanced(EXTERNAL_BOOST_ROOT) -if(EXTERNAL_BOOST_ROOT) - set(BOOST_ROOT ${EXTERNAL_BOOST_ROOT}) +set(EXTERNAL_Boost_ROOT "${Boost_ROOT}" CACHE PATH "Path to Boost directory") +mark_as_advanced(EXTERNAL_Boost_ROOT) +if(EXTERNAL_Boost_ROOT) + set(Boost_ROOT ${EXTERNAL_Boost_ROOT}) endif() if(BUILD_TESTING) set(EXTERNAL_MITK_DATA_DIR "${MITK_DATA_DIR}" CACHE PATH "Path to the MITK data directory") mark_as_advanced(EXTERNAL_MITK_DATA_DIR) if(EXTERNAL_MITK_DATA_DIR) set(MITK_DATA_DIR ${EXTERNAL_MITK_DATA_DIR}) endif() endif() #----------------------------------------------------------------------------- # External project settings #----------------------------------------------------------------------------- include(ExternalProject) include(mitkMacroQueryCustomEPVars) include(mitkFunctionInstallExternalCMakeProject) include(mitkFunctionCleanExternalProject) option(MITK_AUTOCLEAN_EXTERNAL_PROJECTS "Experimental: Clean external project builds if updated" ON) set(ep_prefix "${CMAKE_BINARY_DIR}/ep") set_property(DIRECTORY PROPERTY EP_PREFIX ${ep_prefix}) # Compute -G arg for configuring external projects with the same CMake generator: if(CMAKE_EXTRA_GENERATOR) set(gen "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}") else() set(gen "${CMAKE_GENERATOR}") endif() set(gen_platform ${CMAKE_GENERATOR_PLATFORM}) # Use this value where semi-colons are needed in ep_add args: set(sep "^^") ## if(MSVC_VERSION) set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /bigobj /MP") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj /MP") endif() # This is a workaround for passing linker flags # actually down to the linker invocation set(_cmake_required_flags_orig ${CMAKE_REQUIRED_FLAGS}) set(CMAKE_REQUIRED_FLAGS "-Wl,-rpath") mitkFunctionCheckCompilerFlags(${CMAKE_REQUIRED_FLAGS} _has_rpath_flag) set(CMAKE_REQUIRED_FLAGS ${_cmake_required_flags_orig}) set(_install_rpath_linkflag ) if(_has_rpath_flag) if(APPLE) set(_install_rpath_linkflag "-Wl,-rpath,@loader_path/../lib") else() set(_install_rpath_linkflag "-Wl,-rpath='$ORIGIN/../lib'") endif() endif() set(_install_rpath) if(APPLE) set(_install_rpath "@loader_path/../lib") elseif(UNIX) # this work for libraries as well as executables set(_install_rpath "\$ORIGIN/../lib") endif() set(ep_common_args -DCMAKE_POLICY_DEFAULT_CMP0091:STRING=OLD -DCMAKE_CXX_EXTENSIONS:STRING=${CMAKE_CXX_EXTENSIONS} -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD} -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED} -DCMAKE_MACOSX_RPATH:BOOL=TRUE "-DCMAKE_INSTALL_RPATH:STRING=${_install_rpath}" -DBUILD_TESTING:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE} -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS} "-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${MITK_CXX${MITK_CXX_STANDARD}_FLAG}" #debug flags -DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} -DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG} #release flags -DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE} -DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE} #relwithdebinfo -DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO} #link flags -DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS} -DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS} -DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS} ) if(MSVC_VERSION) list(APPEND ep_common_args -DCMAKE_DEBUG_POSTFIX:STRING=d ) set(DCMTK_CMAKE_DEBUG_POSTFIX d) endif() set(ep_common_cache_args ) set(ep_common_cache_default_args "-DCMAKE_PREFIX_PATH:PATH=<INSTALL_DIR>;${CMAKE_PREFIX_PATH}" "-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}" "-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}" ) # Pass the CMAKE_OSX variables to external projects if(APPLE) set(MAC_OSX_ARCHITECTURE_ARGS -DCMAKE_OSX_ARCHITECTURES:PATH=${CMAKE_OSX_ARCHITECTURES} -DCMAKE_OSX_DEPLOYMENT_TARGET:PATH=${CMAKE_OSX_DEPLOYMENT_TARGET} -DCMAKE_OSX_SYSROOT:PATH=${CMAKE_OSX_SYSROOT} ) set(ep_common_args ${MAC_OSX_ARCHITECTURE_ARGS} ${ep_common_args} ) endif() set(mitk_superbuild_ep_args) set(mitk_depends ) # Include external projects include(CMakeExternals/MITKData.cmake) foreach(p ${external_projects}) set(p_hash "") set(p_file "${CMAKE_SOURCE_DIR}/CMakeExternals/${p}.cmake") if(EXISTS ${p_file}) file(MD5 ${p_file} p_hash) else() foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMakeExternals") set(p_file "${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/${p}.cmake") if(EXISTS "${p_file}") file(MD5 "${p_file}" p_hash) break() endif() endforeach() endif() if(p_hash) set(p_hash_file "${ep_prefix}/tmp/${p}-hash.txt") if(MITK_AUTOCLEAN_EXTERNAL_PROJECTS) if(EXISTS "${p_hash_file}") file(READ "${p_hash_file}" p_prev_hash) if(NOT p_hash STREQUAL p_prev_hash) mitkCleanExternalProject(${p}) endif() endif() endif() file(WRITE "${p_hash_file}" ${p_hash}) endif() include("${p_file}" OPTIONAL) list(APPEND mitk_superbuild_ep_args -DMITK_USE_${p}:BOOL=${MITK_USE_${p}} ) get_property(_package GLOBAL PROPERTY MITK_${p}_PACKAGE) if(_package) list(APPEND mitk_superbuild_ep_args -D${p}_DIR:PATH=${${p}_DIR}) endif() list(APPEND mitk_depends ${${p}_DEPENDS}) endforeach() if (SWIG_EXECUTABLE) list(APPEND mitk_superbuild_ep_args -DSWIG_EXECUTABLE=${SWIG_EXECUTABLE}) endif() #----------------------------------------------------------------------------- # Set superbuild boolean args #----------------------------------------------------------------------------- set(mitk_cmake_boolean_args BUILD_SHARED_LIBS WITH_COVERAGE BUILD_TESTING MITK_BUILD_ALL_PLUGINS MITK_BUILD_ALL_APPS MITK_BUILD_EXAMPLES MITK_USE_Qt5 MITK_USE_SYSTEM_Boost MITK_USE_BLUEBERRY MITK_USE_OpenCL MITK_USE_OpenMP ) #----------------------------------------------------------------------------- # Create the final variable containing superbuild boolean args #----------------------------------------------------------------------------- set(mitk_superbuild_boolean_args) foreach(mitk_cmake_arg ${mitk_cmake_boolean_args}) list(APPEND mitk_superbuild_boolean_args -D${mitk_cmake_arg}:BOOL=${${mitk_cmake_arg}}) endforeach() if(MITK_BUILD_ALL_PLUGINS) list(APPEND mitk_superbuild_boolean_args -DBLUEBERRY_BUILD_ALL_PLUGINS:BOOL=ON) endif() #----------------------------------------------------------------------------- # MITK Utilities #----------------------------------------------------------------------------- set(proj MITK-Utilities) ExternalProject_Add(${proj} DOWNLOAD_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS ${mitk_depends} ) #----------------------------------------------------------------------------- # Additional MITK CXX/C Flags #----------------------------------------------------------------------------- set(MITK_ADDITIONAL_C_FLAGS "" CACHE STRING "Additional C Flags for MITK") set(MITK_ADDITIONAL_C_FLAGS_RELEASE "" CACHE STRING "Additional Release C Flags for MITK") set(MITK_ADDITIONAL_C_FLAGS_DEBUG "" CACHE STRING "Additional Debug C Flags for MITK") mark_as_advanced(MITK_ADDITIONAL_C_FLAGS MITK_ADDITIONAL_C_FLAGS_DEBUG MITK_ADDITIONAL_C_FLAGS_RELEASE) set(MITK_ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CXX Flags for MITK") set(MITK_ADDITIONAL_CXX_FLAGS_RELEASE "" CACHE STRING "Additional Release CXX Flags for MITK") set(MITK_ADDITIONAL_CXX_FLAGS_DEBUG "" CACHE STRING "Additional Debug CXX Flags for MITK") mark_as_advanced(MITK_ADDITIONAL_CXX_FLAGS MITK_ADDITIONAL_CXX_FLAGS_DEBUG MITK_ADDITIONAL_CXX_FLAGS_RELEASE) set(MITK_ADDITIONAL_EXE_LINKER_FLAGS "" CACHE STRING "Additional exe linker flags for MITK") set(MITK_ADDITIONAL_SHARED_LINKER_FLAGS "" CACHE STRING "Additional shared linker flags for MITK") set(MITK_ADDITIONAL_MODULE_LINKER_FLAGS "" CACHE STRING "Additional module linker flags for MITK") mark_as_advanced(MITK_ADDITIONAL_EXE_LINKER_FLAGS MITK_ADDITIONAL_SHARED_LINKER_FLAGS MITK_ADDITIONAL_MODULE_LINKER_FLAGS) #----------------------------------------------------------------------------- # MITK Configure #----------------------------------------------------------------------------- if(MITK_INITIAL_CACHE_FILE) set(mitk_initial_cache_arg -C "${MITK_INITIAL_CACHE_FILE}") endif() set(mitk_optional_cache_args ) foreach(type RUNTIME ARCHIVE LIBRARY) if(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY) list(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY}) endif() endforeach() if(MITK_USE_OpenCV) list(APPEND mitk_optional_cache_args "-DCMAKE_CONFIGURATION_TYPES:STRING=Debug$<SEMICOLON>Release") endif() # Optional python variables if(MITK_USE_Python3) list(APPEND mitk_optional_cache_args -DMITK_USE_Python3:BOOL=${MITK_USE_Python3} "-DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE}" "-DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIRS}" "-DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY}" "-DPython3_STDLIB:FILEPATH=${Python3_STDLIB}" "-DPython3_SITELIB:FILEPATH=${Python3_SITELIB}" ) endif() if(OPENSSL_ROOT_DIR) list(APPEND mitk_optional_cache_args "-DOPENSSL_ROOT_DIR:PATH=${OPENSSL_ROOT_DIR}" ) endif() if(CMAKE_FRAMEWORK_PATH) list(APPEND mitk_optional_cache_args "-DCMAKE_FRAMEWORK_PATH:PATH=${CMAKE_FRAMEWORK_PATH}" ) endif() if(Eigen_INCLUDE_DIR) list(APPEND mitk_optional_cache_args -DEigen_INCLUDE_DIR:PATH=${Eigen_INCLUDE_DIR} ) endif() # Optional pass through of Doxygen if(DOXYGEN_EXECUTABLE) list(APPEND mitk_optional_cache_args -DDOXYGEN_EXECUTABLE:FILEPATH=${DOXYGEN_EXECUTABLE} ) endif() if(MITK_DOXYGEN_BUILD_ALWAYS) list(APPEND mitk_optional_cache_args -DMITK_DOXYGEN_BUILD_ALWAYS:BOOL=${MITK_DOXYGEN_BUILD_ALWAYS} ) endif() set(proj MITK-Configure) ExternalProject_Add(${proj} LIST_SEPARATOR ${sep} DOWNLOAD_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_GENERATOR_PLATFORM ${gen_platform} CMAKE_CACHE_ARGS # --------------- Build options ---------------- -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE} "-DCMAKE_PREFIX_PATH:PATH=${ep_prefix};${CMAKE_PREFIX_PATH}" "-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}" "-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}" # --------------- Compile options ---------------- -DCMAKE_CXX_EXTENSIONS:STRING=${CMAKE_CXX_EXTENSIONS} -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD} -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED} -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} "-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS} ${MITK_ADDITIONAL_C_FLAGS}" "-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${MITK_ADDITIONAL_CXX_FLAGS}" # debug flags "-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} ${MITK_ADDITIONAL_CXX_FLAGS_DEBUG}" "-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG} ${MITK_ADDITIONAL_C_FLAGS_DEBUG}" # release flags "-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE} ${MITK_ADDITIONAL_CXX_FLAGS_RELEASE}" "-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE} ${MITK_ADDITIONAL_C_FLAGS_RELEASE}" # relwithdebinfo -DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO} # link flags "-DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS} ${MITK_ADDITIONAL_EXE_LINKER_FLAGS}" "-DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS} ${MITK_ADDITIONAL_SHARED_LINKER_FLAGS}" "-DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS} ${MITK_ADDITIONAL_MODULE_LINKER_FLAGS}" # Output directories -DMITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY} -DMITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY} -DMITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY} # ------------- Boolean build options -------------- ${mitk_superbuild_boolean_args} ${mitk_optional_cache_args} -DMITK_USE_SUPERBUILD:BOOL=OFF -DMITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION} -DMITK_FAST_TESTING:BOOL=${MITK_FAST_TESTING} -DMITK_XVFB_TESTING:BOOL=${MITK_XVFB_TESTING} -DMITK_XVFB_TESTING_COMMAND:STRING=${MITK_XVFB_TESTING_COMMAND} -DCTEST_USE_LAUNCHERS:BOOL=${CTEST_USE_LAUNCHERS} # ----------------- Miscellaneous --------------- -DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH} -DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH} -DMITK_CTEST_SCRIPT_MODE:STRING=${MITK_CTEST_SCRIPT_MODE} -DMITK_SUPERBUILD_BINARY_DIR:PATH=${MITK_BINARY_DIR} -DMITK_MODULES_TO_BUILD:INTERNAL=${MITK_MODULES_TO_BUILD} -DMITK_WHITELIST:STRING=${MITK_WHITELIST} -DMITK_WHITELISTS_EXTERNAL_PATH:STRING=${MITK_WHITELISTS_EXTERNAL_PATH} -DMITK_WHITELISTS_INTERNAL_PATH:STRING=${MITK_WHITELISTS_INTERNAL_PATH} -DMITK_EXTENSION_DIRS:STRING=${MITK_EXTENSION_DIRS} -DMITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES} -DMITK_ACCESSBYITK_FLOATING_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES} -DMITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES} -DMITK_ACCESSBYITK_VECTOR_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES} -DMITK_ACCESSBYITK_DIMENSIONS:STRING=${MITK_ACCESSBYITK_DIMENSIONS} -DMITK_CUSTOM_REVISION_DESC:STRING=${MITK_CUSTOM_REVISION_DESC} # --------------- External project options --------------- -DMITK_DATA_DIR:PATH=${MITK_DATA_DIR} -DMITK_EXTERNAL_PROJECT_PREFIX:PATH=${ep_prefix} -DCppMicroServices_DIR:PATH=${CppMicroServices_DIR} -DDCMTK_CMAKE_DEBUG_POSTFIX:STRING=${DCMTK_CMAKE_DEBUG_POSTFIX} - -DBOOST_ROOT:PATH=${BOOST_ROOT} + -DBoost_ROOT:PATH=${Boost_ROOT} -DBOOST_LIBRARYDIR:PATH=${BOOST_LIBRARYDIR} -DMITK_USE_Boost_LIBRARIES:STRING=${MITK_USE_Boost_LIBRARIES} -DQt5_DIR:PATH=${Qt5_DIR} CMAKE_ARGS ${mitk_initial_cache_arg} ${MAC_OSX_ARCHITECTURE_ARGS} ${mitk_superbuild_ep_args} SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR} BINARY_DIR ${CMAKE_BINARY_DIR}/MITK-build BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS MITK-Utilities ) mitkFunctionInstallExternalCMakeProject(${proj}) #----------------------------------------------------------------------------- # MITK #----------------------------------------------------------------------------- if(CMAKE_GENERATOR MATCHES ".*Makefiles.*") set(mitk_build_cmd "$(MAKE)") else() set(mitk_build_cmd ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/MITK-build --config ${CMAKE_CFG_INTDIR}) endif() if(NOT DEFINED SUPERBUILD_EXCLUDE_MITKBUILD_TARGET OR NOT SUPERBUILD_EXCLUDE_MITKBUILD_TARGET) set(MITKBUILD_TARGET_ALL_OPTION "ALL") else() set(MITKBUILD_TARGET_ALL_OPTION "") endif() add_custom_target(MITK-build ${MITKBUILD_TARGET_ALL_OPTION} COMMAND ${mitk_build_cmd} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build DEPENDS MITK-Configure ) #----------------------------------------------------------------------------- # Custom target allowing to drive the build of the MITK project itself #----------------------------------------------------------------------------- add_custom_target(MITK COMMAND ${mitk_build_cmd} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY

diff --git a/CMakeExternals/Boost.cmake b/CMakeExternals/Boost.cmake index bf50d36881..323448f549 100644 --- a/CMakeExternals/Boost.cmake +++ b/CMakeExternals/Boost.cmake @@ -1,343 +1,343 @@ #----------------------------------------------------------------------------- # Boost #----------------------------------------------------------------------------- include(mitkFunctionGetMSVCVersion) #[[ Sanity checks ]] -if(DEFINED BOOST_ROOT AND NOT EXISTS ${BOOST_ROOT}) - message(FATAL_ERROR "BOOST_ROOT variable is defined but corresponds to non-existing directory") +if(DEFINED Boost_ROOT AND NOT EXISTS ${Boost_ROOT}) + message(FATAL_ERROR "Boost_ROOT variable is defined but corresponds to non-existing directory") endif() string(REPLACE "^^" ";" MITK_USE_Boost_LIBRARIES "${MITK_USE_Boost_LIBRARIES}") set(proj Boost) set(proj_DEPENDENCIES ) set(Boost_DEPENDS ${proj}) -if(NOT DEFINED BOOST_ROOT AND NOT MITK_USE_SYSTEM_Boost) +if(NOT DEFINED Boost_ROOT AND NOT MITK_USE_SYSTEM_Boost) #[[ Reset variables. ]] set(patch_cmd "") set(configure_cmd "") set(install_cmd "") - set(BOOST_ROOT ${ep_prefix}) - set(Boost_DIR "${BOOST_ROOT}/lib/cmake/Boost-1.82.0") + set(Boost_ROOT ${ep_prefix}) + set(Boost_DIR "${Boost_ROOT}/lib/cmake/Boost-1.82.0") if(WIN32) - set(BOOST_LIBRARYDIR "${BOOST_ROOT}/lib") + set(BOOST_LIBRARYDIR "${Boost_ROOT}/lib") endif() #[[ If you update Boost, make sure that the FindBoost module of the minimum required version of CMake supports the new version of Boost. In case you are using a higher version of CMake, download at least the source code of the minimum required version of CMake to look into the right version of the FindBoost module: /share/cmake-/Modules/FindBoost.cmake Search for a list called _Boost_KNOWN_VERSIONS. If the new version is not included in this list, you have three options: * Update the minimum required version of CMake. This may require adaptions of other parts of our CMake scripts and has the most impact on other MITK developers. Yet this is the safest and cleanest option. * Set Boost_ADDITIONAL_VERSIONS (see the documentation of the FindBoost module). As Boost libraries and dependencies between them are hard-coded in the FindBoost module only for known versions, this may cause trouble for other MITK developers relying on new components of Boost or components with changed dependencies. * Copy a newer version of the FindBoost module into our CMake directory. Our CMake directory has a higher precedence than the default CMake module directory. Doublecheck if the minimum required version of CMake is able to process the newer version of the FindBoost module. Also, DO NOT FORGET to mention this option right above the call of cmake_minimum_required() in the top-level CMakeLists.txt file AND in this file right above the set(url) command below so if we update the minimum required version of CMake or use another option in the future, we do not forget to remove our copy of the FindBoost module again. ]] set(url "${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/boost_1_82_0.tar.gz") set(md5 f7050f554a65f6a42ece221eaeec1660) if(MITK_USE_Boost_LIBRARIES) #[[ Boost has a two-step build process. In the first step, a bootstrap script is called to build b2, an executable that is used to actually build Boost in the second step. The bootstrap script expects a toolset (compiler) argument that is used to build the b2 executable. The scripts and their expected argument format differ between Windows and Unix. ]] if(WIN32) mitkFunctionGetMSVCVersion() if(VISUAL_STUDIO_VERSION_MINOR EQUAL 0) #[[ Use just the major version in the toolset name. ]] set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}) elseif(VISUAL_STUDIO_VERSION_MAJOR EQUAL 14 AND VISUAL_STUDIO_VERSION_MINOR LESS 20) #[[ Assume Visual Studio 2017. ]] set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}1) elseif(VISUAL_STUDIO_VERSION_MAJOR EQUAL 14 AND VISUAL_STUDIO_VERSION_MINOR LESS 30) #[[ Assume Visual Studio 2019. ]] set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}2) elseif(VISUAL_STUDIO_VERSION_MAJOR EQUAL 14 AND VISUAL_STUDIO_VERSION_MINOR LESS 40) #[[ Assume Visual Studio 2022. ]] set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}3) else() #[[ Fallback to the generic case. Be prepared to add another elseif branch above for future versions of Visual Studio. ]] set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}) endif() else() #[[ We support GCC and Clang on Unix. On macOS, the toolset must be set to clang. The actual compiler for all of these toolkits is set further below, after the bootstrap script but before b2. ]] if(CMAKE_CXX_COMPILER_ID STREQUAL GNU) set(toolset gcc) elseif(CMAKE_CXX_COMPILER_ID STREQUAL Clang OR APPLE) set(toolset clang) endif() if(toolset) set(bootstrap_args --with-toolset=${toolset}) endif() #[[ At least give it a shot if the toolset is something else and let the bootstrap script decide on the toolset by not passing any argument. ]] endif() #[[ The call of b2 is more complex. b2 arguments are grouped into options and properties. Options follow the standard format for arguments while properties are plain key-value pairs. ]] set(b2_options --build-dir= --stagedir= --ignore-site-config #[[ Build independent of any site.config file ]] -q #[[ Stop at first error ]] ) if(APPLE AND CMAKE_OSX_SYSROOT) #[[ Specify the macOS platform SDK to be used. ]] list(APPEND b2_options --sysroot=${CMAKE_OSX_SYSROOT}) endif() foreach(lib ${MITK_USE_Boost_LIBRARIES}) list(APPEND b2_options --with-${lib}) endforeach() set(b2_properties threading=multi runtime-link=shared "cxxflags=${MITK_CXX${MITK_CXX_STANDARD}_FLAG} ${CMAKE_CXX_FLAGS}" ) if(CMAKE_SIZEOF_VOID_P EQUAL 8) list(APPEND b2_properties address-model=64) else() list(APPEND b2_properties address-model=32) endif() if(BUILD_SHARED_LIBS) list(APPEND b2_properties link=shared) else() list(APPEND b2_properties link=static) endif() list(APPEND b2_properties "\ $<$:variant=debug>\ $<$:variant=release>\ $<$:variant=release>\ $<$:variant=release>") if(WIN32) set(bootstrap_cmd if not exist b2.exe $ call bootstrap.bat ${bootstrap_args} $) set(b2_cmd b2 ${b2_options} ${b2_properties} stage) else() set(bootstrap_cmd #[[ test -e ./b2 || ]] ./bootstrap.sh ${bootstrap_args}) set(b2_cmd ./b2 ${b2_options} ${b2_properties} stage) #[[ We already told Boost if we want to use GCC or Clang but so far we were not able to specify the exact same compiler we set in CMake when configuring the MITK superbuild for the first time. For example, this can be different from the system default when multiple versions of the same compiler are installed at the same time. The bootstrap script creates a configuration file for b2 that should be modified if necessary before b2 is called. We look for a line like using gcc ; and replace it with something more specific like using gcc : : /usr/bin/gcc-7.3 ; We use the stream editor sed for the replacement but since macOS is based on BSD Unix, we use the limited but portable BSD syntax instead of the more powerful GNU syntax. We also use | instead of the more commonly used / separator for sed because the replacement contains slashes. 2021/06/15: The custom project-config.jam does not work well with SDK paths on macOS anymore, so we use a custom project-config.jam only on Linux for now. ]] if(toolset AND NOT APPLE) set(configure_cmd sed -i.backup "\ s|\ using[[:space:]][[:space:]]*${toolset}[[:space:]]*$|\ using ${toolset} : : ${CMAKE_CXX_COMPILER} $|\ g" /project-config.jam ) endif() endif() endif() if(WIN32) set(dummy_cmd cd .) else() set(dummy_cmd true) #[[ "cd ." does not work reliably ]] endif() if(NOT patch_cmd) set(patch_cmd ${dummy_cmd}) #[[ Do nothing ]] endif() if(NOT configure_cmd) set(configure_cmd ${dummy_cmd}) #[[ Do nothing ]] endif() if(WIN32) set(install_cmd if not exist $ $ ${CMAKE_COMMAND} -E copy_directory /boost /include/boost $ ) else() set(install_cmd # test -e /include/boost/config.hpp || ${CMAKE_COMMAND} -E copy_directory /boost /include/boost ) endif() ExternalProject_Add(${proj} URL ${url} URL_MD5 ${md5} PATCH_COMMAND ${patch_cmd} CONFIGURE_COMMAND ${configure_cmd} BUILD_COMMAND "" INSTALL_COMMAND ${install_cmd} ) ExternalProject_Add_Step(${proj} bootstrap COMMAND ${bootstrap_cmd} DEPENDEES patch DEPENDERS configure WORKING_DIRECTORY ) ExternalProject_Add_Step(${proj} b2 COMMAND ${b2_cmd} DEPENDEES bootstrap DEPENDERS build WORKING_DIRECTORY ) if(WIN32) #[[ Reuse already extracted files. ]] set(stamp_dir ${ep_prefix}/src/Boost-stamp) configure_file( ${CMAKE_CURRENT_LIST_DIR}/extract-Boost.replacement.cmake ${stamp_dir}/extract-Boost.replacement.cmake COPYONLY) ExternalProject_Add_Step(${proj} pre_download COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-pre_download.cmake DEPENDEES mkdir DEPENDERS download WORKING_DIRECTORY ${stamp_dir} ) endif() set(install_manifest_dependees install) if(MITK_USE_Boost_LIBRARIES) if(WIN32) #[[ Move DLLs from lib to bin directory. ]] ExternalProject_Add_Step(${proj} post_install COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-post_install-WIN32.cmake DEPENDEES install WORKING_DIRECTORY /lib ) set(install_manifest_dependees post_install) elseif(APPLE) #[[ Boost does not follow the common practice of either using rpath or absolute paths for referencing dependencies. We have to use the install_name_tool to fix this. ]] ExternalProject_Add_Step(${proj} post_install COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-post_install-APPLE.cmake DEPENDEES install WORKING_DIRECTORY /lib ) set(install_manifest_dependees post_install) endif() endif() ExternalProject_Add_Step(${proj} install_manifest COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-install_manifest.cmake DEPENDEES ${install_manifest_dependees} WORKING_DIRECTORY ${ep_prefix} ) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() diff --git a/CMakeExternals/Poco.cmake b/CMakeExternals/Poco.cmake index 9a3ccd0794..e81f01376e 100644 --- a/CMakeExternals/Poco.cmake +++ b/CMakeExternals/Poco.cmake @@ -1,103 +1,103 @@ #----------------------------------------------------------------------------- # Poco #----------------------------------------------------------------------------- if(MITK_USE_Poco) # Sanity checks if(DEFINED Poco_DIR AND NOT EXISTS ${Poco_DIR}) message(FATAL_ERROR "Poco_DIR variable is defined but corresponds to non-existing directory") endif() set(proj Poco) set(proj_DEPENDENCIES ) set(${proj}_DEPENDS ${proj}) if(NOT DEFINED ${proj}_DIR) set(additional_cmake_args ) if(CTEST_USE_LAUNCHERS) list(APPEND additional_cmake_args "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake" ) endif() mitk_query_custom_ep_vars() set(ssl_args -DENABLE_CRYPTO:BOOL=OFF -DENABLE_NETSSL:BOOL=OFF -DENABLE_NETSSL_WIN:BOOL=OFF ) if(OpenSSL_FOUND) set(ssl_args -DENABLE_CRYPTO:BOOL=ON -DENABLE_NETSSL:BOOL=ON -DFORCE_OPENSSL:BOOL=ON ) if(OPENSSL_ROOT_DIR) list(APPEND ssl_args "-DOPENSSL_ROOT_DIR:PATH=${OPENSSL_ROOT_DIR}" ) endif() endif() ExternalProject_Add(${proj} LIST_SEPARATOR ${sep} - GIT_REPOSITORY https://github.com/pocoproject/poco.git - GIT_TAG poco-1.12.4-release + GIT_REPOSITORY https://github.com/mitk/poco.git + GIT_TAG 7a7d81fd049088d93e42d0f7b8f7f7d5d1af3708 # poco-1.12.4-patched CMAKE_GENERATOR ${gen} CMAKE_GENERATOR_PLATFORM ${gen_platform} CMAKE_ARGS ${ep_common_args} ${additional_cmake_args} ${ssl_args} -DENABLE_ACTIVERECORD:BOOL=OFF -DENABLE_ACTIVERECORD_COMPILER:BOOL=OFF -DENABLE_APACHECONNECTOR:BOOL=OFF -DENABLE_CPPPARSER:BOOL=OFF -DENABLE_DATA:BOOL=OFF -DENABLE_DATA_MYSQL:BOOL=OFF -DENABLE_DATA_ODBC:BOOL=OFF -DENABLE_DATA_POSTGRESQL:BOOL=OFF -DENABLE_DATA_SQLITE:BOOL=OFF -DENABLE_ENCODINGS:BOOL=OFF -DENABLE_ENCODINGS_COMPILER:BOOL=OFF -DENABLE_FOUNDATION:BOOL=ON -DENABLE_JSON:BOOL=ON -DENABLE_JWT:BOOL=OFF -DENABLE_MONGODB:BOOL=OFF -DENABLE_NET:BOOL=ON -DENABLE_PAGECOMPILER:BOOL=OFF -DENABLE_PAGECOMPILER_FILE2PAGE:BOOL=OFF -DENABLE_PDF:BOOL=OFF -DENABLE_POCODOC:BOOL=OFF -DENABLE_PROMETHEUS:BOOL=OFF -DENABLE_REDIS:BOOL=OFF -DENABLE_SEVENZIP:BOOL=OFF -DENABLE_TESTS:BOOL=OFF -DENABLE_UTIL:BOOL=ON -DENABLE_XML:BOOL=ON -DENABLE_ZIP:BOOL=ON ${${proj}_CUSTOM_CMAKE_ARGS} CMAKE_CACHE_ARGS ${ep_common_cache_args} ${${proj}_CUSTOM_CMAKE_CACHE_ARGS} CMAKE_CACHE_DEFAULT_ARGS ${ep_common_cache_default_args} ${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS} DEPENDS ${proj_DEPENDENCIES} ) set(${proj}_DIR ${ep_prefix}) mitkFunctionInstallExternalCMakeProject(${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeLists.txt b/CMakeLists.txt index dd5ce7718a..704c4e583e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,1418 +1,1422 @@ #[[ When increasing the minimum required version, check if Boost_ADDITIONAL_VERSIONS in CMake/PackageDepends/MITK_Boost_Config.cmake can be removed. See the first long comment in CMakeExternals/Boost.cmake for details. ]] set(MITK_CMAKE_MINIMUM_REQUIRED_VERSION 3.18) cmake_minimum_required(VERSION ${MITK_CMAKE_MINIMUM_REQUIRED_VERSION}) if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.19 AND CMAKE_VERSION VERSION_LESS 3.19.2) message(FATAL_ERROR "\ CMake v${CMAKE_VERSION} is defective [1]. \ Please either downgrade to v3.18 or upgrade to at least v3.19.2.\n\ [1] https://gitlab.kitware.com/cmake/cmake/-/issues/21529") endif() #----------------------------------------------------------------------------- # Policies #----------------------------------------------------------------------------- #[[ T28060 https://cmake.org/cmake/help/v3.18/policy/CMP0091.html https://cmake.org/cmake/help/v3.18/variable/CMAKE_MSVC_RUNTIME_LIBRARY.html We pass CMP0091 to all external projects as command-line argument: -DCMAKE_POLICY_DEFAULT_CMP0091:STRING=OLD ]] cmake_policy(SET CMP0091 OLD) +if(POLICY CMP0135) + cmake_policy(SET CMP0135 NEW) # https://cmake.org/cmake/help/v3.24/policy/CMP0135.html +endif() + #----------------------------------------------------------------------------- # Superbuild Option - Enabled by default #----------------------------------------------------------------------------- option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON) if(MITK_USE_SUPERBUILD) project(MITK-superbuild) set(MITK_SOURCE_DIR ${PROJECT_SOURCE_DIR}) set(MITK_BINARY_DIR ${PROJECT_BINARY_DIR}) else() project(MITK VERSION 2023.04.99) include_directories(SYSTEM ${MITK_SUPERBUILD_BINARY_DIR}) endif() #----------------------------------------------------------------------------- # MITK Extension Feature #----------------------------------------------------------------------------- set(MITK_EXTENSION_DIRS "" CACHE STRING "") unset(MITK_ABSOLUTE_EXTENSION_DIRS) foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS}) get_filename_component(MITK_ABSOLUTE_EXTENSION_DIR "${MITK_EXTENSION_DIR}" ABSOLUTE) list(APPEND MITK_ABSOLUTE_EXTENSION_DIRS "${MITK_ABSOLUTE_EXTENSION_DIR}") endforeach() set(MITK_DIR_PLUS_EXTENSION_DIRS "${MITK_SOURCE_DIR}" ${MITK_ABSOLUTE_EXTENSION_DIRS}) #----------------------------------------------------------------------------- # Update CMake module path #----------------------------------------------------------------------------- set(MITK_CMAKE_DIR ${MITK_SOURCE_DIR}/CMake) set(CMAKE_MODULE_PATH ${MITK_CMAKE_DIR}) foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_CMAKE_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMake") if(EXISTS "${MITK_CMAKE_EXTENSION_DIR}") list(APPEND CMAKE_MODULE_PATH "${MITK_CMAKE_EXTENSION_DIR}") endif() endforeach() #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- # Standard CMake macros include(FeatureSummary) include(CTest) include(CMakeParseArguments) include(FindPackageHandleStandardArgs) # MITK macros include(mitkFunctionGetGccVersion) include(mitkFunctionCheckCompilerFlags) include(mitkFunctionSuppressWarnings) # includes several functions include(mitkMacroEmptyExternalProject) include(mitkFunctionEnableBuildConfiguration) include(mitkFunctionWhitelists) include(mitkFunctionAddExternalProject) include(mitkFunctionAddLibrarySearchPaths) SUPPRESS_VC_DEPRECATED_WARNINGS() #----------------------------------------------------------------------------- # Set a default build type if none was specified #----------------------------------------------------------------------------- if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) message(STATUS "Setting build type to 'Debug' as none was specified.") set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE) # Set the possible values of build type for cmake-gui set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") endif() if(CMAKE_COMPILER_IS_GNUCXX) mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION) else() set(GCC_VERSION 0) endif() set(MITK_CXX_STANDARD 17) set(CMAKE_CXX_EXTENSIONS 0) set(CMAKE_CXX_STANDARD ${MITK_CXX_STANDARD}) set(CMAKE_CXX_STANDARD_REQUIRED 1) # This is necessary to avoid problems with compile feature checks. # CMAKE_CXX_STANDARD seems to only set the -std=c++ flag for targets. # However, compile flag checks also need to be done with -std=c++. # The MITK_CXX_FLAG variable is also used for external projects # build during the MITK super-build. mitkFunctionCheckCompilerFlags("-std=c++${MITK_CXX_STANDARD}" MITK_CXX${MITK_CXX_STANDARD}_FLAG) #----------------------------------------------------------------------------- # Warn if source or build path is too long #----------------------------------------------------------------------------- if(WIN32) set(_src_dir_length_max 50) set(_bin_dir_length_max 50) if(MITK_USE_SUPERBUILD) set(_src_dir_length_max 34) # _src_dir_length_max - strlen(ep/src/ITK-build) set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build) endif() string(LENGTH "${MITK_SOURCE_DIR}" _src_n) string(LENGTH "${MITK_BINARY_DIR}" _bin_n) # The warnings should be converted to errors if(_src_n GREATER _src_dir_length_max) message(WARNING "MITK source code directory path length is too long (${_src_n} > ${_src_dir_length_max})." "Please move the MITK source code directory to a directory with a shorter path." ) endif() if(_bin_n GREATER _bin_dir_length_max) message(WARNING "MITK build directory path length is too long (${_bin_n} > ${_bin_dir_length_max})." "Please move the MITK build directory to a directory with a shorter path." ) endif() endif() #----------------------------------------------------------------------------- # Additional MITK Options (also shown during superbuild) #----------------------------------------------------------------------------- # ----------------------------------------- # General build options option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON) option(WITH_COVERAGE "Enable/Disable coverage" OFF) option(BUILD_TESTING "Test the project" ON) option(MITK_FAST_TESTING "Disable long-running tests like packaging" OFF) option(MITK_XVFB_TESTING "Execute test drivers through xvfb-run" OFF) option(MITK_BUILD_ALL_APPS "Build all MITK applications" OFF) option(MITK_BUILD_EXAMPLES "Build the MITK Examples" OFF) mark_as_advanced( MITK_XVFB_TESTING MITK_FAST_TESTING MITK_BUILD_ALL_APPS ) #----------------------------------------------------------------------------- # Set UI testing flags #----------------------------------------------------------------------------- if(MITK_XVFB_TESTING) set(MITK_XVFB_TESTING_COMMAND "xvfb-run" "--auto-servernum" CACHE STRING "Command and options to test through Xvfb") mark_as_advanced(MITK_XVFB_TESTING_COMMAND) endif(MITK_XVFB_TESTING) # ----------------------------------------- # Other options set(MITK_CUSTOM_REVISION_DESC "" CACHE STRING "Override MITK revision description") mark_as_advanced(MITK_CUSTOM_REVISION_DESC) set_property(GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS "") include(CMakeExternals/ExternalProjectList.cmake) foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMakeExternals") if(EXISTS "${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake") include("${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake") endif() endforeach() # ----------------------------------------- # Other MITK_USE_* options not related to # external projects build via the # MITK superbuild option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON) option(MITK_USE_OpenCL "Use OpenCL GPU-Computing library" OFF) option(MITK_USE_OpenMP "Use OpenMP" OFF) option(MITK_USE_Python3 "Use Python 3" OFF) #----------------------------------------------------------------------------- # Build configurations #----------------------------------------------------------------------------- set(_buildConfigs "Custom") file(GLOB _buildConfigFiles CMake/BuildConfigurations/*.cmake) foreach(_buildConfigFile ${_buildConfigFiles}) get_filename_component(_buildConfigFile ${_buildConfigFile} NAME_WE) list(APPEND _buildConfigs ${_buildConfigFile}) endforeach() foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) file(GLOB _extBuildConfigFiles "${MITK_EXTENSION_DIR}/CMake/BuildConfigurations/*.cmake") foreach(_extBuildConfigFile ${_extBuildConfigFiles}) get_filename_component(_extBuildConfigFile "${_extBuildConfigFile}" NAME_WE) list(APPEND _buildConfigs "${_extBuildConfigFile}") endforeach() list(REMOVE_DUPLICATES _buildConfigs) endforeach() set(MITK_BUILD_CONFIGURATION "Custom" CACHE STRING "Use pre-defined MITK configurations") set_property(CACHE MITK_BUILD_CONFIGURATION PROPERTY STRINGS ${_buildConfigs}) mitkFunctionEnableBuildConfiguration() mitkFunctionCreateWhitelistPaths(MITK) mitkFunctionFindWhitelists(MITK) # ----------------------------------------- # Qt version related variables option(MITK_USE_Qt5 "Use Qt 5 library" ON) if(MITK_USE_Qt5) if(WIN32) set(MITK_QT5_MINIMUM_VERSION 5.12.9) else() set(MITK_QT5_MINIMUM_VERSION 5.12) endif() set(MITK_QT5_COMPONENTS Concurrent OpenGL PrintSupport Script Sql Svg Widgets Xml XmlPatterns WebEngineWidgets UiTools Help LinguistTools) if(APPLE) list(APPEND MITK_QT5_COMPONENTS DBus) elseif(UNIX) list(APPEND MITK_QT5_COMPONENTS X11Extras) endif() # Hint at default install locations of Qt if(NOT Qt5_DIR) if(MSVC) set(_dir_candidates "C:/Qt") if(CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)") set(_compilers "msvc${CMAKE_MATCH_1}") elseif(CMAKE_GENERATOR MATCHES "Ninja") include(mitkFunctionGetMSVCVersion) mitkFunctionGetMSVCVersion() if(VISUAL_STUDIO_PRODUCT_NAME MATCHES "^Visual Studio ([0-9]+)") set(_compilers "msvc${CMAKE_MATCH_1}") endif() endif() if(_compilers MATCHES "[0-9]+") if (CMAKE_MATCH_0 EQUAL 2022) list(APPEND _compilers "msvc2019" "msvc2017") # Binary compatible elseif (CMAKE_MATCH_0 EQUAL 2019) list(APPEND _compilers "msvc2017") # Binary compatible endif() endif() else() set(_dir_candidates ~/Qt) if(APPLE) set(_compilers clang) else() list(APPEND _dir_candidates /opt/Qt) set(_compilers gcc) endif() endif() if(CMAKE_SIZEOF_VOID_P EQUAL 8) foreach(_compiler ${_compilers}) list(APPEND _compilers64 "${_compiler}_64") endforeach() set(_compilers ${_compilers64}) endif() foreach(_dir_candidate ${_dir_candidates}) get_filename_component(_dir_candidate ${_dir_candidate} REALPATH) foreach(_compiler ${_compilers}) set(_glob_expression "${_dir_candidate}/5.*/${_compiler}") file(GLOB _hints ${_glob_expression}) list(SORT _hints) list(APPEND MITK_QT5_HINTS ${_hints}) endforeach() endforeach() endif() find_package(Qt5 ${MITK_QT5_MINIMUM_VERSION} COMPONENTS ${MITK_QT5_COMPONENTS} REQUIRED HINTS ${MITK_QT5_HINTS}) endif() # ----------------------------------------- # Custom dependency logic if(WIN32 AND Qt5_DIR) set(_dir_candidate "${Qt5_DIR}/../../../../../Tools/OpenSSL/Win_x64") get_filename_component(_dir_candidate ${_dir_candidate} ABSOLUTE) if(EXISTS "${_dir_candidate}") set(OPENSSL_ROOT_DIR "${_dir_candidate}") endif() endif() find_package(OpenSSL) option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF) set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries") if(MITK_USE_cpprestsdk OR MITK_USE_httplib) if(NOT OpenSSL_FOUND) set(openssl_message "Could not find OpenSSL (dependency of C++ REST SDK and cpp-httplib).\n") if(UNIX) if(APPLE) set(openssl_message "${openssl_message}Please install it using your favorite package management " "system (i.e. Homebrew or MacPorts).\n") else() set(openssl_message "${openssl_message}Please install the dev package of OpenSSL (i.e. libssl-dev).\n") endif() else() set(openssl_message "${openssl_message}Please either install Win32 OpenSSL:\n" " https://slproweb.com/products/Win32OpenSSL.html\n" "Or use the Qt Maintenance tool to install (recommended):\n" " Developer and Designer Tools > OpenSSL Toolkit > OpenSSL 64-bit binaries\n") endif() set(openssl_message "${openssl_message}If it still cannot be found, you can hint CMake to find OpenSSL by " "adding/setting the OPENSSL_ROOT_DIR variable to the root directory of an " "OpenSSL installation. Make sure to clear variables of partly found " "versions of OpenSSL before, or they will be mixed up.") message(FATAL_ERROR ${openssl_message}) endif() list(APPEND MITK_USE_Boost_LIBRARIES date_time regex system) if(UNIX) list(APPEND MITK_USE_Boost_LIBRARIES atomic chrono filesystem random thread) endif() list(REMOVE_DUPLICATES MITK_USE_Boost_LIBRARIES) set(MITK_USE_Boost_LIBRARIES ${MITK_USE_Boost_LIBRARIES} CACHE STRING "A semi-colon separated list of required Boost libraries" FORCE) endif() if(MITK_USE_Python3) set(MITK_USE_ZLIB ON CACHE BOOL "" FORCE) if(APPLE AND CMAKE_FRAMEWORK_PATH AND CMAKE_FRAMEWORK_PATH MATCHES "python3\\.?([0-9]+)") find_package(Python3 3.${CMAKE_MATCH_1} EXACT REQUIRED COMPONENTS Interpreter Development NumPy) else() find_package(Python3 REQUIRED COMPONENTS Interpreter Development NumPy) endif() if(WIN32) string(REPLACE "\\" "/" Python3_STDARCH "${Python3_STDARCH}") string(REPLACE "\\" "/" Python3_STDLIB "${Python3_STDLIB}") string(REPLACE "\\" "/" Python3_SITELIB "${Python3_SITELIB}") endif() endif() if(BUILD_TESTING AND NOT MITK_USE_CppUnit) message("> Forcing MITK_USE_CppUnit to ON because BUILD_TESTING=ON") set(MITK_USE_CppUnit ON CACHE BOOL "Use CppUnit for unit tests" FORCE) endif() if(MITK_USE_BLUEBERRY) option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF) mark_as_advanced(MITK_BUILD_ALL_PLUGINS) if(NOT MITK_USE_CTK) message("> Forcing MITK_USE_CTK to ON because of MITK_USE_BLUEBERRY") set(MITK_USE_CTK ON CACHE BOOL "Use CTK in MITK" FORCE) endif() endif() #----------------------------------------------------------------------------- # Pixel type multiplexing #----------------------------------------------------------------------------- # Customize the default pixel types for multiplex macros set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES "int, unsigned int, short, unsigned short, char, unsigned char" CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES "double, float" CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES "itk::RGBPixel, itk::RGBAPixel" CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_DIMENSIONS "2,3" CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros") mark_as_advanced(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES MITK_ACCESSBYITK_DIMENSIONS ) # consistency checks if(NOT MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES) set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES "int, unsigned int, short, unsigned short, char, unsigned char" CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE) endif() if(NOT MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES) set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES "double, float" CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE) endif() if(NOT MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES) set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES "itk::RGBPixel, itk::RGBAPixel" CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE) endif() if(NOT MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES) string(REPLACE "," ";" _integral_types ${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES}) string(REPLACE "," ";" _floating_types ${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES}) foreach(_scalar_type ${_integral_types} ${_floating_types}) set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}itk::VariableLengthVector<${_scalar_type}>,") endforeach() string(LENGTH "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" _length) math(EXPR _length "${_length} - 1") string(SUBSTRING "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" 0 ${_length} MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES) set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES ${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES} CACHE STRING "List of vector pixel types used in AccessByItk and InstantiateAccessFunction macros for itk::VectorImage types" FORCE) endif() if(NOT MITK_ACCESSBYITK_DIMENSIONS) set(MITK_ACCESSBYITK_DIMENSIONS "2,3" CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros") endif() find_package(Git REQUIRED) #----------------------------------------------------------------------------- # Superbuild script #----------------------------------------------------------------------------- if(MITK_USE_SUPERBUILD) include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") # Print configuration summary message("\n\n") feature_summary( DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------" WHAT ALL) return() endif() #***************************************************************************** #**************************** END OF SUPERBUILD **************************** #***************************************************************************** #----------------------------------------------------------------------------- # Organize MITK targets in folders #----------------------------------------------------------------------------- set_property(GLOBAL PROPERTY USE_FOLDERS ON) set(MITK_ROOT_FOLDER "MITK" CACHE STRING "") mark_as_advanced(MITK_ROOT_FOLDER) #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- include(WriteBasicConfigVersionFile) include(CheckCXXSourceCompiles) include(GenerateExportHeader) include(mitkFunctionAddManifest) include(mitkFunctionAddCustomModuleTest) include(mitkFunctionCheckModuleDependencies) include(mitkFunctionCompileSnippets) include(mitkFunctionConfigureVisualStudioUserProjectFile) include(mitkFunctionCreateBlueBerryApplication) include(mitkFunctionCreateCommandLineApp) include(mitkFunctionCreateModule) include(mitkFunctionCreatePlugin) include(mitkFunctionCreateProvisioningFile) include(mitkFunctionGetLibrarySearchPaths) include(mitkFunctionGetVersion) include(mitkFunctionGetVersionDescription) include(mitkFunctionInstallAutoLoadModules) include(mitkFunctionInstallCTKPlugin) include(mitkFunctionInstallProvisioningFiles) include(mitkFunctionInstallThirdPartyCTKPlugins) include(mitkFunctionOrganizeSources) include(mitkFunctionUseModules) if( ${MITK_USE_MatchPoint} ) include(mitkFunctionCreateMatchPointDeployedAlgorithm) endif() include(mitkMacroConfigureItkPixelTypes) include(mitkMacroCreateExecutable) include(mitkMacroCreateModuleTests) include(mitkMacroGenerateToolsLibrary) include(mitkMacroGetLinuxDistribution) include(mitkMacroGetPMDPlatformString) include(mitkMacroInstall) include(mitkMacroInstallHelperApp) include(mitkMacroInstallTargets) include(mitkMacroMultiplexPicType) # Deprecated include(mitkMacroCreateCTKPlugin) #----------------------------------------------------------------------------- # Global CMake variables #----------------------------------------------------------------------------- if(NOT DEFINED CMAKE_DEBUG_POSTFIX) # We can't do this yet because the CTK Plugin Framework # cannot cope with a postfix yet. #set(CMAKE_DEBUG_POSTFIX d) endif() #----------------------------------------------------------------------------- # Output directories. #----------------------------------------------------------------------------- set(_default_LIBRARY_output_dir lib) set(_default_RUNTIME_output_dir bin) set(_default_ARCHIVE_output_dir lib) foreach(type LIBRARY RUNTIME ARCHIVE) # Make sure the directory exists if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) message("Creating directory MITK_CMAKE_${type}_OUTPUT_DIRECTORY: ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}") file(MAKE_DIRECTORY "${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}") endif() if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY) set(CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) else() set(CMAKE_${type}_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${_default_${type}_output_dir}) set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY}) endif() set(CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY} CACHE INTERNAL "Output directory for ${type} files.") mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY) endforeach() #----------------------------------------------------------------------------- # Set MITK specific options and variables (NOT available during superbuild) #----------------------------------------------------------------------------- if(OpenSSL_FOUND AND WIN32) #[[ On Windows, CMake is able to locate the link libraries for OpenSSL but it does not look for the corresponding DLLs that we need to copy to our binary directories and include in packaging. Setting these paths manually is cumbersome so we try to use a simple heuristic to automatically set them: - Based on the link libraries (usually located in a lib folder), try to find the "../bin" binary directory. - Use the base file names of the link libraries to find corresponding DLLs like "*.dll", that usually are named like "-1_1-x64.dll" or similar. ]] set(openssl_ssl_dll "") set(openssl_crypto_dll "") if(OPENSSL_SSL_LIBRARY AND EXISTS "${OPENSSL_SSL_LIBRARY}") get_filename_component(openssl_bin_dir "${OPENSSL_SSL_LIBRARY}" DIRECTORY) get_filename_component(openssl_bin_dir "${openssl_bin_dir}" DIRECTORY) set(openssl_bin_dir "${openssl_bin_dir}/bin") if(EXISTS "${openssl_bin_dir}") get_filename_component(openssl_ssl_basename "${OPENSSL_SSL_LIBRARY}" NAME_WE) file(GLOB openssl_ssl_dll "${openssl_bin_dir}/${openssl_ssl_basename}*.dll") list(LENGTH openssl_ssl_dll num_findings) if(num_findings GREATER 1) set(openssl_ssl_dll "") endif() get_filename_component(openssl_crypto_basename "${OPENSSL_CRYPTO_LIBRARY}" NAME_WE) file(GLOB openssl_crypto_dll "${openssl_bin_dir}/${openssl_crypto_basename}*.dll") list(LENGTH openssl_crypto_dll num_findings) if(num_findings GREATER 1) set(openssl_crypto_dll "") endif() endif() endif() set(MITK_OPENSSL_SSL_DLL "${openssl_ssl_dll}" CACHE FILEPATH "") if(DEFINED CACHE{MITK_OPENSSL_SSL_DLL} AND NOT MITK_OPENSSL_SSL_DLL AND openssl_ssl_dll) set(MITK_OPENSSL_SSL_DLL "${openssl_ssl_dll}" CACHE FILEPATH "" FORCE) endif() set(MITK_OPENSSL_CRYPTO_DLL "${openssl_crypto_dll}" CACHE FILEPATH "") if(DEFINED CACHE{MITK_OPENSSL_CRYPTO_DLL} AND NOT MITK_OPENSSL_CRYPTO_DLL AND openssl_crypto_dll) set(MITK_OPENSSL_CRYPTO_DLL "${openssl_crypto_dll}" CACHE FILEPATH "" FORCE) endif() if(MITK_OPENSSL_SSL_DLL AND EXISTS "${MITK_OPENSSL_SSL_DLL}" AND MITK_OPENSSL_CRYPTO_DLL AND EXISTS "${MITK_OPENSSL_CRYPTO_DLL}") foreach(config_type ${CMAKE_CONFIGURATION_TYPES}) execute_process(COMMAND "${CMAKE_COMMAND}" -E make_directory "${MITK_BINARY_DIR}/bin/${config_type}") configure_file("${MITK_OPENSSL_SSL_DLL}" "${MITK_BINARY_DIR}/bin/${config_type}/" COPYONLY) configure_file("${MITK_OPENSSL_CRYPTO_DLL}" "${MITK_BINARY_DIR}/bin/${config_type}/" COPYONLY) endforeach() MITK_INSTALL(FILES "${MITK_OPENSSL_SSL_DLL}" "${MITK_OPENSSL_CRYPTO_DLL}" ) endif() endif() # Look for optional Doxygen package find_package(Doxygen) option(BLUEBERRY_DEBUG_SMARTPOINTER "Enable code for debugging smart pointers" OFF) mark_as_advanced(BLUEBERRY_DEBUG_SMARTPOINTER) # Ask the user to show the console window for applications option(MITK_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting MITK GUI Applications" ON) mark_as_advanced(MITK_SHOW_CONSOLE_WINDOW) if(NOT MITK_FAST_TESTING) if(MITK_CTEST_SCRIPT_MODE STREQUAL "Continuous" OR MITK_CTEST_SCRIPT_MODE STREQUAL "Experimental") set(MITK_FAST_TESTING ON) endif() endif() if(NOT UNIX) set(MITK_WIN32_FORCE_STATIC "STATIC" CACHE INTERNAL "Use this variable to always build static libraries on non-unix platforms") endif() if(MITK_BUILD_ALL_PLUGINS) set(MITK_BUILD_ALL_PLUGINS_OPTION "FORCE_BUILD_ALL") endif() # Configure pixel types used for ITK image access multiplexing mitkMacroConfigureItkPixelTypes() # Configure module naming conventions set(MITK_MODULE_NAME_REGEX_MATCH "^[A-Z].*$") set(MITK_MODULE_NAME_REGEX_NOT_MATCH "^[Mm][Ii][Tt][Kk].*$") set(MITK_DEFAULT_MODULE_NAME_PREFIX "Mitk") set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX}) set(MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME 1) #----------------------------------------------------------------------------- # Get MITK version info #----------------------------------------------------------------------------- mitkFunctionGetVersion(${MITK_SOURCE_DIR} MITK) mitkFunctionGetVersionDescription(${MITK_SOURCE_DIR} MITK) # MITK_VERSION set(MITK_VERSION_STRING "${MITK_VERSION_MAJOR}.${MITK_VERSION_MINOR}.${MITK_VERSION_PATCH}") if(MITK_VERSION_PATCH STREQUAL "99") set(MITK_VERSION_STRING "${MITK_VERSION_STRING}-${MITK_REVISION_SHORTID}") endif() #----------------------------------------------------------------------------- # Installation preparation # # These should be set before any MITK install macros are used #----------------------------------------------------------------------------- # on macOS all BlueBerry plugins get copied into every # application bundle (.app directory) specified here if(MITK_USE_BLUEBERRY AND APPLE) foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") set(MITK_APPS "") include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") foreach(mitk_app ${MITK_APPS}) # extract option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 1 option_name) list(GET target_info_list 0 app_name) # check if the application is enabled if(${option_name} OR MITK_BUILD_ALL_APPS) set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} Mitk${app_name}) endif() endforeach() endif() endforeach() endif() #----------------------------------------------------------------------------- # Set coverage Flags #----------------------------------------------------------------------------- if(WITH_COVERAGE) if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG") set(COVERAGE_CXX_FLAGS ${coverage_flags}) set(COVERAGE_C_FLAGS ${coverage_flags}) endif() endif() #----------------------------------------------------------------------------- # MITK C/CXX Flags #----------------------------------------------------------------------------- set(MITK_C_FLAGS "${COVERAGE_C_FLAGS}") set(MITK_C_FLAGS_DEBUG ) set(MITK_C_FLAGS_RELEASE ) set(MITK_CXX_FLAGS "${COVERAGE_CXX_FLAGS} ${MITK_CXX${MITK_CXX_STANDARD}_FLAG}") set(MITK_CXX_FLAGS_DEBUG ) set(MITK_CXX_FLAGS_RELEASE ) set(MITK_EXE_LINKER_FLAGS ) set(MITK_SHARED_LINKER_FLAGS ) if(WIN32) set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DWIN32_LEAN_AND_MEAN -DNOMINMAX") mitkFunctionCheckCompilerFlags("/wd4005" MITK_CXX_FLAGS) # warning C4005: macro redefinition mitkFunctionCheckCompilerFlags("/wd4231" MITK_CXX_FLAGS) # warning C4231: nonstandard extension used : 'extern' before template explicit instantiation # the following line should be removed after fixing bug 17637 mitkFunctionCheckCompilerFlags("/wd4316" MITK_CXX_FLAGS) # warning C4316: object alignment on heap mitkFunctionCheckCompilerFlags("/wd4180" MITK_CXX_FLAGS) # warning C4180: qualifier applied to function type has no meaning mitkFunctionCheckCompilerFlags("/wd4251" MITK_CXX_FLAGS) # warning C4251: 'identifier' : class 'type' needs to have dll-interface to be used by clients of class 'type2' endif() if(APPLE) set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DGL_SILENCE_DEPRECATION") # Apple deprecated OpenGL in macOS 10.14 endif() if(NOT MSVC_VERSION) foreach(_flag -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -Wno-error=gnu -Wno-error=unknown-pragmas # The strict-overflow warning is generated by ITK template code -Wno-error=strict-overflow -Woverloaded-virtual -Wstrict-null-sentinel #-Wold-style-cast #-Wsign-promo -Wno-deprecated-copy -Wno-array-bounds -Wno-cast-function-type -Wno-maybe-uninitialized -Wno-error=stringop-overread -fdiagnostics-show-option ) mitkFunctionCheckCAndCXXCompilerFlags(${_flag} MITK_C_FLAGS MITK_CXX_FLAGS) endforeach() endif() if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE) mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" MITK_SHARED_LINKER_FLAGS) mitkFunctionCheckCompilerFlags("-Wl,--as-needed" MITK_SHARED_LINKER_FLAGS) endif() if(CMAKE_COMPILER_IS_GNUCXX) mitkFunctionCheckCAndCXXCompilerFlags("-fstack-protector-all" MITK_C_FLAGS MITK_CXX_FLAGS) set(MITK_CXX_FLAGS_RELEASE "-U_FORTIFY_SOURCES -D_FORTIFY_SOURCE=2 ${MITK_CXX_FLAGS_RELEASE}") endif() set(MITK_MODULE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS}) set(MITK_EXE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS}) #----------------------------------------------------------------------------- # MITK Packages #----------------------------------------------------------------------------- set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends) set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR}) foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_PACKAGE_DEPENDS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMake/PackageDepends") if(EXISTS "${MITK_PACKAGE_DEPENDS_EXTENSION_DIR}") list(APPEND MODULES_PACKAGE_DEPENDS_DIRS "${MITK_PACKAGE_DEPENDS_EXTENSION_DIR}") endif() endforeach() if(NOT MITK_USE_SYSTEM_Boost) set(Boost_NO_SYSTEM_PATHS 1) endif() set(Boost_USE_MULTITHREADED 1) set(Boost_USE_STATIC_LIBS 0) set(Boost_USE_STATIC_RUNTIME 0) set(Boost_ADDITIONAL_VERSIONS 1.74 1.74.0) # We need this later for a DCMTK workaround set(_dcmtk_dir_orig ${DCMTK_DIR}) # This property is populated at the top half of this file get_property(MITK_EXTERNAL_PROJECTS GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS) foreach(ep ${MITK_EXTERNAL_PROJECTS}) get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE) get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS) if(MITK_USE_${ep} AND _package) if(_components) find_package(${_package} COMPONENTS ${_components} REQUIRED CONFIG) else() # Prefer config mode first because it finds external # Config.cmake files pointed at by _DIR variables. # Otherwise, existing Find.cmake files could fail. if(DEFINED ${_package}_DIR) #we store the information because it will be overwritten by find_package #and would get lost for all EPs that use on Find.cmake instead of config #files. set(_temp_EP_${_package}_dir ${${_package}_DIR}) endif(DEFINED ${_package}_DIR) find_package(${_package} QUIET CONFIG) string(TOUPPER "${_package}" _package_uc) if(NOT (${_package}_FOUND OR ${_package_uc}_FOUND)) if(DEFINED _temp_EP_${_package}_dir) set(${_package}_DIR ${_temp_EP_${_package}_dir} CACHE PATH "externaly set dir of the package ${_package}" FORCE) endif(DEFINED _temp_EP_${_package}_dir) find_package(${_package} REQUIRED) endif() endif() endif() endforeach() # Ensure that the MITK CMake module path comes first set(CMAKE_MODULE_PATH ${MITK_CMAKE_DIR} ${CMAKE_MODULE_PATH} ) if(MITK_USE_DCMTK) if(${_dcmtk_dir_orig} MATCHES "${MITK_EXTERNAL_PROJECT_PREFIX}.*") # Help our FindDCMTK.cmake script find our super-build DCMTK set(DCMTK_DIR ${MITK_EXTERNAL_PROJECT_PREFIX}) else() # Use the original value set(DCMTK_DIR ${_dcmtk_dir_orig}) endif() endif() if(MITK_USE_DCMQI) # Due to the preferred CONFIG mode in find_package calls above, # the DCMQIConfig.cmake file is read, which does not provide useful # package information. We explictly need MODULE mode to find DCMQI. # Help our FindDCMQI.cmake script find our super-build DCMQI set(DCMQI_DIR ${MITK_EXTERNAL_PROJECT_PREFIX}) find_package(DCMQI REQUIRED) endif() if(MITK_USE_OpenIGTLink) link_directories(${OpenIGTLink_LIBRARY_DIRS}) endif() if(MITK_USE_OpenCL) find_package(OpenCL REQUIRED) endif() if(MITK_USE_OpenMP) find_package(OpenMP REQUIRED COMPONENTS CXX) else() find_package(OpenMP QUIET COMPONENTS CXX) if(OpenMP_FOUND) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) elseif(APPLE AND OpenMP_libomp_LIBRARY AND NOT OpenMP_CXX_LIB_NAMES) set(OpenMP_CXX_LIB_NAMES libomp CACHE STRING "" FORCE) get_filename_component(openmp_lib_dir "${OpenMP_libomp_LIBRARY}" DIRECTORY) set(openmp_include_dir "${openmp_lib_dir}/../include") if(EXISTS "${openmp_include_dir}") get_filename_component(openmp_include_dir "${openmp_include_dir}" REALPATH) set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${openmp_include_dir}" CACHE STRING "" FORCE) find_package(OpenMP QUIET COMPONENTS CXX) if(OpenMP_FOUND) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) endif() endif() endif() endif() # Qt support if(MITK_USE_Qt5) find_package(Qt5Core ${MITK_QT5_MINIMUM_VERSION} REQUIRED) # at least Core required get_target_property(_qmake_exec Qt5::qmake LOCATION) execute_process(COMMAND ${_qmake_exec} -query QT_INSTALL_BINS RESULT_VARIABLE _result OUTPUT_VARIABLE QT_BINARY_DIR ERROR_VARIABLE _error ) string(STRIP "${QT_BINARY_DIR}" QT_BINARY_DIR) if(_result OR NOT EXISTS "${QT_BINARY_DIR}") message(FATAL_ERROR "Could not determine Qt binary directory: ${_result} ${QT_BINARY_DIR} ${_error}") endif() find_program(QT_HELPGENERATOR_EXECUTABLE NAMES qhelpgenerator qhelpgenerator-qt5 qhelpgenerator5 PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) find_program(QT_COLLECTIONGENERATOR_EXECUTABLE NAMES qcollectiongenerator qcollectiongenerator-qt5 qcollectiongenerator5 PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) find_program(QT_ASSISTANT_EXECUTABLE NAMES assistant assistant-qt5 assistant5 PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) find_program(QT_XMLPATTERNS_EXECUTABLE NAMES xmlpatterns PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) mark_as_advanced(QT_HELPGENERATOR_EXECUTABLE QT_COLLECTIONGENERATOR_EXECUTABLE QT_ASSISTANT_EXECUTABLE QT_XMLPATTERNS_EXECUTABLE ) if(MITK_USE_BLUEBERRY) option(BLUEBERRY_USE_QT_HELP "Enable support for integrating plugin documentation into Qt Help" ${DOXYGEN_FOUND}) mark_as_advanced(BLUEBERRY_USE_QT_HELP) # Sanity checks for in-application BlueBerry plug-in help generation if(BLUEBERRY_USE_QT_HELP) set(_force_blueberry_use_qt_help_to_off 0) if(NOT DOXYGEN_FOUND) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen was not found.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(DOXYGEN_FOUND AND DOXYGEN_VERSION VERSION_LESS 1.8.7) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(NOT QT_HELPGENERATOR_EXECUTABLE) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because QT_HELPGENERATOR_EXECUTABLE is empty.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(NOT MITK_USE_Qt5) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because MITK_USE_Qt5 is OFF.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(NOT QT_XMLPATTERNS_EXECUTABLE) message("You have enabled Qt Help support, but QT_XMLPATTERNS_EXECUTABLE is empty") set(_force_blueberry_use_qt_help_to_off 1) endif() if(_force_blueberry_use_qt_help_to_off) set(BLUEBERRY_USE_QT_HELP OFF CACHE BOOL "Enable support for integrating plugin documentation into Qt Help" FORCE) endif() endif() if(BLUEBERRY_QT_HELP_REQUIRED AND NOT BLUEBERRY_USE_QT_HELP) message(FATAL_ERROR "BLUEBERRY_USE_QT_HELP is required to be set to ON") endif() endif() endif() #----------------------------------------------------------------------------- # Testing #----------------------------------------------------------------------------- if(BUILD_TESTING) # Configuration for the CMake-generated test driver set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include ") set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN " try {") set(CMAKE_TESTDRIVER_AFTER_TESTMAIN " } catch (const std::exception& e) { fprintf(stderr, \"%s\\n\", e.what()); return EXIT_FAILURE; } catch (...) { printf(\"Exception caught in the test driver\\n\"); return EXIT_FAILURE; }") set(MITK_TEST_OUTPUT_DIR "${MITK_BINARY_DIR}/test_output") if(NOT EXISTS ${MITK_TEST_OUTPUT_DIR}) file(MAKE_DIRECTORY ${MITK_TEST_OUTPUT_DIR}) endif() # Test the package target include(mitkPackageTest) endif() configure_file(mitkTestingConfig.h.in ${MITK_BINARY_DIR}/mitkTestingConfig.h) #----------------------------------------------------------------------------- # MITK_SUPERBUILD_BINARY_DIR #----------------------------------------------------------------------------- # If MITK_SUPERBUILD_BINARY_DIR isn't defined, it means MITK is *NOT* build using Superbuild. # In that specific case, MITK_SUPERBUILD_BINARY_DIR should default to MITK_BINARY_DIR if(NOT DEFINED MITK_SUPERBUILD_BINARY_DIR) set(MITK_SUPERBUILD_BINARY_DIR ${MITK_BINARY_DIR}) endif() #----------------------------------------------------------------------------- # Set C/CXX and linker flags for MITK code #----------------------------------------------------------------------------- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MITK_CXX_FLAGS}") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${MITK_CXX_FLAGS_DEBUG}") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${MITK_CXX_FLAGS_RELEASE}") set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MITK_C_FLAGS}") set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} ${MITK_C_FLAGS_DEBUG}") set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${MITK_C_FLAGS_RELEASE}") set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MITK_EXE_LINKER_FLAGS}") set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${MITK_SHARED_LINKER_FLAGS}") set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${MITK_MODULE_LINKER_FLAGS}") #----------------------------------------------------------------------------- # Add subdirectories #----------------------------------------------------------------------------- add_subdirectory(Utilities) add_subdirectory(Modules) include("${CMAKE_CURRENT_SOURCE_DIR}/Modules/ModuleList.cmake") mitkFunctionWhitelistModules(MITK MITK_MODULES) set(MITK_ROOT_FOLDER_BACKUP "${MITK_ROOT_FOLDER}") foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) get_filename_component(MITK_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME) set(MITK_MODULES_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Modules") if(EXISTS "${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake") set(MITK_MODULES "") include("${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake") foreach(mitk_module ${MITK_MODULES}) add_subdirectory("${MITK_MODULES_EXTENSION_DIR}/${mitk_module}" "Modules/${mitk_module}") endforeach() endif() set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX}) endforeach() set(MITK_ROOT_FOLDER "${MITK_ROOT_FOLDER_BACKUP}") add_subdirectory(Wrapping) set(MITK_DOXYGEN_OUTPUT_DIR "${PROJECT_BINARY_DIR}/Documentation/Doxygen" CACHE PATH "Output directory for doxygen generated documentation.") if(MITK_USE_BLUEBERRY) include("${CMAKE_CURRENT_SOURCE_DIR}/Plugins/PluginList.cmake") mitkFunctionWhitelistPlugins(MITK MITK_PLUGINS) set(mitk_plugins_fullpath "") foreach(mitk_plugin ${MITK_PLUGINS}) list(APPEND mitk_plugins_fullpath Plugins/${mitk_plugin}) endforeach() set(MITK_PLUGIN_REGEX_LIST "") foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_PLUGINS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Plugins") if(EXISTS "${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake") set(MITK_PLUGINS "") include("${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake") foreach(mitk_plugin ${MITK_PLUGINS}) list(APPEND mitk_plugins_fullpath "${MITK_PLUGINS_EXTENSION_DIR}/${mitk_plugin}") endforeach() endif() endforeach() if(EXISTS ${MITK_PRIVATE_MODULES}/PluginList.cmake) include(${MITK_PRIVATE_MODULES}/PluginList.cmake) foreach(mitk_plugin ${MITK_PRIVATE_PLUGINS}) list(APPEND mitk_plugins_fullpath ${MITK_PRIVATE_MODULES}/${mitk_plugin}) endforeach() endif() if(MITK_BUILD_EXAMPLES) include("${CMAKE_CURRENT_SOURCE_DIR}/Examples/Plugins/PluginList.cmake") set(mitk_example_plugins_fullpath ) foreach(mitk_example_plugin ${MITK_EXAMPLE_PLUGINS}) list(APPEND mitk_example_plugins_fullpath Examples/Plugins/${mitk_example_plugin}) list(APPEND mitk_plugins_fullpath Examples/Plugins/${mitk_example_plugin}) endforeach() endif() # Specify which plug-ins belong to this project macro(GetMyTargetLibraries all_target_libraries varname) set(re_ctkplugin_mitk "^org_mitk_[a-zA-Z0-9_]+$") set(re_ctkplugin_bb "^org_blueberry_[a-zA-Z0-9_]+$") set(_tmp_list) list(APPEND _tmp_list ${all_target_libraries}) ctkMacroListFilter(_tmp_list re_ctkplugin_mitk re_ctkplugin_bb MITK_PLUGIN_REGEX_LIST OUTPUT_VARIABLE ${varname}) endmacro() # Get infos about application directories and build options set(mitk_apps_fullpath "") foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") set(MITK_APPS "") include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") foreach(mitk_app ${MITK_APPS}) # extract option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 directory_name) list(GET target_info_list 1 option_name) if(${option_name}) list(APPEND mitk_apps_fullpath "${MITK_APPLICATIONS_EXTENSION_DIR}/${directory_name}^^${option_name}") endif() endforeach() endif() endforeach() if (mitk_plugins_fullpath) ctkMacroSetupPlugins(${mitk_plugins_fullpath} BUILD_OPTION_PREFIX MITK_BUILD_ APPS ${mitk_apps_fullpath} BUILD_ALL ${MITK_BUILD_ALL_PLUGINS} COMPACT_OPTIONS) endif() set(MITK_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkPluginUseFile.cmake") if(${PROJECT_NAME}_PLUGIN_LIBRARIES) ctkFunctionGeneratePluginUseFile(${MITK_PLUGIN_USE_FILE}) else() file(REMOVE ${MITK_PLUGIN_USE_FILE}) set(MITK_PLUGIN_USE_FILE ) endif() endif() #----------------------------------------------------------------------------- # Documentation #----------------------------------------------------------------------------- set(MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS) set(MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS) foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS}) set(MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS "${MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS} \"${MITK_EXTENSION_DIR}\"") set(MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS "${MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS} \"${MITK_EXTENSION_DIR}\"") endforeach() if(DOXYGEN_FOUND) add_subdirectory(Documentation) endif() #----------------------------------------------------------------------------- # Installation #----------------------------------------------------------------------------- # set MITK cpack variables # These are the default variables, which can be overwritten ( see below ) include(mitkSetupCPack) set(use_default_config ON) set(ALL_MITK_APPS "") set(activated_apps_no 0) foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") set(MITK_APPS "") include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") foreach(mitk_app ${MITK_APPS}) string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 directory_name) list(GET target_info_list 1 option_name) list(GET target_info_list 2 executable_name) list(APPEND ALL_MITK_APPS "${MITK_EXTENSION_DIR}/Applications/${directory_name}^^${option_name}^^${executable_name}") if(${option_name} OR MITK_BUILD_ALL_APPS) MATH(EXPR activated_apps_no "${activated_apps_no} + 1") endif() endforeach() endif() endforeach() list(LENGTH ALL_MITK_APPS app_count) if(app_count EQUAL 1 AND (activated_apps_no EQUAL 1 OR MITK_BUILD_ALL_APPS)) # Corner case if there is only one app in total set(use_project_cpack ON) elseif(activated_apps_no EQUAL 1 AND NOT MITK_BUILD_ALL_APPS) # Only one app is enabled (no "build all" flag set) set(use_project_cpack ON) else() # Less or more then one app is enabled set(use_project_cpack OFF) endif() foreach(mitk_app ${ALL_MITK_APPS}) # extract target_dir and option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 target_dir) list(GET target_info_list 1 option_name) list(GET target_info_list 2 executable_name) # check if the application is enabled if(${option_name} OR MITK_BUILD_ALL_APPS) # check whether application specific configuration files will be used if(use_project_cpack) # use files if they exist if(EXISTS "${target_dir}/CPackOptions.cmake") include("${target_dir}/CPackOptions.cmake") endif() if(EXISTS "${target_dir}/CPackConfig.cmake.in") set(CPACK_PROJECT_CONFIG_FILE "${target_dir}/CPackConfig.cmake") configure_file(${target_dir}/CPackConfig.cmake.in ${CPACK_PROJECT_CONFIG_FILE} @ONLY) set(use_default_config OFF) endif() endif() # add link to the list list(APPEND CPACK_CREATE_DESKTOP_LINKS "${executable_name}") endif() endforeach() # if no application specific configuration file was used, use default if(use_default_config) configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in ${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY) set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake") endif() # include CPack model once all variables are set include(CPack) # Additional installation rules include(mitkInstallRules) #----------------------------------------------------------------------------- # Last configuration steps #----------------------------------------------------------------------------- # ---------------- Export targets ----------------- set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake") file(REMOVE ${MITK_EXPORTS_FILE}) set(targets_to_export) get_property(module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS) if(module_targets) list(APPEND targets_to_export ${module_targets}) endif() if(MITK_USE_BLUEBERRY) if(MITK_PLUGIN_LIBRARIES) list(APPEND targets_to_export ${MITK_PLUGIN_LIBRARIES}) endif() endif() export(TARGETS ${targets_to_export} APPEND FILE ${MITK_EXPORTS_FILE}) set(MITK_EXPORTED_TARGET_PROPERTIES ) foreach(target_to_export ${targets_to_export}) get_target_property(autoload_targets ${target_to_export} MITK_AUTOLOAD_TARGETS) if(autoload_targets) set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES} set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_TARGETS \"${autoload_targets}\")") endif() get_target_property(autoload_dir ${target_to_export} MITK_AUTOLOAD_DIRECTORY) if(autoload_dir) set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES} set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_DIRECTORY \"${autoload_dir}\")") endif() get_target_property(deprecated_module ${target_to_export} MITK_MODULE_DEPRECATED_SINCE) if(deprecated_module) set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES} set_target_properties(${target_to_export} PROPERTIES MITK_MODULE_DEPRECATED_SINCE \"${deprecated_module}\")") endif() endforeach() # ---------------- External projects ----------------- get_property(MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS_CONFIG GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS) set(MITK_CONFIG_EXTERNAL_PROJECTS ) #string(REPLACE "^^" ";" _mitk_external_projects ${MITK_EXTERNAL_PROJECTS}) foreach(ep ${MITK_EXTERNAL_PROJECTS}) get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS) set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS} set(MITK_USE_${ep} ${MITK_USE_${ep}}) set(MITK_${ep}_DIR \"${${ep}_DIR}\") set(MITK_${ep}_COMPONENTS ${_components}) ") endforeach() foreach(ep ${MITK_EXTERNAL_PROJECTS}) get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE) get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS) if(_components) set(_components_arg COMPONENTS \${_components}) else() set(_components_arg) endif() if(_package) set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS} if(MITK_USE_${ep}) set(${ep}_DIR \${MITK_${ep}_DIR}) if(MITK_${ep}_COMPONENTS) mitkMacroFindDependency(${_package} COMPONENTS \${MITK_${ep}_COMPONENTS}) else() mitkMacroFindDependency(${_package}) endif() endif()") endif() endforeach() # ---------------- Tools ----------------- configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY) # ---------------- Configure files ----------------- configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc) set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY) write_basic_config_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake VERSION ${MITK_VERSION_STRING} COMPATIBILITY AnyNewerVersion) #----------------------------------------------------------------------------- # MITK Applications #----------------------------------------------------------------------------- # This must come after MITKConfig.h was generated, since applications # might do a find_package(MITK REQUIRED). add_subdirectory(Applications) if(MSVC AND TARGET MitkWorkbench) set_directory_properties(PROPERTIES VS_STARTUP_PROJECT MitkWorkbench) endif() foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/CMakeLists.txt") add_subdirectory("${MITK_APPLICATIONS_EXTENSION_DIR}" "Applications") endif() endforeach() #----------------------------------------------------------------------------- # MITK Examples #----------------------------------------------------------------------------- if(MITK_BUILD_EXAMPLES) # This must come after MITKConfig.h was generated, since applications # might do a find_package(MITK REQUIRED). add_subdirectory(Examples) endif() #----------------------------------------------------------------------------- # Print configuration summary #----------------------------------------------------------------------------- message("\n\n") feature_summary( DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------" WHAT ALL ) diff --git a/MITKConfig.cmake.in b/MITKConfig.cmake.in index 530ee7c6e3..4e7ef7c55b 100644 --- a/MITKConfig.cmake.in +++ b/MITKConfig.cmake.in @@ -1,314 +1,314 @@ if(CMAKE_VERSION VERSION_LESS @MITK_CMAKE_MINIMUM_REQUIRED_VERSION@) message(FATAL_ERROR "MITK requires at least CMake Version @MITK_CMAKE_MINIMUM_REQUIRED_VERSION@") endif() # The MITK version number set(MITK_VERSION_MAJOR "@MITK_VERSION_MAJOR@") set(MITK_VERSION_MINOR "@MITK_VERSION_MINOR@") set(MITK_VERSION_PATCH "@MITK_VERSION_PATCH@") set(MITK_VERSION_STRING "@MITK_VERSION_STRING@") #----------------------------------------------------------------------------- # C++ language standard #----------------------------------------------------------------------------- set(MITK_CXX_STANDARD @MITK_CXX_STANDARD@) #----------------------------------------------------------------------------- # Include required CMake scripts #----------------------------------------------------------------------------- # Update the CMake module path set(MITK_CMAKE_MODULE_PATH "@MITK_SOURCE_DIR@/CMake") list(APPEND CMAKE_MODULE_PATH ${MITK_CMAKE_MODULE_PATH}) # Standard CMake macros include(CMakeParseArguments) include(FeatureSummary) include(FindPackageHandleStandardArgs) include(GenerateExportHeader) # Include MITK macros include(MacroParseArguments) include(mitkFunctionAddManifest) include(mitkFunctionAddCustomModuleTest) include(mitkFunctionCheckMitkCompatibility) include(mitkFunctionCheckModuleDependencies) include(mitkFunctionConfigureVisualStudioUserProjectFile) include(mitkFunctionCreateBlueBerryApplication) include(mitkFunctionCreateCommandLineApp) include(mitkFunctionCreateModule) include(mitkFunctionCreatePlugin) include(mitkFunctionCreateProvisioningFile) include(mitkFunctionCreateWindowsBatchScript) include(mitkFunctionGetLibrarySearchPaths) include(mitkFunctionInstallAutoLoadModules) include(mitkFunctionInstallCTKPlugin) include(mitkFunctionInstallProvisioningFiles) include(mitkFunctionInstallThirdPartyCTKPlugins) include(mitkFunctionOrganizeSources) include(mitkFunctionUseModules) include(mitkMacroCreateExecutable) include(mitkMacroCreateModuleTests) include(mitkMacroFindDependency) include(mitkMacroGenerateToolsLibrary) include(mitkMacroGetPMDPlatformString) include(mitkMacroInstall) include(mitkMacroInstallHelperApp) include(mitkMacroInstallTargets) include(mitkMacroMultiplexPicType) #----------------------------------------------------------------------------- # MITK flags and directories #----------------------------------------------------------------------------- # MITK compiler flags set(MITK_C_FLAGS "@MITK_C_FLAGS@") set(MTTK_C_FLAGS_DEBUG "@MITK_C_FLAGS_DEBUG@") set(MITK_C_FLAGS_RELEASE "@MITK_C_FLAGS_RELEASE@") set(MITK_CXX_FLAGS "@MITK_CXX_FLAGS@") set(MTTK_CXX_FLAGS_DEBUG "@MITK_CXX_FLAGS_DEBUG@") set(MITK_CXX_FLAGS_RELEASE "@MITK_CXX_FLAGS_RELEASE@") # MITK linker flags set(MITK_EXE_LINKER_FLAGS "@MITK_EXE_LINKER_FLAGS@") set(MITK_SHARED_LINKER_FLAGS "@MITK_SHARED_LINKER_FLAGS@") set(MITK_MODULE_LINKER_FLAGS "@MITK_MODULE_LINKER_FLAGS@") # MITK specific directories set(MITK_SOURCE_DIR "@MITK_SOURCE_DIR@") set(MITK_BINARY_DIR "@MITK_BINARY_DIR@") set(MITK_CMAKE_DIR "@MITK_CMAKE_DIR@") # MITK output directories set(MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY "@MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY@") set(MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY "@MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY@") set(MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY "@MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY@") #----------------------------------------------------------------------------- # Miscellaneous variables #----------------------------------------------------------------------------- # Internal version numbers, used for approximate compatibility checks # of a MITK development version (non-release). set(MITK_VERSION_PLUGIN_SYSTEM 2) # dropped legacy BlueBerry plug-in CMake support set(MITK_DATA_DIR "@MITK_DATA_DIR@") set(UTILITIES_DIR "@UTILITIES_DIR@") set(REGISTER_QFUNCTIONALITY_CPP_IN "@REGISTER_QFUNCTIONALITY_CPP_IN@") set(MITK_DOXYGEN_TAGFILE_NAME "@MITK_DOXYGEN_TAGFILE_NAME@") set(MITK_LEGACY_EXPORT_MACRO_NAME 1) set(DCMTK_CMAKE_DEBUG_POSTFIX @DCMTK_CMAKE_DEBUG_POSTFIX@) # Get the canonical name of the directory to avoid potential case mismatch, # e.g. in the drive letter on Windows. get_filename_component(CMAKE_CURRENT_LIST_DIR_REALPATH ${CMAKE_CURRENT_LIST_DIR} REALPATH) if(CMAKE_CURRENT_LIST_DIR_REALPATH STREQUAL MITK_BINARY_DIR) set(MITK_EXTERNAL_PROJECT_PREFIX @MITK_EXTERNAL_PROJECT_PREFIX@) endif() set(MITK_MODULES_PACKAGE_DEPENDS_DIR "@MITK_MODULES_PACKAGE_DEPENDS_DIR@") if(MODULES_PACKAGE_DEPENDS_DIRS) list(APPEND MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR}) list(REMOVE_DUPLICATES MODULES_PACKAGE_DEPENDS_DIRS) else() set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR}) endif() #----------------------------------------------------------------------------- # External dependencies #----------------------------------------------------------------------------- list(APPEND CMAKE_PREFIX_PATH "@MITK_EXTERNAL_PROJECT_PREFIX@") # ----------------------------------------- # Qt variables and dependencies set(MITK_USE_Qt5 @MITK_USE_Qt5@) if(MITK_USE_Qt5) set(MITK_QT5_MINIMUM_VERSION @MITK_QT5_MINIMUM_VERSION@) set(MITK_QT5_COMPONENTS @MITK_QT5_COMPONENTS@) mitkMacroFindDependency(Qt5 ${MITK_QT5_MINIMUM_VERSION} COMPONENTS ${MITK_QT5_COMPONENTS}) endif() # ----------------------------------------- # Special Python variables set(MITK_USE_Python3 @MITK_USE_Python3@) if(MITK_USE_Python3) set(PYTHON_EXECUTABLE "@PYTHON_EXECUTABLE@" CACHE FILEPATH "") set(PYTHON_INCLUDE_DIR "@PYTHON_INCLUDE_DIR@" CACHE PATH "") set(PYTHON_LIBRARY "@PYTHON_LIBRARY@" CACHE FILEPATH "") set(PYTHON_INCLUDE_DIR2 "@PYTHON_INCLUDE_DIR2@" CACHE PATH "") mitkMacroFindDependency(Python3 COMPONENTS Interpreter Development NumPy) endif() # ----------------------------------------- # Special Boost variables set(MITK_USE_Boost_LIBRARIES @MITK_USE_Boost_LIBRARIES@) set(MITK_USE_SYSTEM_Boost @MITK_USE_SYSTEM_Boost@) -set(BOOST_ROOT "@BOOST_ROOT@" CACHE PATH "") +set(Boost_ROOT "@Boost_ROOT@" CACHE PATH "") set(BOOST_LIBRARYDIR "@BOOST_LIBRARYDIR@" CACHE PATH "") set(Boost_ADDITIONAL_VERSIONS 1.74 1.74.0) # We need this later for a DCMTK workaround set(_dcmtk_dir_orig "@DCMTK_DIR@") # ----------------------------------------- # External dependencies from the superbuild # or injected from somewhere else via # _DIR variables. @MITK_CONFIG_EXTERNAL_PROJECTS@ # Ensure the MITK module path comes first set(CMAKE_MODULE_PATH ${MITK_CMAKE_MODULE_PATH} ${CMAKE_MODULE_PATH}) # ----------------------------------------- # Special handling for DCMTK if(MITK_USE_DCMTK) # Due to the preferred CONFIG mode in find_package calls above, # the DCMTKConfig.cmake file is read, which does not provide useful # package information. We explictly need MODULE mode to find DCMTK. if(${_dcmtk_dir_orig} MATCHES "${MITK_EXTERNAL_PROJECT_PREFIX}.*") # Help our FindDCMTK.cmake script find our super-build DCMTK set(DCMTK_DIR ${MITK_EXTERNAL_PROJECT_PREFIX}) else() # Use the original value set(DCMTK_DIR ${_dcmtk_dir_orig}) endif() find_package(DCMTK REQUIRED MODULE) endif() # ----------------------------------------- # Special handling for DCMQI if(MITK_USE_DCMQI) # Due to the preferred CONFIG mode in find_package calls above, # the DCMQIConfig.cmake file is read, which does not provide useful # package information. We explictly need MODULE mode to find DCMQI. # Help our FindDCMQI.cmake script find our super-build DCMQI set(DCMQI_DIR ${MITK_EXTERNAL_PROJECT_PREFIX}) find_package(DCMQI REQUIRED) endif() # ----------------------------------------- # Special handling for Boost if(MITK_USE_Boost) link_directories(${Boost_LIBRARY_DIRS}) endif() # ----------------------------------------- # Special handling for OpenIGTLink if(MITK_USE_OpenIGTLink) link_directories(${OpenIGTLink_LIBRARY_DIRS}) endif() # ----------------------------------------- # Internal project dependencies set(CppMicroServices_DIR "@CppMicroServices_DIR@") mitkMacroFindDependency(CppMicroServices) set(MITK_USE_BLUEBERRY @MITK_USE_BLUEBERRY@) if(MITK_USE_BLUEBERRY) set(MITK_PLUGIN_USE_FILE "@MITK_PLUGIN_USE_FILE@") if(MITK_PLUGIN_USE_FILE) if(EXISTS "${MITK_PLUGIN_USE_FILE}") include("${MITK_PLUGIN_USE_FILE}") endif() endif() set(MITK_PLUGIN_PROVISIONING_FILE "@MITK_EXTAPP_PROVISIONING_FILE@") set(MITK_PROVISIONING_FILES "${BLUEBERRY_PLUGIN_PROVISIONING_FILE}" "${MITK_PLUGIN_PROVISIONING_FILE}") endif() set(BLUEBERRY_USE_QT_HELP @BLUEBERRY_USE_QT_HELP@) if(BLUEBERRY_USE_QT_HELP AND DOXYGEN_VERSION VERSION_LESS "1.8.7") message("Setting BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.") set(BLUEBERRY_USE_QT_HELP OFF) endif() set(BLUEBERRY_QTPLUGIN_PATH "@BLUEBERRY_QTPLUGIN_PATH@") set(QT_HELPGENERATOR_EXECUTABLE "@QT_HELPGENERATOR_EXECUTABLE@") set(QT_COLLECTIONGENERATOR_EXECUTABLE "@QT_COLLECTIONGENERATOR_EXECUTABLE@") set(QT_ASSISTANT_EXECUTABLE "@QT_ASSISTANT_EXECUTABLE@") set(QT_XMLPATTERNS_EXECUTABLE "@QT_XMLPATTERNS_EXECUTABLE@") #----------------------------------------------------------------------------- # MITK sub-project variables #----------------------------------------------------------------------------- # External SDK directories set(MITK_PMD_SDK_DIR @MITK_PMD_SDK_DIR@) # MITK ToF use variables set(MITK_TOF_PMDCAMCUBE_AVAILABLE @MITK_USE_TOF_PMDCAMCUBE@) if(MITK_TOF_PMDCAMCUBE_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK") option(MITK_USE_TOF_PMDCAMCUBE "Enable support for PMD Cam Cube" @MITK_USE_TOF_PMDCAMCUBE@) mark_as_advanced(MITK_USE_TOF_PMDCAMCUBE) endif() set(MITK_TOF_PMDCAMBOARD_AVAILABLE @MITK_USE_TOF_PMDCAMBOARD@) if(MITK_TOF_PMDCAMBOARD_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK") option(MITK_USE_TOF_PMDCAMBOARD "Enable support for PMD Cam Board" @MITK_USE_TOF_PMDCAMBOARD@) mark_as_advanced(MITK_USE_TOF_PMDCAMBOARD) endif() set(MITK_TOF_PMDO3_AVAILABLE @MITK_USE_TOF_PMDO3@) if(MITK_TOF_PMDO3_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK") option(MITK_USE_TOF_PMDO3 "Enable support for PMD =3" @MITK_USE_TOF_PMDO3@) mark_as_advanced(MITK_USE_TOF_PMDO3) endif() set(MITK_TOF_KINECT_AVAILABLE @MITK_USE_TOF_KINECT@) if(MITK_TOF_KINECT_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK") option(MITK_USE_TOF_KINECT "Enable support for Kinect" @MITK_USE_TOF_KINECT@) mark_as_advanced(MITK_USE_TOF_KINECT) endif() set(MITK_TOF_MESASR4000_AVAILABLE @MITK_USE_TOF_MESASR4000@) if(MITK_TOF_MESASR4000_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK") option(MITK_USE_TOF_MESASR4000 "Enable support for MESA SR4000" @MITK_USE_TOF_MESASR4000@) mark_as_advanced(MITK_USE_TOF_MESASR4000) endif() if(MITK_USE_IGT) #include("${MITK_DIR}/mitkIGTConfig.cmake") endif() #----------------------------------------------------------------------------- # Import MITK targets and set custom properties #----------------------------------------------------------------------------- if(NOT MITK_EXPORTS_FILE_INCLUDED) if(EXISTS "@MITK_EXPORTS_FILE@") set(MITK_EXPORTS_FILE_INCLUDED 1) include("@MITK_EXPORTS_FILE@") endif() endif() # Set properties on exported targets @MITK_EXPORTED_TARGET_PROPERTIES@ #----------------------------------------------------------------------------- # Install rules #----------------------------------------------------------------------------- # Install rules for ToF libraries loaded at runtime if(EXISTS "@MITK_BINARY_DIR@/mitkToFHardwareInstallRules.cmake") include("@MITK_BINARY_DIR@/mitkToFHardwareInstallRules.cmake") endif() diff --git a/Modules/Core/include/mitkBaseGeometry.h b/Modules/Core/include/mitkBaseGeometry.h index 833189965d..4d00557d8d 100644 --- a/Modules/Core/include/mitkBaseGeometry.h +++ b/Modules/Core/include/mitkBaseGeometry.h @@ -1,752 +1,763 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkBaseGeometry_h #define mitkBaseGeometry_h #include "mitkOperationActor.h" #include #include #include "itkScalableAffineTransform.h" #include "mitkNumericTypes.h" #include #include #include #include #include #include class vtkMatrix4x4; class vtkMatrixToLinearTransform; class vtkLinearTransform; namespace mitk { //##Documentation //## @brief Standard 3D-BoundingBox typedef //## //## Standard 3D-BoundingBox typedef to get rid of template arguments (3D, type). typedef itk::BoundingBox BoundingBox; //##Documentation //## @brief Standard typedef for time-bounds typedef itk::FixedArray TimeBounds; typedef itk::FixedArray FixedArrayType; //##Documentation //## @brief BaseGeometry Describes the geometry of a data object //## //## The class holds //## \li a bounding box which is axes-parallel in intrinsic coordinates //## (often integer indices of pixels), to be accessed by //## GetBoundingBox() //## \li a transform to convert intrinsic coordinates into a //## world-coordinate system with coordinates in millimeters //## and milliseconds (all are floating point values), to //## be accessed by GetIndexToWorldTransform() //## \li an origin and spacing to define the geometry //## //## BaseGeometry and its sub-classes allow converting between //## intrinsic coordinates (called index or unit coordinates) //## and world-coordinates (called world or mm coordinates), //## e.g. WorldToIndex. //## In case you need integer index coordinates, provide an //## mitk::Index3D (or itk::Index) as target variable to //## WorldToIndex, otherwise you will get a continuous index //## (floating point values). //## //## An important sub-class is SlicedGeometry3D, which describes //## data objects consisting of slices, e.g., objects of type Image. //## Conversions between world coordinates (in mm) and unit coordinates //## (e.g., pixels in the case of an Image) can be performed. //## //## For more information on related classes, see \ref Geometry. //## //## BaseGeometry instances referring to an Image need a slightly //## different definition of corners, see SetImageGeometry. This //## is usually automatically called by Image. //## //## BaseGeometry have to be initialized in the method GenerateOutputInformation() //## of BaseProcess (or CopyInformation/ UpdateOutputInformation of BaseData, //## if possible, e.g., by analyzing pic tags in Image) subclasses. See also //## itk::ProcessObject::GenerateOutputInformation(), //## itk::DataObject::CopyInformation() and //## itk::DataObject::UpdateOutputInformation(). //## //## At least, it can return the bounding box of the data object. //## //## The BaseGeometry class is an abstract class. The most simple implementation //## is the subclass Geometry3D. //## //## Rule: everything is in mm (ms) if not stated otherwise. //## @ingroup Geometry class MITKCORE_EXPORT BaseGeometry : public itk::Object, public OperationActor { public: mitkClassMacroItkParent(BaseGeometry, itk::Object); itkCloneMacro(Self); // ********************************** TypeDef ********************************** typedef GeometryTransformHolder::TransformType TransformType; typedef itk::BoundingBox BoundingBoxType; typedef BoundingBoxType::BoundsArrayType BoundsArrayType; typedef BoundingBoxType::Pointer BoundingBoxPointer; // ********************************** Origin, Spacing ********************************** //##Documentation //## @brief Get the origin, e.g. the upper-left corner of the plane const Point3D GetOrigin() const; //##Documentation //## @brief Set the origin, i.e. the upper-left corner of the plane //## void SetOrigin(const Point3D &origin); //##Documentation //## @brief Get the spacing (size of a pixel). //## const mitk::Vector3D GetSpacing() const; //##Documentation //## @brief Set the spacing (m_Spacing). //## //##The spacing is also changed in the IndexToWorldTransform. void SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing = false); //##Documentation //## @brief Get the origin as VnlVector //## //## \sa GetOrigin VnlVector GetOriginVnl() const; // ********************************** other functions ********************************** //##Documentation //## @brief Get the DICOM FrameOfReferenceID referring to the //## used world coordinate system itkGetConstMacro(FrameOfReferenceID, unsigned int); //##Documentation //## @brief Set the DICOM FrameOfReferenceID referring to the //## used world coordinate system itkSetMacro(FrameOfReferenceID, unsigned int); itkGetConstMacro(IndexToWorldTransformLastModified, unsigned long); //##Documentation //## @brief Overload of function Modified() to prohibit several calls of Modified() using the ModifiedLock class. //## //## For the use of Modified(), see class ModifiedLock. void Modified() const override; friend class ModifiedLock; //##Documentation //## @brief Is this BaseGeometry in a state that is valid? //## //## This function returns always true in the BaseGeometry class. Other implementations are possible in subclasses. virtual bool IsValid() const; // ********************************** Initialize ********************************** //##Documentation //## @brief Initialize the BaseGeometry void Initialize(); void InitializeGeometry(Self *newGeometry) const; // ********************************** Transformations Set/Get ********************************** //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates mitk::AffineTransform3D *GetIndexToWorldTransform(); //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates const mitk::AffineTransform3D *GetIndexToWorldTransform() const; //## @brief Set the transformation used to convert from index //## to world coordinates. The spacing of the new transform is //## copied to m_spacing. void SetIndexToWorldTransform(mitk::AffineTransform3D *transform); //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4.The spacing of //## the new transform is copied to m_spacing. //## \sa SetIndexToWorldTransform void SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4 *vtkmatrix); //## @brief Set the transformation used to convert from index //## to world coordinates.This function keeps the original spacing. void SetIndexToWorldTransformWithoutChangingSpacing(mitk::AffineTransform3D *transform); //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4. This function keeps the original spacing. //## \sa SetIndexToWorldTransform void SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkMatrix4x4 *vtkmatrix); //## Get the Vtk Matrix which describes the transform. vtkMatrix4x4 *GetVtkMatrix(); //##Documentation //## @brief Get the m_IndexToWorldTransform as a vtkLinearTransform vtkLinearTransform *GetVtkTransform() const; //##Documentation //## @brief Set the transform to identity, the spacing to 1 and origin to 0 //## void SetIdentity(); // ********************************** Transformations ********************************** //##Documentation //## @brief Compose new IndexToWorldTransform with a given transform. //## //## This method composes m_IndexToWorldTransform with another transform, //## modifying self to be the composition of self and other. //## If the argument pre is true, then other is precomposed with self; //## that is, the resulting transformation consists of first applying //## other to the source, followed by self. If pre is false or omitted, //## then other is post-composed with self; that is the resulting //## transformation consists of first applying self to the source, //## followed by other. //## This method also changes m_spacing. void Compose(const TransformType *other, bool pre = false); //##Documentation //## @brief Compose new IndexToWorldTransform with a given vtkMatrix4x4. //## //## Converts the vtkMatrix4x4 into a itk-transform and calls the previous method. void Compose(const vtkMatrix4x4 *vtkmatrix, bool pre = false); //##Documentation //## @brief Translate the origin by a vector //## void Translate(const Vector3D &vector); //##Documentation //##@brief executes affine operations (translate, rotate, scale) void ExecuteOperation(Operation *operation) override; //##Documentation //## @brief Convert world coordinates (in mm) of a \em point to (continuous!) index coordinates //## \warning If you need (discrete) integer index coordinates (e.g., for iterating easily over an image), //## use WorldToIndex(const mitk::Point3D& pt_mm, itk::Index &index). //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em point to (discrete!) index coordinates. //## This method rounds to integer indices! //## For further information about coordinates types, please see the Geometry documentation template void WorldToIndex(const mitk::Point3D &pt_mm, itk::Index &index) const { typedef itk::Index IndexType; mitk::Point3D pt_units; this->WorldToIndex(pt_mm, pt_units); int i, dim = index.GetIndexDimension(); if (dim > 3) { index.Fill(0); dim = 3; } for (i = 0; i < dim; ++i) { index[i] = itk::Math::RoundHalfIntegerUp(pt_units[i]); } } //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em point to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const; //##Documentation //## @brief Convert (discrete) index coordinates of a \em point to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation template void IndexToWorld(const itk::Index &index, mitk::Point3D &pt_mm) const { mitk::Point3D pt_units; pt_units.Fill(0); int i, dim = index.GetIndexDimension(); if (dim > 3) { dim = 3; } for (i = 0; i < dim; ++i) { pt_units[i] = index[i]; } IndexToWorld(pt_units, pt_mm); } //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point3D) is not used. If possible, please use void IndexToWorld(const // mitk::Vector3D& vec_units, mitk::Vector3D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Point3D &atPt3d_units, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point3D) is not used. If possible, please use void WorldToIndex(const // mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const; //##Documentation //## @brief Deprecated for use with ITK version 3.10 or newer. //## Convert ITK physical coordinates of a \em point (in mm, //## but without a rotation) into MITK world coordinates (in mm) //## //## For more information, see WorldToItkPhysicalPoint. template void ItkPhysicalPointToWorld(const itk::Point &itkPhysicalPoint, mitk::Point3D &pt_mm) const { mitk::vtk2itk(itkPhysicalPoint, pt_mm); } //##Documentation //## @brief Deprecated for use with ITK version 3.10 or newer. //## Convert world coordinates (in mm) of a \em point to //## ITK physical coordinates (in mm, but without a possible rotation) //## //## This method is useful if you have want to access an mitk::Image //## via an itk::Image. ITK v3.8 and older did not support rotated (tilted) //## images, i.e., ITK images are always parallel to the coordinate axes. //## When accessing a (possibly rotated) mitk::Image via an itk::Image //## the rotational part of the transformation in the BaseGeometry is //## simply discarded; in other word: only the origin and spacing is //## used by ITK, not the complete matrix available in MITK. //## With WorldToItkPhysicalPoint you can convert an MITK world //## coordinate (including the rotation) into a coordinate that //## can be used with the ITK image as a ITK physical coordinate //## (excluding the rotation). template void WorldToItkPhysicalPoint(const mitk::Point3D &pt_mm, itk::Point &itkPhysicalPoint) const { mitk::vtk2itk(pt_mm, itkPhysicalPoint); } // ********************************** BoundingBox ********************************** /** Get the bounding box */ itkGetConstObjectMacro(BoundingBox, BoundingBoxType); // a bit of a misuse, but we want only doxygen to see the following: #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get bounding box (in index/unit coordinates) itkGetConstObjectMacro(BoundingBox, BoundingBoxType); //##Documentation //## @brief Get bounding box (in index/unit coordinates) as a BoundsArrayType const BoundsArrayType GetBounds() const; #endif const BoundsArrayType GetBounds() const; //##Documentation //## \brief Set the bounding box (in index/unit coordinates) //## //## Only possible via the BoundsArray to make clear that a //## copy of the bounding-box is stored, not a reference to it. void SetBounds(const BoundsArrayType &bounds); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a float array void SetFloatBounds(const float bounds[6]); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a double array void SetFloatBounds(const double bounds[6]); //##Documentation //## @brief Get a VnlVector along bounding-box in the specified //## @a direction, length is spacing //## //## \sa GetAxisVector VnlVector GetMatrixColumn(unsigned int direction) const; //##Documentation //## @brief Calculates a bounding-box around the geometry relative //## to a coordinate system defined by a transform //## mitk::BoundingBox::Pointer CalculateBoundingBoxRelativeToTransform(const mitk::AffineTransform3D *transform) const; //##Documentation //## @brief Set the time bounds (in ms) // void SetTimeBounds(const TimeBounds& timebounds); // ********************************** Geometry ********************************** #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get the extent of the bounding box (in index/unit coordinates) //## //## To access the extent in mm use GetExtentInMM ScalarType GetExtent(unsigned int direction) const; #endif /** Get the extent of the bounding box */ ScalarType GetExtent(unsigned int direction) const; //##Documentation //## @brief Get the extent of the bounding-box in the specified @a direction in mm //## //## Equals length of GetAxisVector(direction). ScalarType GetExtentInMM(int direction) const; //##Documentation //## @brief Get vector along bounding-box in the specified @a direction in mm //## //## The length of the vector is the size of the bounding-box in the //## specified @a direction in mm //## \sa GetMatrixColumn Vector3D GetAxisVector(unsigned int direction) const; //##Documentation //## @brief Checks, if the given geometry can be converted to 2D without information loss //## e.g. when a 2D image is saved, the matrix is usually cropped to 2x2, and when you load it back to MITK //## it will be filled with standard values. This function checks, if information would be lost during this //## procedure virtual bool Is2DConvertable(); //##Documentation //## @brief Get the center of the bounding-box in mm //## Point3D GetCenter() const; //##Documentation //## @brief Get the squared length of the diagonal of the bounding-box in mm //## double GetDiagonalLength2() const; //##Documentation //## @brief Get the length of the diagonal of the bounding-box in mm //## double GetDiagonalLength() const; //##Documentation //## @brief Get the position of the corner number \a id (in world coordinates) //## //## See SetImageGeometry for how a corner is defined on images. Point3D GetCornerPoint(int id) const; //##Documentation //## @brief Get the position of a corner (in world coordinates) //## //## See SetImageGeometry for how a corner is defined on images. Point3D GetCornerPoint(bool xFront = true, bool yFront = true, bool zFront = true) const; //##Documentation //## @brief Set the extent of the bounding-box in the specified @a direction in mm //## //## @note This changes the matrix in the transform, @a not the bounds, which are given in units! void SetExtentInMM(int direction, ScalarType extentInMM); //##Documentation //## @brief Test whether the point \a p (world coordinates in mm) is //## inside the bounding box bool IsInside(const mitk::Point3D &p) const; //##Documentation //## @brief Test whether the point \a p ((continuous!)index coordinates in units) is //## inside the bounding box bool IsIndexInside(const mitk::Point3D &index) const; //##Documentation //## @brief Convenience method for working with ITK indices template bool IsIndexInside(const itk::Index &index) const { int i, dim = index.GetIndexDimension(); Point3D pt_index; pt_index.Fill(0); for (i = 0; i < dim; ++i) { pt_index[i] = index[i]; } return IsIndexInside(pt_index); } // ********************************* Image Geometry ******************************** //##Documentation //## @brief When switching from an Image Geometry to a normal Geometry (and the other way around), you have to //change // the origin as well (See Geometry Documentation)! This function will change the "isImageGeometry" bool flag and // changes the origin respectively. virtual void ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry); //##Documentation //## @brief Is this an ImageGeometry? //## //## For more information, see SetImageGeometry itkGetConstMacro(ImageGeometry, bool) //##Documentation //## @brief Define that this BaseGeometry is referring to an Image //## //## A geometry referring to an Image needs a slightly different //## definition of the position of the corners (see GetCornerPoint). //## The position of a voxel is defined by the position of its center. //## If we would use the origin (position of the (center of) the first //## voxel) as a corner and display this point, it would seem to be //## \em not at the corner but a bit within the image. Even worse for //## the opposite corner of the image: here the corner would appear //## outside the image (by half of the voxel diameter). Thus, we have //## to correct for this and to be able to do that, we need to know //## that the BaseGeometry is referring to an Image. itkSetMacro(ImageGeometry, bool); itkBooleanMacro(ImageGeometry); const GeometryTransformHolder *GetGeometryTransformHolder() const; + //##Documentation + //## @brief One to one mapping of axes to world orientations. + //## + //## The result is stored in the output argument that must be an array of three int values. + //## The elements of the array will be the axis indices that correspond to the sagittal, + //## coronal and axial orientations, in this order. It is guaranteed that each axis will + //## be mapped to different orientations. + //## + //## @param axes Output argument that will store the axis indices for each orientation. + void MapAxesToOrientations(int axes[]) const; + protected: // ********************************** Constructor ********************************** BaseGeometry(); BaseGeometry(const BaseGeometry &other); ~BaseGeometry() override; itk::LightObject::Pointer InternalClone() const override = 0; void PrintSelf(std::ostream &os, itk::Indent indent) const override; static const std::string GetTransformAsString(TransformType *transformType); itkGetConstMacro(NDimensions, unsigned int); bool IsBoundingBoxNull() const; bool IsIndexToWorldTransformNull() const; void SetVtkMatrixDeepCopy(vtkTransform *vtktransform); void _SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing = false); //##Documentation //## @brief PreSetSpacing //## //## These virtual function allows a different beahiour in subclasses. //## Do implement them in every subclass of BaseGeometry. If not needed, use //## {Superclass::PreSetSpacing();}; virtual void PreSetSpacing(const mitk::Vector3D & /*aSpacing*/){}; //##Documentation //## @brief CheckBounds //## //## This function is called in SetBounds. Assertions can be implemented in this function (see PlaneGeometry.cpp). //## If you implement this function in a subclass, make sure, that all classes were your class inherits from //## have an implementation of CheckBounds //## (e.g. inheritance BaseGeometry <- A <- B. Implementation of CheckBounds in class B needs implementation in A as // well!) virtual void CheckBounds(const BoundsArrayType & /*bounds*/){}; //##Documentation //## @brief CheckIndexToWorldTransform //## //## This function is called in SetIndexToWorldTransform. Assertions can be implemented in this function (see // PlaneGeometry.cpp). //## In Subclasses of BaseGeometry, implement own conditions or call Superclass::CheckBounds(bounds);. virtual void CheckIndexToWorldTransform(mitk::AffineTransform3D * /*transform*/){}; private: GeometryTransformHolder *m_GeometryTransform; void InitializeGeometryTransformHolder(const BaseGeometry *otherGeometry); //##Documentation //## @brief Bounding Box, which is axes-parallel in intrinsic coordinates //## (often integer indices of pixels) BoundingBoxPointer m_BoundingBox; unsigned int m_FrameOfReferenceID; // mitk::TimeBounds m_TimeBounds; static const unsigned int m_NDimensions = 3; mutable TransformType::Pointer m_InvertedTransform; mutable unsigned long m_IndexToWorldTransformLastModified; bool m_ImageGeometry; //##Documentation //## @brief ModifiedLockFlag is used to prohibit the call of Modified() //## //## For the use of this Flag, see class ModifiedLock. This flag should only be set //## by the ModifiedLock class! bool m_ModifiedLockFlag; //##Documentation //## @brief ModifiedcalledFlag is used to collect calls of Modified(). //## //## For the use of this Flag, see class ModifiedLock. This flag should only be set //## by the Modified() function! mutable bool m_ModifiedCalledFlag; }; // ********************************** Equal Functions ********************************** // // Static compare functions mainly for testing // /** * @brief Equal A function comparing two geometries for being identical. * * @ingroup MITKTestingAPI * * The function compares the spacing, origin, axisvectors, extents, the matrix of the * IndexToWorldTransform (elementwise), the bounding (elementwise) and the ImageGeometry flag. * * The parameter eps is a tolarence value for all methods which are internally used for comparison. * If you want to use different tolerance values for different parts of the geometry, feel free to use * the other comparison methods and write your own implementation of Equal. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param coordinateEps Tolerance for comparison of all spatial aspects (spacing, origin and grid alignment). * You can use mitk::eps in most cases. * @param directionEps Tolerance for comparison of all directional aspects (axis). You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry& leftHandSide, const mitk::BaseGeometry& rightHandSide, ScalarType coordinateEps, ScalarType directionEps, bool verbose = false); /** * @brief Equal A function comparing two geometries for being identical. * * @ingroup MITKTestingAPI * * This is an overloaded version that uses a single tolerance for spatial and directional aspects. For more details, * see the other overloaded version. * * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry &leftHandSide, const mitk::BaseGeometry &rightHandSide, ScalarType eps = mitk::eps, bool verbose = false); /** * @brief Equal A function comparing two transforms (TransformType) for being identical. * * @ingroup MITKTestingAPI * * The function compares the IndexToWorldTransform (elementwise). * * The parameter eps is a tolarence value for all methods which are internally used for comparison. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::TransformType &leftHandSide, const mitk::BaseGeometry::TransformType &rightHandSide, ScalarType eps, bool verbose); /** * @brief Equal A function comparing two bounding boxes (BoundingBoxType) for being identical. * * @ingroup MITKTestingAPI * * The function compares the bounds (elementwise). * * The parameter eps is a tolarence value for all methods which are internally used for comparison. * @param rightHandSide Compare this against leftHandSide. * @param leftHandSide Compare this against rightHandSide. * @param eps Tolarence for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False in any other case. */ MITKCORE_EXPORT bool Equal(const mitk::BaseGeometry::BoundingBoxType &leftHandSide, const mitk::BaseGeometry::BoundingBoxType &rightHandSide, ScalarType eps, bool verbose); /** * @brief A function checks if a test geometry is a sub geometry of * a given reference geometry. * * Sub geometry means that both geometries have the same voxel grid (same spacing, same axes, * origin is on voxel grid), but the bounding box of the checked geometry is contained or equal * to the bounding box of the reference geometry.\n * By this definition equal geometries are always sub geometries of each other. * * The function checks the spacing, origin, axis vectors, extents, the matrix of the * IndexToWorldTransform (elementwise), the bounding (elementwise) and the ImageGeometry flag. * * The parameter eps is a tolerance value for all methods which are internally used for comparison. * @param testGeo Geometry that should be checked if it is a sub geometry of referenceGeo. * @param referenceGeo Geometry that should contain testedGeometry as sub geometry. * @param coordinateEps Tolerance for comparison of all spatial aspects (spacing, origin and grid alignment). * You can use mitk::eps in most cases. * @param directionEps Tolerance for comparison of all directional aspects (axis). You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparisons are true. False otherwise. */ MITKCORE_EXPORT bool IsSubGeometry(const mitk::BaseGeometry& testGeo, const mitk::BaseGeometry& referenceGeo, ScalarType coordinateEps, ScalarType directionEps, bool verbose = false); /** * @brief A function checks if a test geometry is a sub geometry of * a given reference geometry. * * This is a overloaded version that uses a single tolerance for spatial and directional aspects. For more details, * see the other overloaded version. * * @param testGeo Geometry that should be checked if it is a sub geometry of referenceGeo. * @param referenceGeo Geometry that should contain testedGeometry as sub geometry. * @param eps Tolarence for comparison (both spatial and directional). You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return True, if all comparison are true. False otherwise. */ MITKCORE_EXPORT bool IsSubGeometry(const mitk::BaseGeometry& testGeo, const mitk::BaseGeometry& referenceGeo, ScalarType eps = mitk::eps, bool verbose = false); } // namespace mitk #endif diff --git a/Modules/Core/include/mitkPlaneGeometry.h b/Modules/Core/include/mitkPlaneGeometry.h index 0fec6a0794..81a0c3c0e1 100644 --- a/Modules/Core/include/mitkPlaneGeometry.h +++ b/Modules/Core/include/mitkPlaneGeometry.h @@ -1,608 +1,606 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkPlaneGeometry_h #define mitkPlaneGeometry_h #include #include #include #include #include namespace mitk { template class Line; typedef Line Line3D; /** * \brief Describes the geometry of a plane object * * Describes a two-dimensional manifold, i.e., to put it simply, * an object that can be described using a 2D coordinate-system. * * PlaneGeometry can map points between 3D world coordinates * (in mm) and the described 2D coordinate-system (in mm) by first projecting * the 3D point onto the 2D manifold and then calculating the 2D-coordinates * (in mm). These 2D-mm-coordinates can be further converted into * 2D-unit-coordinates (e.g., pixels), giving a parameter representation of * the object with parameter values inside a rectangle * (e.g., [0,0]..[width, height]), which is the bounding box (bounding range * in z-direction always [0]..[1]). * * A PlaneGeometry describes the 2D representation within a 3D object (derived from BaseGeometry). For example, * a single CT-image (slice) is 2D in the sense that you can access the * pixels using 2D-coordinates, but is also 3D, as the pixels are really * voxels, thus have an extension (thickness) in the 3rd dimension. * * * Optionally, a reference BaseGeometry can be specified, which usually would * be the geometry associated with the underlying dataset. This is currently * used for calculating the intersection of inclined / rotated planes * (represented as PlaneGeometry) with the bounding box of the associated * BaseGeometry. * * \warning The PlaneGeometry are not necessarily up-to-date and not even * initialized. As described in the previous paragraph, one of the * Generate-/Copy-/UpdateOutputInformation methods have to initialize it. * mitk::BaseData::GetPlaneGeometry() makes sure, that the PlaneGeometry is * up-to-date before returning it (by setting the update extent appropriately * and calling UpdateOutputInformation). * * Rule: everything is in mm (or ms for temporal information) if not * stated otherwise. * \ingroup Geometry */ class PlaneGeometry; /** \deprecatedSince{2014_10} This class is deprecated. Please use PlaneGeometry instead. */ DEPRECATED(typedef PlaneGeometry Geometry2D); /** * \brief Describes a two-dimensional, rectangular plane * * \ingroup Geometry */ class MITKCORE_EXPORT PlaneGeometry : public BaseGeometry { public: mitkClassMacro(PlaneGeometry, BaseGeometry); /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); virtual void IndexToWorld(const Point2D &pt_units, Point2D &pt_mm) const; virtual void WorldToIndex(const Point2D &pt_mm, Point2D &pt_units) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point2D) is not used. If possible, please use void IndexToWorld(const // mitk::Vector2D& vec_units, mitk::Vector2D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Point2D &atPt2d_untis, const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point2D) is not used. If possible, please use void WorldToIndex(const // mitk::Vector2D& vec_mm, mitk::Vector2D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Point2D &atPt2d_mm, const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; /** * \brief Initialize a plane with orientation \a AnatomicalPlane * (default: axial) with respect to \a BaseGeometry (default: identity). * Spacing also taken from \a BaseGeometry. * * \warning A former version of this method created a geometry with unit * spacing. For unit spacing use * * \code * // for in-plane unit spacing: * thisgeometry->SetSizeInUnits(thisgeometry->GetExtentInMM(0), * thisgeometry->GetExtentInMM(1)); * // additionally, for unit spacing in normal direction (former version * // did not do this): * thisgeometry->SetExtentInMM(2, 1.0); * \endcode */ virtual void InitializeStandardPlane(const BaseGeometry *geometry3D, AnatomicalPlane planeorientation = AnatomicalPlane::Axial, ScalarType zPosition = 0, bool frontside = true, bool rotated = false, bool top = true); /** * \brief Initialize a plane with orientation \a AnatomicalPlane * (default: axial) with respect to \a BaseGeometry (default: identity). * Spacing also taken from \a BaseGeometry. * * \param geometry3D * \param top if \a true, create plane at top, otherwise at bottom * (for AnatomicalPlane Axial, for other plane locations respectively) * \param planeorientation * \param frontside * \param rotated */ virtual void InitializeStandardPlane(const BaseGeometry *geometry3D, bool top, AnatomicalPlane planeorientation = AnatomicalPlane::Axial, bool frontside = true, bool rotated = false); /** * \brief Initialize a plane with orientation \a AnatomicalPlane * (default: axial) with respect to \a transform (default: identity) * given width and height in units. * * \a Rotated means rotated by 180 degrees (1/2 rotation) within the plane. * Rotation by 90 degrees (1/4 rotation) is not implemented as of now. * * \a Frontside/Backside: * Viewed from below = frontside in the axial case; * (radiologist's view versus neuro-surgeon's view, see: * http://www.itk.org/Wiki/images/e/ed/DICOM-OrientationDiagram-Radiologist-vs-NeuroSurgeon.png ) * Viewed from front = frontside in the coronal case; * Viewed from left = frontside in the sagittal case. * * \a Cave/Caution: Currently only RPI, LAI, LPS and RAS in the three standard planes are covered, * i.e. 12 cases of 144: 3 standard planes * 48 coordinate orientations = 144 cases. */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const AffineTransform3D *transform = nullptr, AnatomicalPlane planeorientation = AnatomicalPlane::Axial, ScalarType zPosition = 0, bool frontside = true, bool rotated = false, bool top = true); /** * \brief Initialize plane with orientation \a AnatomicalPlane * (default: axial) given width, height and spacing. * */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const Vector3D &spacing, AnatomicalPlane planeorientation = AnatomicalPlane::Axial, ScalarType zPosition = 0, bool frontside = true, bool rotated = false, bool top = true); /** * \brief Initialize plane by width and height in pixels, right-/down-vector * (itk) to describe orientation in world-space (vectors will be normalized) * and spacing (default: 1.0 mm in all directions). * * The vectors are normalized and multiplied by the respective spacing before * they are set in the matrix. * * This overloaded version of InitializeStandardPlane() creates only righthanded * coordinate orientations, unless spacing contains 1 or 3 negative entries. * */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by width and height in pixels, * right-/down-vector (vnl) to describe orientation in world-space (vectors * will be normalized) and spacing (default: 1.0 mm in all directions). * * The vectors are normalized and multiplied by the respective spacing * before they are set in the matrix. * * This overloaded version of InitializeStandardPlane() creates only righthanded * coordinate orientations, unless spacing contains 1 or 3 negative entries. * */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by right-/down-vector (itk) and spacing * (default: 1.0 mm in all directions). * * The length of the right-/-down-vector is used as width/height in units, * respectively. Then, the vectors are normalized and multiplied by the * respective spacing before they are set in the matrix. */ virtual void InitializeStandardPlane(const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by right-/down-vector (vnl) and spacing * (default: 1.0 mm in all directions). * * The length of the right-/-down-vector is used as width/height in units, * respectively. Then, the vectors are normalized and multiplied by the * respective spacing before they are set in the matrix. */ virtual void InitializeStandardPlane(const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by origin and normal (size is 1.0 mm in * all directions, direction of right-/down-vector valid but * undefined). * \warning This function can only produce righthanded coordinate orientation, not lefthanded. */ virtual void InitializePlane(const Point3D &origin, const Vector3D &normal); /** * \brief Initialize plane by right-/down-vector. * * \warning The vectors are set into the matrix as they are, * \em without normalization! * This function creates a righthanded IndexToWorldTransform, * only a negative thickness could still make it lefthanded. */ void SetMatrixByVectors(const VnlVector &rightVector, const VnlVector &downVector, ScalarType thickness = 1.0); /** * \brief Check if matrix is a rotation matrix: * - determinant is 1? * - R*R^T is ID? * Output warning otherwise. */ static bool CheckRotationMatrix(AffineTransform3D *transform, double epsilon=1e-6); /** * \brief Normal of the plane * */ Vector3D GetNormal() const; /** * \brief Normal of the plane as VnlVector * */ VnlVector GetNormalVnl() const; virtual ScalarType SignedDistance(const Point3D &pt3d_mm) const; /** * \brief Calculates, whether a point is below or above the plane. There are two different *calculation methods, with or without consideration of the bounding box. */ virtual bool IsAbove(const Point3D &pt3d_mm, bool considerBoundingBox = false) const; /** * \brief Distance of the point from the plane * (bounding-box \em not considered) * */ ScalarType DistanceFromPlane(const Point3D &pt3d_mm) const; /** * \brief Signed distance of the point from the plane * (bounding-box \em not considered) * * > 0 : point is in the direction of the direction vector. */ inline ScalarType SignedDistanceFromPlane(const Point3D &pt3d_mm) const { ScalarType len = GetNormalVnl().two_norm(); if (len == 0) return 0; return (pt3d_mm - GetOrigin()) * GetNormal() / len; } /** * \brief Distance of the plane from another plane * (bounding-box \em not considered) * * Result is 0 if planes are not parallel. */ ScalarType DistanceFromPlane(const PlaneGeometry *plane) const { return fabs(SignedDistanceFromPlane(plane)); } /** * \brief Signed distance of the plane from another plane * (bounding-box \em not considered) * * Result is 0 if planes are not parallel. */ inline ScalarType SignedDistanceFromPlane(const PlaneGeometry *plane) const { if (IsParallel(plane)) { return SignedDistance(plane->GetOrigin()); } return 0; } /** * \brief Calculate the intersecting line of two planes * * \return \a true planes are intersecting * \return \a false planes do not intersect */ bool IntersectionLine(const PlaneGeometry *plane, Line3D &crossline) const; /** * \brief Calculate two points where another plane intersects the border of this plane * * \return number of intersection points (0..2). First interection point (if existing) * is returned in \a lineFrom, second in \a lineTo. */ unsigned int IntersectWithPlane2D(const PlaneGeometry *plane, Point2D &lineFrom, Point2D &lineTo) const; /** * \brief Calculate the angle between two planes * * \return angle in radiants */ double Angle(const PlaneGeometry *plane) const; /** * \brief Calculate the angle between the plane and a line * * \return angle in radiants */ double Angle(const Line3D &line) const; /** * \brief Calculate intersection point between the plane and a line * * \param line * \param intersectionPoint intersection point * \return \a true if \em unique intersection exists, i.e., if line * is \em not on or parallel to the plane */ bool IntersectionPoint(const Line3D &line, Point3D &intersectionPoint) const; /** * \brief Calculate line parameter of intersection point between the * plane and a line * * \param line * \param t parameter of line: intersection point is * line.GetPoint()+t*line.GetDirection() * \return \a true if \em unique intersection exists, i.e., if line * is \em not on or parallel to the plane */ bool IntersectionPointParam(const Line3D &line, double &t) const; /** * \brief Returns whether the plane is parallel to another plane * * @return true iff the normal vectors both point to the same or exactly oposit direction */ bool IsParallel(const PlaneGeometry *plane) const; /** * \brief Returns whether the point is on the plane * (bounding-box \em not considered) */ bool IsOnPlane(const Point3D &point) const; /** * \brief Returns whether the line is on the plane * (bounding-box \em not considered) */ bool IsOnPlane(const Line3D &line) const; /** * \brief Returns whether the plane is on the plane * (bounding-box \em not considered) * * @return true if the normal vector of the planes point to the same or the exactly oposit direction and * the distance of the planes is < eps * */ bool IsOnPlane(const PlaneGeometry *plane) const; /** * \brief Returns the lot from the point to the plane */ Point3D ProjectPointOntoPlane(const Point3D &pt) const; itk::LightObject::Pointer InternalClone() const override; /** Implements operation to re-orient the plane */ void ExecuteOperation(Operation *operation) override; /** * \brief Project a 3D point given in mm (\a pt3d_mm) onto the 2D * geometry. The result is a 2D point in mm (\a pt2d_mm). * * The result is a 2D point in mm (\a pt2d_mm) relative to the upper-left * corner of the geometry. To convert this point into units (e.g., pixels * in case of an image), use WorldToIndex. * \return true projection was possible * \sa Project(const mitk::Point3D &pt3d_mm, mitk::Point3D * &projectedPt3d_mm) */ virtual bool Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const; /** * \brief Converts a 2D point given in mm (\a pt2d_mm) relative to the * upper-left corner of the geometry into the corresponding * world-coordinate (a 3D point in mm, \a pt3d_mm). * * To convert a 2D point given in units (e.g., pixels in case of an * image) into a 2D point given in mm (as required by this method), use * IndexToWorld. */ virtual void Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const; /** * \brief Set the width and height of this 2D-geometry in units by calling * SetBounds. This does \a not change the extent in mm! * * For an image, this is the number of pixels in x-/y-direction. * \note In contrast to calling SetBounds directly, this does \a not change * the extent in mm! */ virtual void SetSizeInUnits(mitk::ScalarType width, mitk::ScalarType height); /** * \brief Project a 3D point given in mm (\a pt3d_mm) onto the 2D * geometry. The result is a 3D point in mm (\a projectedPt3d_mm). * * \return true projection was possible */ virtual bool Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 2D vector in mm (\a vec2d_mm). * * The result is a 2D vector in mm (\a vec2d_mm) relative to the * upper-left * corner of the geometry. To convert this point into units (e.g., pixels * in case of an image), use WorldToIndex. * \return true projection was possible * \sa Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D * &projectedVec3d_mm) */ virtual bool Map(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const; /** * \brief Converts a 2D vector given in mm (\a vec2d_mm) relative to the * upper-left corner of the geometry into the corresponding * world-coordinate (a 3D vector in mm, \a vec3d_mm). * * To convert a 2D vector given in units (e.g., pixels in case of an * image) into a 2D vector given in mm (as required by this method), use * IndexToWorld. */ virtual void Map(const mitk::Point2D &atPt2d_mm, const mitk::Vector2D &vec2d_mm, mitk::Vector3D &vec3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 3D vector in mm (\a projectedVec3d_mm). * * DEPRECATED. Use Project(vector,vector) instead * * \return true projection was possible */ virtual bool Project(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 3D vector in mm (\a projectedVec3d_mm). * * \return true projection was possible */ virtual bool Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief Distance of the point from the geometry * (bounding-box \em not considered) * */ inline ScalarType Distance(const Point3D &pt3d_mm) const { return fabs(SignedDistance(pt3d_mm)); } /** * \brief Set the geometrical frame of reference in which this PlaneGeometry * is placed. * * This would usually be the BaseGeometry of the underlying dataset, but * setting it is optional. */ void SetReferenceGeometry(const mitk::BaseGeometry *geometry); /** * \brief Get the geometrical frame of reference for this PlaneGeometry. */ const BaseGeometry *GetReferenceGeometry() const; bool HasReferenceGeometry() const; - static std::vector< int > CalculateDominantAxes(mitk::AffineTransform3D::MatrixType::InternalMatrixType& rotation_matrix); - protected: PlaneGeometry(); PlaneGeometry(const PlaneGeometry &other); ~PlaneGeometry() override; void PrintSelf(std::ostream &os, itk::Indent indent) const override; const mitk::BaseGeometry *m_ReferenceGeometry; //##Documentation //## @brief PreSetSpacing //## //## These virtual function allows a different beahiour in subclasses. //## Do implement them in every subclass of BaseGeometry. If not needed, use //## {Superclass::PreSetSpacing();}; void PreSetSpacing(const mitk::Vector3D &aSpacing) override { Superclass::PreSetSpacing(aSpacing); }; //##Documentation //## @brief CheckBounds //## //## This function is called in SetBounds. Assertions can be implemented in this function (see PlaneGeometry.cpp). //## If you implement this function in a subclass, make sure, that all classes were your class inherits from //## have an implementation of CheckBounds //## (e.g. inheritance BaseGeometry <- A <- B. Implementation of CheckBounds in class B needs implementation in A as // well!) void CheckBounds(const BoundsArrayType &bounds) override; //##Documentation //## @brief CheckIndexToWorldTransform //## //## This function is called in SetIndexToWorldTransform. Assertions can be implemented in this function (see // PlaneGeometry.cpp). //## In Subclasses of BaseGeometry, implement own conditions or call Superclass::CheckBounds(bounds);. void CheckIndexToWorldTransform(mitk::AffineTransform3D *transform) override; private: /** * \brief Compares plane with another plane: \a true if IsOnPlane * (bounding-box \em not considered) */ virtual bool operator==(const PlaneGeometry *) const { return false; }; /** * \brief Compares plane with another plane: \a false if IsOnPlane * (bounding-box \em not considered) */ virtual bool operator!=(const PlaneGeometry *) const { return false; }; }; } // namespace mitk #endif diff --git a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp index 55ea6e4b07..6a3a8352e7 100644 --- a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp @@ -1,1101 +1,1185 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include "mitkApplyTransformMatrixOperation.h" #include "mitkBaseGeometry.h" #include "mitkGeometryTransformHolder.h" #include "mitkInteractionConst.h" #include "mitkMatrixConvert.h" #include "mitkModifiedLock.h" #include "mitkPointOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkRotationOperation.h" #include "mitkScaleOperation.h" #include "mitkVector.h" #include "mitkMatrix.h" mitk::BaseGeometry::BaseGeometry() : Superclass(), mitk::OperationActor(), m_FrameOfReferenceID(0), m_IndexToWorldTransformLastModified(0), m_ImageGeometry(false), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) { m_GeometryTransform = new GeometryTransformHolder(); Initialize(); } mitk::BaseGeometry::BaseGeometry(const BaseGeometry &other) : Superclass(), mitk::OperationActor(), m_FrameOfReferenceID(other.m_FrameOfReferenceID), m_IndexToWorldTransformLastModified(other.m_IndexToWorldTransformLastModified), m_ImageGeometry(other.m_ImageGeometry), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) { m_GeometryTransform = new GeometryTransformHolder(*other.GetGeometryTransformHolder()); other.InitializeGeometry(this); } mitk::BaseGeometry::~BaseGeometry() { delete m_GeometryTransform; } void mitk::BaseGeometry::SetVtkMatrixDeepCopy(vtkTransform *vtktransform) { m_GeometryTransform->SetVtkMatrixDeepCopy(vtktransform); } const mitk::Point3D mitk::BaseGeometry::GetOrigin() const { return m_GeometryTransform->GetOrigin(); } void mitk::BaseGeometry::SetOrigin(const Point3D &origin) { mitk::ModifiedLock lock(this); if (origin != GetOrigin()) { m_GeometryTransform->SetOrigin(origin); Modified(); } } const mitk::Vector3D mitk::BaseGeometry::GetSpacing() const { return m_GeometryTransform->GetSpacing(); } void mitk::BaseGeometry::Initialize() { float b[6] = {0, 1, 0, 1, 0, 1}; SetFloatBounds(b); m_GeometryTransform->Initialize(); m_FrameOfReferenceID = 0; m_ImageGeometry = false; } void mitk::BaseGeometry::SetFloatBounds(const float bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const float *input = bounds; int i = 0; for (mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6; ++i) *it++ = (mitk::ScalarType)*input++; SetBounds(b); } void mitk::BaseGeometry::SetFloatBounds(const double bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const double *input = bounds; int i = 0; for (mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6; ++i) *it++ = (mitk::ScalarType)*input++; SetBounds(b); } /** Initialize the geometry */ void mitk::BaseGeometry::InitializeGeometry(BaseGeometry *newGeometry) const { newGeometry->SetBounds(m_BoundingBox->GetBounds()); newGeometry->SetFrameOfReferenceID(GetFrameOfReferenceID()); newGeometry->InitializeGeometryTransformHolder(this); newGeometry->m_ImageGeometry = m_ImageGeometry; } void mitk::BaseGeometry::InitializeGeometryTransformHolder(const BaseGeometry *otherGeometry) { this->m_GeometryTransform->Initialize(otherGeometry->GetGeometryTransformHolder()); } /** Set the bounds */ void mitk::BaseGeometry::SetBounds(const BoundsArrayType &bounds) { mitk::ModifiedLock lock(this); this->CheckBounds(bounds); m_BoundingBox = BoundingBoxType::New(); BoundingBoxType::PointsContainer::Pointer pointscontainer = BoundingBoxType::PointsContainer::New(); BoundingBoxType::PointType p; BoundingBoxType::PointIdentifier pointid; for (pointid = 0; pointid < 2; ++pointid) { unsigned int i; for (i = 0; i < m_NDimensions; ++i) { p[i] = bounds[2 * i + pointid]; } pointscontainer->InsertElement(pointid, p); } m_BoundingBox->SetPoints(pointscontainer); m_BoundingBox->ComputeBoundingBox(); this->Modified(); } void mitk::BaseGeometry::SetIndexToWorldTransform(mitk::AffineTransform3D *transform) { mitk::ModifiedLock lock(this); CheckIndexToWorldTransform(transform); m_GeometryTransform->SetIndexToWorldTransform(transform); Modified(); } void mitk::BaseGeometry::SetIndexToWorldTransformWithoutChangingSpacing(mitk::AffineTransform3D *transform) { // security check mitk::Vector3D originalSpacing = this->GetSpacing(); mitk::ModifiedLock lock(this); CheckIndexToWorldTransform(transform); m_GeometryTransform->SetIndexToWorldTransformWithoutChangingSpacing(transform); Modified(); // Security check. Spacig must not have changed if (!mitk::Equal(originalSpacing, this->GetSpacing())) { MITK_WARN << "Spacing has changed in a method, where the spacing must not change."; assert(false); } } const mitk::BaseGeometry::BoundsArrayType mitk::BaseGeometry::GetBounds() const { assert(m_BoundingBox.IsNotNull()); return m_BoundingBox->GetBounds(); } bool mitk::BaseGeometry::IsValid() const { return true; } void mitk::BaseGeometry::SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing) { PreSetSpacing(aSpacing); _SetSpacing(aSpacing, enforceSetSpacing); } void mitk::BaseGeometry::_SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing) { m_GeometryTransform->SetSpacing(aSpacing, enforceSetSpacing); } mitk::Vector3D mitk::BaseGeometry::GetAxisVector(unsigned int direction) const { Vector3D frontToBack; frontToBack.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction).as_ref()); frontToBack *= GetExtent(direction); return frontToBack; } mitk::ScalarType mitk::BaseGeometry::GetExtent(unsigned int direction) const { assert(m_BoundingBox.IsNotNull()); if (direction >= m_NDimensions) mitkThrow() << "Direction is too big. This geometry is for 3D Data"; BoundsArrayType bounds = m_BoundingBox->GetBounds(); return bounds[direction * 2 + 1] - bounds[direction * 2]; } bool mitk::BaseGeometry::Is2DConvertable() { bool isConvertableWithoutLoss = true; do { if (this->GetSpacing()[2] != 1) { isConvertableWithoutLoss = false; break; } if (this->GetOrigin()[2] != 0) { isConvertableWithoutLoss = false; break; } mitk::Vector3D col0, col1, col2; col0.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(0).as_ref()); col1.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(1).as_ref()); col2.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2).as_ref()); if ((col0[2] != 0) || (col1[2] != 0) || (col2[0] != 0) || (col2[1] != 0) || (col2[2] != 1)) { isConvertableWithoutLoss = false; break; } } while (false); return isConvertableWithoutLoss; } mitk::Point3D mitk::BaseGeometry::GetCenter() const { assert(m_BoundingBox.IsNotNull()); Point3D c = m_BoundingBox->GetCenter(); if (m_ImageGeometry) { // Get Center returns the middel of min and max pixel index. In corner based images, this is the right position. // In center based images (imageGeometry == true), the index needs to be shifted back. c[0] -= 0.5; c[1] -= 0.5; c[2] -= 0.5; } this->IndexToWorld(c, c); return c; } double mitk::BaseGeometry::GetDiagonalLength2() const { Vector3D diagonalvector = GetCornerPoint() - GetCornerPoint(false, false, false); return diagonalvector.GetSquaredNorm(); } double mitk::BaseGeometry::GetDiagonalLength() const { return sqrt(GetDiagonalLength2()); } mitk::Point3D mitk::BaseGeometry::GetCornerPoint(int id) const { assert(id >= 0); assert(this->IsBoundingBoxNull() == false); BoundingBox::BoundsArrayType bounds = this->GetBoundingBox()->GetBounds(); Point3D cornerpoint; switch (id) { case 0: FillVector3D(cornerpoint, bounds[0], bounds[2], bounds[4]); break; case 1: FillVector3D(cornerpoint, bounds[0], bounds[2], bounds[5]); break; case 2: FillVector3D(cornerpoint, bounds[0], bounds[3], bounds[4]); break; case 3: FillVector3D(cornerpoint, bounds[0], bounds[3], bounds[5]); break; case 4: FillVector3D(cornerpoint, bounds[1], bounds[2], bounds[4]); break; case 5: FillVector3D(cornerpoint, bounds[1], bounds[2], bounds[5]); break; case 6: FillVector3D(cornerpoint, bounds[1], bounds[3], bounds[4]); break; case 7: FillVector3D(cornerpoint, bounds[1], bounds[3], bounds[5]); break; default: { itkExceptionMacro(<< "A cube only has 8 corners. These are labeled 0-7."); } } if (m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based FillVector3D(cornerpoint, cornerpoint[0] - 0.5, cornerpoint[1] - 0.5, cornerpoint[2] - 0.5); } return this->GetIndexToWorldTransform()->TransformPoint(cornerpoint); } mitk::Point3D mitk::BaseGeometry::GetCornerPoint(bool xFront, bool yFront, bool zFront) const { assert(this->IsBoundingBoxNull() == false); BoundingBox::BoundsArrayType bounds = this->GetBoundingBox()->GetBounds(); Point3D cornerpoint; cornerpoint[0] = (xFront ? bounds[0] : bounds[1]); cornerpoint[1] = (yFront ? bounds[2] : bounds[3]); cornerpoint[2] = (zFront ? bounds[4] : bounds[5]); if (m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based FillVector3D(cornerpoint, cornerpoint[0] - 0.5, cornerpoint[1] - 0.5, cornerpoint[2] - 0.5); } return this->GetIndexToWorldTransform()->TransformPoint(cornerpoint); } mitk::ScalarType mitk::BaseGeometry::GetExtentInMM(int direction) const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction).magnitude() * GetExtent(direction); } void mitk::BaseGeometry::SetExtentInMM(int direction, ScalarType extentInMM) { mitk::ModifiedLock lock(this); ScalarType len = GetExtentInMM(direction); if (fabs(len - extentInMM) >= mitk::eps) { AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_GeometryTransform->GetVnlMatrix(); if (len > extentInMM) vnlmatrix.set_column(direction, vnlmatrix.get_column(direction) / len * extentInMM); else vnlmatrix.set_column(direction, vnlmatrix.get_column(direction) * extentInMM / len); Matrix3D matrix; matrix = vnlmatrix; m_GeometryTransform->SetMatrix(matrix); Modified(); } } bool mitk::BaseGeometry::IsInside(const mitk::Point3D &p) const { mitk::Point3D index; WorldToIndex(p, index); return IsIndexInside(index); } bool mitk::BaseGeometry::IsIndexInside(const mitk::Point3D &index) const { bool inside = false; // if it is an image geometry, we need to convert the index to discrete values // this is done by applying the rounding function also used in WorldToIndex (see line 323) if (m_ImageGeometry) { mitk::Point3D discretIndex; discretIndex[0] = itk::Math::RoundHalfIntegerUp(index[0]); discretIndex[1] = itk::Math::RoundHalfIntegerUp(index[1]); discretIndex[2] = itk::Math::RoundHalfIntegerUp(index[2]); inside = this->GetBoundingBox()->IsInside(discretIndex); // we have to check if the index is at the upper border of each dimension, // because the boundingbox is not centerbased if (inside) { const BoundingBox::BoundsArrayType &bounds = this->GetBoundingBox()->GetBounds(); if ((discretIndex[0] == bounds[1]) || (discretIndex[1] == bounds[3]) || (discretIndex[2] == bounds[5])) inside = false; } } else inside = this->GetBoundingBox()->IsInside(index); return inside; } void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const { mitk::Vector3D tempIn, tempOut; const TransformType::OffsetType &offset = this->GetIndexToWorldTransform()->GetOffset(); tempIn = pt_mm.GetVectorFromOrigin() - offset; WorldToIndex(tempIn, tempOut); pt_units = Point3D(tempOut); } void mitk::BaseGeometry::WorldToIndex(const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != this->GetIndexToWorldTransform()->GetMTime()) { if (!m_InvertedTransform) { m_InvertedTransform = TransformType::New(); } if (!this->GetIndexToWorldTransform()->GetInverse(m_InvertedTransform.GetPointer())) { itkExceptionMacro("Internal ITK matrix inversion error, cannot proceed."); } m_IndexToWorldTransformLastModified = this->GetIndexToWorldTransform()->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType &inverse = m_InvertedTransform->GetMatrix(); if (inverse.GetVnlMatrix().has_nans()) { itkExceptionMacro("Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << this->GetIndexToWorldTransform()->GetMatrix() << "Suggested inverted matrix is:" << std::endl << inverse); } vec_units = inverse * vec_mm; } void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D & /*atPt3d_mm*/, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { MITK_WARN << "Warning! Call of the deprecated function BaseGeometry::WorldToIndex(point, vec, vec). Use " "BaseGeometry::WorldToIndex(vec, vec) instead!"; this->WorldToIndex(vec_mm, vec_units); } mitk::VnlVector mitk::BaseGeometry::GetOriginVnl() const { return GetOrigin().GetVnlVector(); } vtkLinearTransform *mitk::BaseGeometry::GetVtkTransform() const { return m_GeometryTransform->GetVtkTransform(); } void mitk::BaseGeometry::SetIdentity() { mitk::ModifiedLock lock(this); m_GeometryTransform->SetIdentity(); Modified(); } void mitk::BaseGeometry::Compose(const mitk::BaseGeometry::TransformType *other, bool pre) { mitk::ModifiedLock lock(this); m_GeometryTransform->Compose(other, pre); Modified(); } void mitk::BaseGeometry::Compose(const vtkMatrix4x4 *vtkmatrix, bool pre) { mitk::BaseGeometry::TransformType::Pointer itkTransform = mitk::BaseGeometry::TransformType::New(); TransferVtkMatrixToItkTransform(vtkmatrix, itkTransform.GetPointer()); Compose(itkTransform, pre); } void mitk::BaseGeometry::Translate(const Vector3D &vector) { if ((vector[0] != 0) || (vector[1] != 0) || (vector[2] != 0)) { this->SetOrigin(this->GetOrigin() + vector); } } void mitk::BaseGeometry::IndexToWorld(const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const { pt_mm = this->GetIndexToWorldTransform()->TransformPoint(pt_units); } void mitk::BaseGeometry::IndexToWorld(const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { vec_mm = this->GetIndexToWorldTransform()->TransformVector(vec_units); } void mitk::BaseGeometry::ExecuteOperation(Operation *operation) { mitk::ModifiedLock lock(this); vtkTransform *vtktransform = vtkTransform::New(); vtktransform->SetMatrix(this->GetVtkMatrix()); switch (operation->GetOperationType()) { case OpNOTHING: break; case OpMOVE: { auto *pointOp = dynamic_cast(operation); if (pointOp == nullptr) { MITK_ERROR << "Point move operation is null!"; return; } mitk::Point3D newPos = pointOp->GetPoint(); ScalarType data[3]; vtktransform->GetPosition(data); vtktransform->PostMultiply(); vtktransform->Translate(newPos[0], newPos[1], newPos[2]); vtktransform->PreMultiply(); break; } case OpSCALE: { auto *scaleOp = dynamic_cast(operation); if (scaleOp == nullptr) { MITK_ERROR << "Scale operation is null!"; return; } mitk::Point3D newScale = scaleOp->GetScaleFactor(); ScalarType scalefactor[3]; scalefactor[0] = 1 + (newScale[0] / GetMatrixColumn(0).magnitude()); scalefactor[1] = 1 + (newScale[1] / GetMatrixColumn(1).magnitude()); scalefactor[2] = 1 + (newScale[2] / GetMatrixColumn(2).magnitude()); mitk::Point3D anchor = scaleOp->GetScaleAnchorPoint(); vtktransform->PostMultiply(); vtktransform->Translate(-anchor[0], -anchor[1], -anchor[2]); vtktransform->Scale(scalefactor[0], scalefactor[1], scalefactor[2]); vtktransform->Translate(anchor[0], anchor[1], anchor[2]); break; } case OpROTATE: { auto *rotateOp = dynamic_cast(operation); if (rotateOp == nullptr) { MITK_ERROR << "Rotation operation is null!"; return; } Vector3D rotationVector = rotateOp->GetVectorOfRotation(); Point3D center = rotateOp->GetCenterOfRotation(); ScalarType angle = rotateOp->GetAngleOfRotation(); vtktransform->PostMultiply(); vtktransform->Translate(-center[0], -center[1], -center[2]); vtktransform->RotateWXYZ(angle, rotationVector[0], rotationVector[1], rotationVector[2]); vtktransform->Translate(center[0], center[1], center[2]); vtktransform->PreMultiply(); break; } case OpRESTOREPLANEPOSITION: { // Copy necessary to avoid vtk warning vtkMatrix4x4 *matrix = vtkMatrix4x4::New(); TransferItkTransformToVtkMatrix( dynamic_cast(operation)->GetTransform().GetPointer(), matrix); vtktransform->SetMatrix(matrix); matrix->Delete(); break; } case OpAPPLYTRANSFORMMATRIX: { auto *applyMatrixOp = dynamic_cast(operation); vtktransform->SetMatrix(applyMatrixOp->GetMatrix()); break; } default: vtktransform->Delete(); return; } this->SetVtkMatrixDeepCopy(vtktransform); Modified(); vtktransform->Delete(); } mitk::VnlVector mitk::BaseGeometry::GetMatrixColumn(unsigned int direction) const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction).as_ref(); } mitk::BoundingBox::Pointer mitk::BaseGeometry::CalculateBoundingBoxRelativeToTransform( const mitk::AffineTransform3D *transform) const { mitk::BoundingBox::PointsContainer::Pointer pointscontainer = mitk::BoundingBox::PointsContainer::New(); mitk::BoundingBox::PointIdentifier pointid = 0; unsigned char i; if (transform != nullptr) { mitk::AffineTransform3D::Pointer inverse = mitk::AffineTransform3D::New(); transform->GetInverse(inverse); for (i = 0; i < 8; ++i) pointscontainer->InsertElement(pointid++, inverse->TransformPoint(GetCornerPoint(i))); } else { for (i = 0; i < 8; ++i) pointscontainer->InsertElement(pointid++, GetCornerPoint(i)); } mitk::BoundingBox::Pointer result = mitk::BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); return result; } const std::string mitk::BaseGeometry::GetTransformAsString(TransformType *transformType) { std::ostringstream out; out << '['; for (int i = 0; i < 3; ++i) { out << '['; for (int j = 0; j < 3; ++j) out << transformType->GetMatrix().GetVnlMatrix().get(i, j) << ' '; out << ']'; } out << "]["; for (int i = 0; i < 3; ++i) out << transformType->GetOffset()[i] << ' '; out << "]\0"; return out.str(); } void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4 *vtkmatrix) { m_GeometryTransform->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); } void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkMatrix4x4 *vtkmatrix) { m_GeometryTransform->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkmatrix); } void mitk::BaseGeometry::IndexToWorld(const mitk::Point3D & /*atPt3d_units*/, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { MITK_WARN << "Warning! Call of the deprecated function BaseGeometry::IndexToWorld(point, vec, vec). Use " "BaseGeometry::IndexToWorld(vec, vec) instead!"; // vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); this->IndexToWorld(vec_units, vec_mm); } vtkMatrix4x4 *mitk::BaseGeometry::GetVtkMatrix() { return m_GeometryTransform->GetVtkMatrix(); } bool mitk::BaseGeometry::IsBoundingBoxNull() const { return m_BoundingBox.IsNull(); } bool mitk::BaseGeometry::IsIndexToWorldTransformNull() const { return m_GeometryTransform->IsIndexToWorldTransformNull(); } void mitk::BaseGeometry::ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry) { // If Geometry is switched to ImageGeometry, you have to put an offset to the origin, because // imageGeometries origins are pixel-center-based // ... and remove the offset, if you switch an imageGeometry back to a normal geometry // For more information please see the Geometry documentation page if (m_ImageGeometry == isAnImageGeometry) return; const BoundingBox::BoundsArrayType &boundsarray = this->GetBoundingBox()->GetBounds(); Point3D originIndex; FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]); if (isAnImageGeometry == true) FillVector3D(originIndex, originIndex[0] + 0.5, originIndex[1] + 0.5, originIndex[2] + 0.5); else FillVector3D(originIndex, originIndex[0] - 0.5, originIndex[1] - 0.5, originIndex[2] - 0.5); Point3D originWorld; originWorld = GetIndexToWorldTransform()->TransformPoint(originIndex); // instead could as well call IndexToWorld(originIndex,originWorld); SetOrigin(originWorld); this->SetImageGeometry(isAnImageGeometry); } void mitk::BaseGeometry::PrintSelf(std::ostream &os, itk::Indent indent) const { os << indent << " IndexToWorldTransform: "; if (this->IsIndexToWorldTransformNull()) os << "nullptr" << std::endl; else { // from itk::MatrixOffsetTransformBase unsigned int i, j; os << std::endl; os << indent << "Matrix: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << this->GetIndexToWorldTransform()->GetMatrix()[i][j] << " "; } os << std::endl; } os << indent << "Offset: " << this->GetIndexToWorldTransform()->GetOffset() << std::endl; os << indent << "Center: " << this->GetIndexToWorldTransform()->GetCenter() << std::endl; os << indent << "Translation: " << this->GetIndexToWorldTransform()->GetTranslation() << std::endl; auto inverse = mitk::AffineTransform3D::New(); if (this->GetIndexToWorldTransform()->GetInverse(inverse)) { os << indent << "Inverse: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << inverse->GetMatrix()[i][j] << " "; } os << std::endl; } } // from itk::ScalableAffineTransform os << indent << "Scale : "; for (i = 0; i < 3; i++) { os << this->GetIndexToWorldTransform()->GetScale()[i] << " "; } os << std::endl; } os << indent << " BoundingBox: "; if (this->IsBoundingBoxNull()) os << "nullptr" << std::endl; else { os << indent << "( "; for (unsigned int i = 0; i < 3; i++) { os << this->GetBoundingBox()->GetBounds()[2 * i] << "," << this->GetBoundingBox()->GetBounds()[2 * i + 1] << " "; } os << " )" << std::endl; } os << indent << " Origin: " << this->GetOrigin() << std::endl; os << indent << " ImageGeometry: " << this->GetImageGeometry() << std::endl; os << indent << " Spacing: " << this->GetSpacing() << std::endl; } void mitk::BaseGeometry::Modified() const { if (!m_ModifiedLockFlag) Superclass::Modified(); else m_ModifiedCalledFlag = true; } mitk::AffineTransform3D *mitk::BaseGeometry::GetIndexToWorldTransform() { return m_GeometryTransform->GetIndexToWorldTransform(); } const mitk::AffineTransform3D *mitk::BaseGeometry::GetIndexToWorldTransform() const { return m_GeometryTransform->GetIndexToWorldTransform(); } const mitk::GeometryTransformHolder *mitk::BaseGeometry::GetGeometryTransformHolder() const { return m_GeometryTransform; } +void mitk::BaseGeometry::MapAxesToOrientations(int axes[]) const +{ + auto affineTransform = this->GetIndexToWorldTransform(); + auto matrix = affineTransform->GetMatrix(); + matrix.GetVnlMatrix().normalize_columns(); + auto inverseMatrix = matrix.GetInverse(); + + bool mapped[3] = {false, false, false}; + + // We need to allow an epsilon difference to ignore rounding. + const double eps = 0.0001; + + for (int orientation = 0; orientation < 3; ++orientation) + { + auto absX = std::abs(inverseMatrix[0][orientation]); + auto absY = std::abs(inverseMatrix[1][orientation]); + auto absZ = std::abs(inverseMatrix[2][orientation]); + + // First we check if there is a single maximum value. If there is, we found the axis + // that corresponds to the given orientation. If there is no single maximum value, + // we choose one from the the two or three axes that have the maximum value, but we + // need to make sure that we do not map the same axis to different orientations. + // Equal values are valid if the volume is rotated by exactly 45 degrees around one + // axis. If the volume is rotated by 45 degrees around two axes, you will get single + // maximum values at the same axes for two different orientations. In this case, + // the axis is mapped to one of the orientations, and for the other orientation we + // choose a different axis that has not been mapped yet, even if it is not a maximum. + + if (absX > absY + eps) + { + if (absX > absZ + eps) + { + // x is the greatest + int axis = !mapped[0] ? 0 : !mapped[1] ? 1 : 2; + axes[orientation] = axis; + mapped[axis] = true; + } + else + { + // z is the greatest OR x and z are equal and greater than y + int axis = !mapped[2] ? 2 : !mapped[0] ? 0 : 1; + axes[orientation] = axis; + mapped[axis] = true; + } + } + else if (absY > absX + eps) + { + if (absY > absZ + eps) + { + // y is the greatest + int axis = !mapped[1] ? 1 : !mapped[2] ? 2 : 0; + axes[orientation] = axis; + mapped[axis] = true; + } + else + { + // z is the greatest OR y and z are equal and greater than x + int axis = !mapped[2] ? 2 : !mapped[1] ? 1 : 0; + axes[orientation] = axis; + mapped[axis] = true; + } + } + else + { + if (absZ > absX + eps) + { + // z is the greatest + int axis = !mapped[2] ? 2 : !mapped[0] ? 0 : 1; + axes[orientation] = axis; + mapped[axis] = true; + } + else + { + // x and y are equal and greater than z OR x and y and z are equal + int axis = !mapped[0] ? 0 : !mapped[1] ? 1 : 2; + axes[orientation] = axis; + mapped[axis] = true; + } + } + } + + assert(mapped[0] && mapped[1] && mapped[2]); +} + bool mitk::Equal(const mitk::BaseGeometry::BoundingBoxType &leftHandSide, const mitk::BaseGeometry::BoundingBoxType &rightHandSide, ScalarType eps, bool verbose) { bool result = true; BaseGeometry::BoundsArrayType rightBounds = rightHandSide.GetBounds(); BaseGeometry::BoundsArrayType leftBounds = leftHandSide.GetBounds(); BaseGeometry::BoundsArrayType::Iterator itLeft = leftBounds.Begin(); for (BaseGeometry::BoundsArrayType::Iterator itRight = rightBounds.Begin(); itRight != rightBounds.End(); ++itRight) { if ((!mitk::Equal(*itLeft, *itRight, eps))) { if (verbose) { MITK_INFO << "[( Geometry3D::BoundingBoxType )] bounds are not equal."; MITK_INFO << "rightHandSide is " << setprecision(12) << *itRight << " : leftHandSide is " << *itLeft << " and tolerance is " << eps; } result = false; } itLeft++; } return result; } bool mitk::Equal(const mitk::BaseGeometry &leftHandSide, const mitk::BaseGeometry &rightHandSide, ScalarType coordinateEps, ScalarType directionEps, bool verbose) { bool result = true; // Compare spacings if (!mitk::Equal(leftHandSide.GetSpacing(), rightHandSide.GetSpacing(), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Spacing differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetSpacing() << " : leftHandSide is " << leftHandSide.GetSpacing() << " and tolerance is " << coordinateEps; } result = false; } // Compare Origins if (!mitk::Equal(leftHandSide.GetOrigin(), rightHandSide.GetOrigin(), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Origin differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetOrigin() << " : leftHandSide is " << leftHandSide.GetOrigin() << " and tolerance is " << coordinateEps; } result = false; } // Compare Axis and Extents for (unsigned int i = 0; i < 3; ++i) { if (!mitk::Equal(leftHandSide.GetAxisVector(i), rightHandSide.GetAxisVector(i), directionEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] AxisVector #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetAxisVector(i) << " : leftHandSide is " << leftHandSide.GetAxisVector(i) << " and tolerance is " << directionEps; } result = false; } if (!mitk::Equal(leftHandSide.GetExtent(i), rightHandSide.GetExtent(i), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Extent #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetExtent(i) << " : leftHandSide is " << leftHandSide.GetExtent(i) << " and tolerance is " << coordinateEps; } result = false; } } // Compare ImageGeometry Flag if (rightHandSide.GetImageGeometry() != leftHandSide.GetImageGeometry()) { if (verbose) { MITK_INFO << "[( Geometry3D )] GetImageGeometry is different."; MITK_INFO << "rightHandSide is " << rightHandSide.GetImageGeometry() << " : leftHandSide is " << leftHandSide.GetImageGeometry(); } result = false; } // Compare FrameOfReference ID if (rightHandSide.GetFrameOfReferenceID() != leftHandSide.GetFrameOfReferenceID()) { if (verbose) { MITK_INFO << "[( Geometry3D )] GetFrameOfReferenceID is different."; MITK_INFO << "rightHandSide is " << rightHandSide.GetFrameOfReferenceID() << " : leftHandSide is " << leftHandSide.GetFrameOfReferenceID(); } result = false; } // Compare BoundingBoxes if (!mitk::Equal(*leftHandSide.GetBoundingBox(), *rightHandSide.GetBoundingBox(), coordinateEps, verbose)) { result = false; } // Compare IndexToWorldTransform Matrix if (!mitk::Equal(*leftHandSide.GetIndexToWorldTransform(), *rightHandSide.GetIndexToWorldTransform(), directionEps, verbose)) { result = false; } return result; } bool mitk::Equal(const mitk::BaseGeometry& leftHandSide, const mitk::BaseGeometry& rightHandSide, ScalarType eps, bool verbose) { return Equal(leftHandSide, rightHandSide, eps, eps, verbose); } bool mitk::Equal(const mitk::BaseGeometry::TransformType &leftHandSide, const mitk::BaseGeometry::TransformType &rightHandSide, ScalarType eps, bool verbose) { // Compare IndexToWorldTransform Matrix if (!mitk::MatrixEqualElementWise(leftHandSide.GetMatrix(), rightHandSide.GetMatrix(), eps)) { if (verbose) { MITK_INFO << "[( Geometry3D::TransformType )] Index to World Transformation matrix differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetMatrix() << " : leftHandSide is " << leftHandSide.GetMatrix() << " and tolerance is " << eps; } return false; } return true; } bool mitk::IsSubGeometry(const mitk::BaseGeometry& testGeo, const mitk::BaseGeometry& referenceGeo, ScalarType coordinateEps, ScalarType directionEps, bool verbose) { bool result = true; // Compare spacings (must be equal) const auto testedSpacing = testGeo.GetSpacing(); if (!mitk::Equal(testedSpacing, referenceGeo.GetSpacing(), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Spacing differs."; MITK_INFO << "testedGeometry is " << setprecision(12) << testedSpacing << " : referenceGeometry is " << referenceGeo.GetSpacing() << " and tolerance is " << coordinateEps; } result = false; } // Compare ImageGeometry Flag (must be equal) if (referenceGeo.GetImageGeometry() != testGeo.GetImageGeometry()) { if (verbose) { MITK_INFO << "[( Geometry3D )] GetImageGeometry is different."; MITK_INFO << "referenceGeo is " << referenceGeo.GetImageGeometry() << " : testGeo is " << testGeo.GetImageGeometry(); } result = false; } // Compare IndexToWorldTransform Matrix (must be equal -> same axis directions) if (!Equal(*(testGeo.GetIndexToWorldTransform()), *(referenceGeo.GetIndexToWorldTransform()), directionEps, verbose)) { result = false; } //check if the geometry is within or equal to the bounds of reference geomentry. for (int i = 0; i<8; ++i) { auto testCorner = testGeo.GetCornerPoint(i); bool isInside = false; mitk::Point3D testCornerIndex; referenceGeo.WorldToIndex(testCorner, testCornerIndex); std::bitset bs(i); //To regard the coordinateEps, we subtract or add it to the index elements //depending on whether it was constructed by a lower or an upper bound value //(see implementation of BaseGeometry::GetCorner()). if (bs.test(0)) { testCornerIndex[2] -= coordinateEps; } else { testCornerIndex[2] += coordinateEps; } if (bs.test(1)) { testCornerIndex[1] -= coordinateEps; } else { testCornerIndex[1] += coordinateEps; } if (bs.test(2)) { testCornerIndex[0] -= coordinateEps; } else { testCornerIndex[0] += coordinateEps; } isInside = referenceGeo.IsIndexInside(testCornerIndex); if (!isInside) { if (verbose) { MITK_INFO << "[( Geometry3D )] corner point is not inside. "; MITK_INFO << "referenceGeo is " << setprecision(12) << referenceGeo << " : tested corner is " << testGeo.GetCornerPoint(i); } result = false; } } // check grid of test geometry is on the grid of the reference geometry. This is important as the // boundingbox is only checked for containing the tested geometry, but if a corner (one is enough // as we know that axis and spacing are equal, due to equal transfor (see above)) of the tested geometry // is on the grid it is really a sub geometry (as they have the same spacing and axis). auto cornerOffset = testGeo.GetCornerPoint(0) - referenceGeo.GetCornerPoint(0); mitk::Vector3D cornerIndexOffset; referenceGeo.WorldToIndex(cornerOffset, cornerIndexOffset); for (unsigned int i = 0; i < 3; ++i) { auto pixelCountContinous = cornerIndexOffset[i]; auto pixelCount = std::round(pixelCountContinous); if (std::abs(pixelCount - pixelCountContinous) > coordinateEps) { if (verbose) { MITK_INFO << "[( Geometry3D )] Tested geometry is not on the grid of the reference geometry. "; MITK_INFO << "referenceGeo is " << setprecision(15) << referenceGeo << " : tested corner offset in pixels is " << pixelCountContinous << " for axis "< #include #include namespace mitk { PlaneGeometry::PlaneGeometry() : Superclass(), m_ReferenceGeometry(nullptr) { Initialize(); } PlaneGeometry::~PlaneGeometry() {} PlaneGeometry::PlaneGeometry(const PlaneGeometry &other) : Superclass(other), m_ReferenceGeometry(other.m_ReferenceGeometry) { } bool PlaneGeometry::CheckRotationMatrix(mitk::AffineTransform3D *transform, double epsilon) { bool rotation = true; auto matrix = transform->GetMatrix().GetVnlMatrix(); matrix.normalize_columns(); auto det = vnl_determinant(matrix); if (fabs(det-1.0) > epsilon) { MITK_WARN << "Invalid rotation matrix! Determinant != 1 (" << det << ")"; rotation = false; } vnl_matrix_fixed id; id.set_identity(); auto should_be_id = matrix*matrix.transpose(); should_be_id -= id; auto max = should_be_id.absolute_value_max(); if (max > epsilon) { MITK_WARN << "Invalid rotation matrix! R*R^T != ID. Max value: " << max << " (should be 0)"; rotation = false; } return rotation; } void PlaneGeometry::CheckIndexToWorldTransform(mitk::AffineTransform3D *transform) { this->CheckRotationMatrix(transform); } void PlaneGeometry::CheckBounds(const BoundingBox::BoundsArrayType &bounds) { // error: unused parameter 'bounds' // this happens in release mode, where the assert macro is defined empty // hence we "use" the parameter: (void)bounds; // currently the unit rectangle must be starting at the origin [0,0] assert(bounds[0] == 0); assert(bounds[2] == 0); // the unit rectangle must be two-dimensional assert(bounds[1] > 0); assert(bounds[3] > 0); } void PlaneGeometry::IndexToWorld(const Point2D &pt_units, Point2D &pt_mm) const { pt_mm[0] = GetExtentInMM(0) / GetExtent(0) * pt_units[0]; pt_mm[1] = GetExtentInMM(1) / GetExtent(1) * pt_units[1]; } void PlaneGeometry::WorldToIndex(const Point2D &pt_mm, Point2D &pt_units) const { pt_units[0] = pt_mm[0] * (1.0 / (GetExtentInMM(0) / GetExtent(0))); pt_units[1] = pt_mm[1] * (1.0 / (GetExtentInMM(1) / GetExtent(1))); } void PlaneGeometry::IndexToWorld(const Point2D & /*atPt2d_units*/, const Vector2D &vec_units, Vector2D &vec_mm) const { MITK_WARN << "Warning! Call of the deprecated function PlaneGeometry::IndexToWorld(point, vec, vec). Use " "PlaneGeometry::IndexToWorld(vec, vec) instead!"; this->IndexToWorld(vec_units, vec_mm); } void PlaneGeometry::IndexToWorld(const Vector2D &vec_units, Vector2D &vec_mm) const { vec_mm[0] = (GetExtentInMM(0) / GetExtent(0)) * vec_units[0]; vec_mm[1] = (GetExtentInMM(1) / GetExtent(1)) * vec_units[1]; } void PlaneGeometry::WorldToIndex(const Point2D & /*atPt2d_mm*/, const Vector2D &vec_mm, Vector2D &vec_units) const { MITK_WARN << "Warning! Call of the deprecated function PlaneGeometry::WorldToIndex(point, vec, vec). Use " "PlaneGeometry::WorldToIndex(vec, vec) instead!"; this->WorldToIndex(vec_mm, vec_units); } void PlaneGeometry::WorldToIndex(const Vector2D &vec_mm, Vector2D &vec_units) const { vec_units[0] = vec_mm[0] * (1.0 / (GetExtentInMM(0) / GetExtent(0))); vec_units[1] = vec_mm[1] * (1.0 / (GetExtentInMM(1) / GetExtent(1))); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, ScalarType height, const Vector3D &spacing, AnatomicalPlane planeorientation, ScalarType zPosition, bool frontside, bool rotated, bool top) { AffineTransform3D::Pointer transform; transform = AffineTransform3D::New(); AffineTransform3D::MatrixType matrix; AffineTransform3D::MatrixType::InternalMatrixType &vnlmatrix = matrix.GetVnlMatrix(); vnlmatrix.set_identity(); vnlmatrix(0, 0) = spacing[0]; vnlmatrix(1, 1) = spacing[1]; vnlmatrix(2, 2) = spacing[2]; transform->SetIdentity(); transform->SetMatrix(matrix); InitializeStandardPlane(width, height, transform.GetPointer(), planeorientation, zPosition, frontside, rotated, top); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, mitk::ScalarType height, const AffineTransform3D *transform /* = nullptr */, AnatomicalPlane planeorientation /* = Axial */, mitk::ScalarType zPosition /* = 0 */, bool frontside /* = true */, bool rotated /* = false */, bool top /* = true */) { Superclass::Initialize(); /// construct standard view. // We define at the moment "frontside" as: axial from above, // coronal from front (nose), sagittal from right. // TODO: Double check with medicals doctors or radiologists [ ]. // We define the orientation in patient's view, e.g. LAI is in a axial cut // (parallel to the triangle ear-ear-nose): // first axis: To the left ear of the patient // seecond axis: To the nose of the patient // third axis: To the legs of the patient. // Options are: L/R left/right; A/P anterior/posterior; I/S inferior/superior // (AKA caudal/cranial). // We note on all cases in the following switch block r.h. for right handed // or l.h. for left handed to describe the different cases. // However, which system is chosen is defined at the end of the switch block. // CAVE / be careful: the vectors right and bottom are relative to the plane // and do NOT describe e.g. the right side of the patient. Point3D origin; /** Bottom means downwards, DV means Direction Vector. Both relative to the image! */ VnlVector rightDV(3), bottomDV(3); /** Origin of this plane is by default a zero vector and implicitly in the top-left corner: */ origin.Fill(0); /** This is different to all definitions in MITK, except the QT mouse clicks. * But it is like this here and we don't want to change a running system. * Just be aware, that IN THIS FUNCTION we define the origin at the top left (e.g. your screen). */ /** NormalDirection defines which axis (i.e. column index in the transform matrix) * is perpendicular to the plane: */ int normalDirection; switch (planeorientation) // Switch through our limited choice of standard planes: { case AnatomicalPlane::Original: /** Orientation 'Original' shall be done like the axial plane, * for whatever reasons. */ case AnatomicalPlane::Axial: if (frontside) // Radiologist's view from below. A cut along the triangle ear-ear-nose. { if (rotated == false) /** Origin in the top-left corner, x=[1; 0; 0], y=[0; 1; 0], z=[0; 0; 1], * origin=[0,0,zpos]: LAI (r.h.) * * 0---rightDV----> | * | | * | Picture of a finite, rectangular plane | * | ( insert LOLCAT-scan here ^_^ ) | * | | * v _________________________________________| * */ { FillVector3D(origin, 0, 0, zPosition); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 1, 0); } else // Origin rotated to the bottom-right corner, x=[-1; 0; 0], y=[0; -1; 0], z=[0; 0; 1], // origin=[w,h,zpos]: RPI (r.h.) { // Caveat emptor: Still using top-left as origin of index coordinate system! FillVector3D(origin, width, height, zPosition); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, -1, 0); } } else // 'Backside, not frontside.' Neuro-Surgeons's view from above patient. { if (rotated == false) // x=[-1; 0; 0], y=[0; 1; 0], z=[0; 0; 1], origin=[w,0,zpos]: RAS (r.h.) { FillVector3D(origin, width, 0, zPosition); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 1, 0); } else // Origin in the bottom-left corner, x=[1; 0; 0], y=[0; -1; 0], z=[0; 0; 1], // origin=[0,h,zpos]: LPS (r.h.) { FillVector3D(origin, 0, height, zPosition); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, -1, 0); } } normalDirection = 2; // That is S=Superior=z=third_axis=middlefinger in righthanded LPS-system. break; case AnatomicalPlane::Coronal: // Coronal=Frontal plane; cuts through patient's ear-ear-heel-heel: if (frontside) { if (rotated == false) // x=[1; 0; 0], y=[0; 0; 1], z=[0; 1; 0], origin=[0,zpos,0]: LAI (r.h.) { FillVector3D(origin, 0, zPosition, 0); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[-1;0;0], y=[0;0;-1], z=[0;1;0], origin=[w,zpos,h]: RAS (r.h.) { FillVector3D(origin, width, zPosition, height); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 0, -1); } } else { if (rotated == false) // x=[-1;0;0], y=[0;0;1], z=[0;1;0], origin=[w,zpos,0]: RPI (r.h.) { FillVector3D(origin, width, zPosition, 0); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[1;0;0], y=[0;1;0], z=[0;0;-1], origin=[0,zpos,h]: LPS (r.h.) { FillVector3D(origin, 0, zPosition, height); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 0, -1); } } normalDirection = 1; // Normal vector = posterior direction. break; case AnatomicalPlane::Sagittal: // Sagittal=Medial plane, the symmetry-plane mirroring your face. if (frontside) { if (rotated == false) // x=[0;1;0], y=[0;0;1], z=[1;0;0], origin=[zpos,0,0]: LAI (r.h.) { FillVector3D(origin, zPosition, 0, 0); FillVector3D(rightDV, 0, 1, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[0;-1;0], y=[0;0;-1], z=[1;0;0], origin=[zpos,w,h]: LPS (r.h.) { FillVector3D(origin, zPosition, width, height); FillVector3D(rightDV, 0, -1, 0); FillVector3D(bottomDV, 0, 0, -1); } } else { if (rotated == false) // x=[0;-1;0], y=[0;0;1], z=[1;0;0], origin=[zpos,w,0]: RPI (r.h.) { FillVector3D(origin, zPosition, width, 0); FillVector3D(rightDV, 0, -1, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[0;1;0], y=[0;0;-1], z=[1;0;0], origin=[zpos,0,h]: RAS (r.h.) { FillVector3D(origin, zPosition, 0, height); FillVector3D(rightDV, 0, 1, 0); FillVector3D(bottomDV, 0, 0, -1); } } normalDirection = 0; // Normal vector = Lateral direction: Left in a LPS-system. break; default: itkExceptionMacro("unknown AnatomicalPlane"); } VnlVector normal(3); FillVector3D(normal, 0, 0, 0); normal[normalDirection] = top ? 1 : -1; if ( transform != nullptr ) { origin = transform->TransformPoint( origin ); rightDV = transform->TransformVector( rightDV ).as_ref(); bottomDV = transform->TransformVector( bottomDV ).as_ref(); normal = transform->TransformVector( normal ).as_ref(); } ScalarType bounds[6] = {0, width, 0, height, 0, 1}; this->SetBounds(bounds); AffineTransform3D::Pointer planeTransform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightDV.as_ref()); matrix.GetVnlMatrix().set_column(1, bottomDV.as_ref()); matrix.GetVnlMatrix().set_column(2, normal.as_ref()); planeTransform->SetMatrix(matrix); planeTransform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); this->SetIndexToWorldTransform(planeTransform); this->SetOrigin(origin); } - - std::vector< int > PlaneGeometry::CalculateDominantAxes(mitk::AffineTransform3D::MatrixType::InternalMatrixType& rotation_matrix) - { - std::vector< int > axes; - - bool dominant_axis_error = false; - for (int i = 0; i < 3; ++i) - { - int dominantAxis = itk::Function::Max3( - rotation_matrix[0][i], - rotation_matrix[1][i], - rotation_matrix[2][i] - ); - - for (int j=0; jSetReferenceGeometry(geometry3D); ScalarType width, height; - // Inspired by: - // http://www.na-mic.org/Wiki/index.php/Coordinate_System_Conversion_Between_ITK_and_Slicer3 - - mitk::AffineTransform3D::MatrixType matrix = geometry3D->GetIndexToWorldTransform()->GetMatrix(); - + auto matrix = geometry3D->GetIndexToWorldTransform()->GetMatrix(); matrix.GetVnlMatrix().normalize_columns(); - mitk::AffineTransform3D::MatrixType::InternalMatrixType inverseMatrix = matrix.GetTranspose(); + auto inverseMatrix = matrix.GetInverse(); + + // The index of the sagittal, coronal and axial axes in the reference geometry. + int axes[3]; + geometry3D->MapAxesToOrientations(axes); - /// The index of the sagittal, coronal and axial axes in the reference geometry. - auto axes = CalculateDominantAxes(inverseMatrix); - /// The direction of the sagittal, coronal and axial axes in the reference geometry. - /// +1 means that the direction is straight, i.e. greater index translates to greater - /// world coordinate. -1 means that the direction is inverted. + // The direction of the sagittal, coronal and axial axes in the reference geometry. + // +1 means that the direction is straight, i.e. greater index translates to greater + // world coordinate. -1 means that the direction is inverted. int directions[3]; ScalarType extents[3]; ScalarType spacings[3]; for (int i=0; i<3; ++i) { - int dominantAxis = axes.at(i); - directions[i] = itk::Function::Sign(inverseMatrix[dominantAxis][i]); - extents[i] = geometry3D->GetExtent(dominantAxis); - spacings[i] = geometry3D->GetSpacing()[dominantAxis]; + int axis = axes[i]; + directions[i] = itk::Function::Sign(inverseMatrix[axis][i]); + extents[i] = geometry3D->GetExtent(axis); + spacings[i] = geometry3D->GetSpacing()[axis]; } // matrix(column) = inverseTransformMatrix(row) * flippedAxes * spacing matrix[0][0] = inverseMatrix[axes[0]][0] * directions[0] * spacings[0]; matrix[1][0] = inverseMatrix[axes[0]][1] * directions[0] * spacings[0]; matrix[2][0] = inverseMatrix[axes[0]][2] * directions[0] * spacings[0]; matrix[0][1] = inverseMatrix[axes[1]][0] * directions[1] * spacings[1]; matrix[1][1] = inverseMatrix[axes[1]][1] * directions[1] * spacings[1]; matrix[2][1] = inverseMatrix[axes[1]][2] * directions[1] * spacings[1]; matrix[0][2] = inverseMatrix[axes[2]][0] * directions[2] * spacings[2]; matrix[1][2] = inverseMatrix[axes[2]][1] * directions[2] * spacings[2]; matrix[2][2] = inverseMatrix[axes[2]][2] * directions[2] * spacings[2]; /// The "world origin" is the corner with the lowest physical coordinates. /// We use it as a reference point so that we get the correct anatomical /// orientations. Point3D worldOrigin = geometry3D->GetOrigin(); for (int i = 0; i < 3; ++i) { /// The distance of the plane origin from the world origin in voxels. double offset = directions[i] > 0 ? 0.0 : extents[i]; if (geometry3D->GetImageGeometry()) { offset += directions[i] * 0.5; } for (int j = 0; j < 3; ++j) { worldOrigin[j] -= offset * matrix[j][i]; } } switch(planeorientation) { case AnatomicalPlane::Original: /** Orientation 'Original' shall be done like the axial plane orientation, * for whatever reasons. */ case AnatomicalPlane::Axial: width = extents[0]; height = extents[1]; break; case AnatomicalPlane::Coronal: width = extents[0]; height = extents[2]; break; case AnatomicalPlane::Sagittal: width = extents[1]; height = extents[2]; break; default: itkExceptionMacro("unknown AnatomicalPlane"); } ScalarType bounds[6]= { 0, width, 0, height, 0, 1 }; this->SetBounds( bounds ); AffineTransform3D::Pointer transform = AffineTransform3D::New(); transform->SetMatrix(matrix); transform->SetOffset(worldOrigin.GetVectorFromOrigin()); InitializeStandardPlane( width, height, transform, planeorientation, zPosition, frontside, rotated, top); } void PlaneGeometry::InitializeStandardPlane(const BaseGeometry *geometry3D, bool top, AnatomicalPlane planeorientation, bool frontside, bool rotated) { /// The index of the sagittal, coronal and axial axes in world coordinate system. int worldAxis; switch(planeorientation) { case AnatomicalPlane::Original: /** Orientation 'Original' shall be done like the axial plane orientation, * for whatever reasons. */ case AnatomicalPlane::Axial: worldAxis = 2; break; case AnatomicalPlane::Coronal: worldAxis = 1; break; case AnatomicalPlane::Sagittal: worldAxis = 0; break; default: itkExceptionMacro("unknown AnatomicalPlane"); } - // Inspired by: - // http://www.na-mic.org/Wiki/index.php/Coordinate_System_Conversion_Between_ITK_and_Slicer3 - - mitk::AffineTransform3D::ConstPointer affineTransform = geometry3D->GetIndexToWorldTransform(); - mitk::AffineTransform3D::MatrixType matrix = affineTransform->GetMatrix(); - matrix.GetVnlMatrix().normalize_columns(); - mitk::AffineTransform3D::MatrixType::InternalMatrixType inverseMatrix = matrix.GetInverse(); - - /// The index of the sagittal, coronal and axial axes in the reference geometry. - int dominantAxis = CalculateDominantAxes(inverseMatrix).at(worldAxis); + int axes[3]; + geometry3D->MapAxesToOrientations(axes); + int axis = axes[worldAxis]; - ScalarType zPosition = top ? 0.5 : geometry3D->GetExtent(dominantAxis) - 0.5; + ScalarType zPosition = top ? 0.5 : geometry3D->GetExtent(axis) - 0.5; InitializeStandardPlane(geometry3D, planeorientation, zPosition, frontside, rotated, top); } void PlaneGeometry::InitializeStandardPlane(const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing) { InitializeStandardPlane(rightVector.GetVnlVector(), downVector.GetVnlVector(), spacing); } void PlaneGeometry::InitializeStandardPlane(const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing) { ScalarType width = rightVector.two_norm(); ScalarType height = downVector.two_norm(); InitializeStandardPlane(width, height, rightVector, downVector, spacing); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, ScalarType height, const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing) { InitializeStandardPlane(width, height, rightVector.GetVnlVector(), downVector.GetVnlVector(), spacing); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, ScalarType height, const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing) { assert(width > 0); assert(height > 0); VnlVector rightDV = rightVector; rightDV.normalize(); VnlVector downDV = downVector; downDV.normalize(); VnlVector normal = vnl_cross_3d(rightVector, downVector); normal.normalize(); // Crossproduct vnl_cross_3d is always righthanded, but that is okay here // because in this method we create a new IndexToWorldTransform and // spacing with 1 or 3 negative components could still make it lefthanded. if (spacing != nullptr) { rightDV *= (*spacing)[0]; downDV *= (*spacing)[1]; normal *= (*spacing)[2]; } AffineTransform3D::Pointer transform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightDV); matrix.GetVnlMatrix().set_column(1, downDV); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); ScalarType bounds[6] = {0, width, 0, height, 0, 1}; this->SetBounds(bounds); this->SetIndexToWorldTransform(transform); } void PlaneGeometry::InitializePlane(const Point3D &origin, const Vector3D &normal) { VnlVector rightVectorVnl(3), downVectorVnl; if (Equal(normal[1], 0.0f) == false) { FillVector3D(rightVectorVnl, 1.0f, -normal[0] / normal[1], 0.0f); rightVectorVnl.normalize(); } else { FillVector3D(rightVectorVnl, 0.0f, 1.0f, 0.0f); } downVectorVnl = vnl_cross_3d(normal.GetVnlVector(), rightVectorVnl); downVectorVnl.normalize(); // Crossproduct vnl_cross_3d is always righthanded. InitializeStandardPlane(rightVectorVnl, downVectorVnl); SetOrigin(origin); } void PlaneGeometry::SetMatrixByVectors(const VnlVector &rightVector, const VnlVector &downVector, ScalarType thickness /* = 1.0 */) { VnlVector normal = vnl_cross_3d(rightVector, downVector); normal.normalize(); normal *= thickness; // Crossproduct vnl_cross_3d is always righthanded, but that is okay here // because in this method we create a new IndexToWorldTransform and // a negative thickness could still make it lefthanded. AffineTransform3D::Pointer transform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightVector); matrix.GetVnlMatrix().set_column(1, downVector); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); SetIndexToWorldTransform(transform); } Vector3D PlaneGeometry::GetNormal() const { Vector3D frontToBack; frontToBack.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2).as_ref()); return frontToBack; } VnlVector PlaneGeometry::GetNormalVnl() const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2).as_ref(); } ScalarType PlaneGeometry::DistanceFromPlane(const Point3D &pt3d_mm) const { return fabs(SignedDistance(pt3d_mm)); } ScalarType PlaneGeometry::SignedDistance(const Point3D &pt3d_mm) const { return SignedDistanceFromPlane(pt3d_mm); } bool PlaneGeometry::IsAbove(const Point3D &pt3d_mm, bool considerBoundingBox) const { if (considerBoundingBox) { Point3D pt3d_units; BaseGeometry::WorldToIndex(pt3d_mm, pt3d_units); return (pt3d_units[2] > this->GetBoundingBox()->GetBounds()[4]); } else return SignedDistanceFromPlane(pt3d_mm) > 0; } bool PlaneGeometry::IntersectionLine(const PlaneGeometry* plane, Line3D& crossline) const { Vector3D normal = this->GetNormal(); normal.Normalize(); Vector3D planeNormal = plane->GetNormal(); planeNormal.Normalize(); Vector3D direction = itk::CrossProduct(normal, planeNormal); if (direction.GetSquaredNorm() < eps) return false; crossline.SetDirection(direction); double N1dN2 = normal * planeNormal; double determinant = 1.0 - N1dN2 * N1dN2; Vector3D origin = this->GetOrigin().GetVectorFromOrigin(); Vector3D planeOrigin = plane->GetOrigin().GetVectorFromOrigin(); double d1 = normal * origin; double d2 = planeNormal * planeOrigin; double c1 = (d1 - d2 * N1dN2) / determinant; double c2 = (d2 - d1 * N1dN2) / determinant; Vector3D p = normal * c1 + planeNormal * c2; crossline.GetPoint()[0] = p.GetVnlVector()[0]; crossline.GetPoint()[1] = p.GetVnlVector()[1]; crossline.GetPoint()[2] = p.GetVnlVector()[2]; return true; } unsigned int PlaneGeometry::IntersectWithPlane2D(const PlaneGeometry *plane, Point2D &lineFrom, Point2D &lineTo) const { Line3D crossline; if (this->IntersectionLine(plane, crossline) == false) return 0; Point2D point2; Vector2D direction2; this->Map(crossline.GetPoint(), point2); this->Map(crossline.GetPoint(), crossline.GetDirection(), direction2); return Line3D::RectangleLineIntersection( 0, 0, GetExtentInMM(0), GetExtentInMM(1), point2, direction2, lineFrom, lineTo); } double PlaneGeometry::Angle(const PlaneGeometry *plane) const { return angle(plane->GetMatrixColumn(2), GetMatrixColumn(2)); } double PlaneGeometry::Angle(const Line3D &line) const { return vnl_math::pi_over_2 - angle(line.GetDirection().GetVnlVector(), GetMatrixColumn(2)); } bool PlaneGeometry::IntersectionPoint(const Line3D &line, Point3D &intersectionPoint) const { Vector3D planeNormal = this->GetNormal(); planeNormal.Normalize(); Vector3D lineDirection = line.GetDirection(); lineDirection.Normalize(); double t = planeNormal * lineDirection; if (fabs(t) < eps) { return false; } Vector3D diff; diff = this->GetOrigin() - line.GetPoint(); t = (planeNormal * diff) / t; intersectionPoint = line.GetPoint() + lineDirection * t; return true; } bool PlaneGeometry::IntersectionPointParam(const Line3D &line, double &t) const { Vector3D planeNormal = this->GetNormal(); Vector3D lineDirection = line.GetDirection(); t = planeNormal * lineDirection; if (fabs(t) < eps) { return false; } Vector3D diff; diff = this->GetOrigin() - line.GetPoint(); t = (planeNormal * diff) / t; return true; } bool PlaneGeometry::IsParallel(const PlaneGeometry *plane) const { return ((Angle(plane) < 10.0 * mitk::sqrteps) || (Angle(plane) > (vnl_math::pi - 10.0 * sqrteps))); } bool PlaneGeometry::IsOnPlane(const Point3D &point) const { return Distance(point) < eps; } bool PlaneGeometry::IsOnPlane(const Line3D &line) const { return ((Distance(line.GetPoint()) < eps) && (Distance(line.GetPoint2()) < eps)); } bool PlaneGeometry::IsOnPlane(const PlaneGeometry *plane) const { return (IsParallel(plane) && (Distance(plane->GetOrigin()) < eps)); } Point3D PlaneGeometry::ProjectPointOntoPlane(const Point3D &pt) const { ScalarType len = this->GetNormalVnl().two_norm(); return pt - this->GetNormal() * this->SignedDistanceFromPlane(pt) / len; } itk::LightObject::Pointer PlaneGeometry::InternalClone() const { Self::Pointer newGeometry = new PlaneGeometry(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } void PlaneGeometry::ExecuteOperation(Operation *operation) { vtkTransform *transform = vtkTransform::New(); transform->SetMatrix(this->GetVtkMatrix()); switch (operation->GetOperationType()) { case OpORIENT: { auto *planeOp = dynamic_cast(operation); if (planeOp == nullptr) { return; } Point3D center = planeOp->GetPoint(); Vector3D orientationVector = planeOp->GetNormal(); Vector3D defaultVector; FillVector3D(defaultVector, 0.0, 0.0, 1.0); Vector3D rotationAxis = itk::CrossProduct(orientationVector, defaultVector); // double rotationAngle = acos( orientationVector[2] / orientationVector.GetNorm() ); double rotationAngle = atan2((double)rotationAxis.GetNorm(), (double)(orientationVector * defaultVector)); rotationAngle *= 180.0 / vnl_math::pi; transform->PostMultiply(); transform->Identity(); transform->Translate(center[0], center[1], center[2]); transform->RotateWXYZ(rotationAngle, rotationAxis[0], rotationAxis[1], rotationAxis[2]); transform->Translate(-center[0], -center[1], -center[2]); break; } case OpRESTOREPLANEPOSITION: { auto *op = dynamic_cast(operation); if (op == nullptr) { return; } AffineTransform3D::Pointer transform2 = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(0)); matrix.GetVnlMatrix().set_column(1, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(1)); matrix.GetVnlMatrix().set_column(2, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(2)); transform2->SetMatrix(matrix); Vector3D offset = op->GetTransform()->GetOffset(); transform2->SetOffset(offset); this->SetIndexToWorldTransform(transform2); ScalarType bounds[6] = {0, op->GetWidth(), 0, op->GetHeight(), 0, 1}; this->SetBounds(bounds); this->Modified(); transform->Delete(); return; } default: Superclass::ExecuteOperation(operation); transform->Delete(); return; } this->SetVtkMatrixDeepCopy(transform); this->Modified(); transform->Delete(); } void PlaneGeometry::PrintSelf(std::ostream &os, itk::Indent indent) const { Superclass::PrintSelf(os, indent); os << indent << " ScaleFactorMMPerUnitX: " << GetExtentInMM(0) / GetExtent(0) << std::endl; os << indent << " ScaleFactorMMPerUnitY: " << GetExtentInMM(1) / GetExtent(1) << std::endl; os << indent << " Normal: " << GetNormal() << std::endl; } bool PlaneGeometry::Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const { assert(this->IsBoundingBoxNull() == false); Point3D pt3d_units; Superclass::WorldToIndex(pt3d_mm, pt3d_units); pt2d_mm[0] = pt3d_units[0] * GetExtentInMM(0) / GetExtent(0); pt2d_mm[1] = pt3d_units[1] * GetExtentInMM(1) / GetExtent(1); pt3d_units[2] = 0; return this->GetBoundingBox()->IsInside(pt3d_units); } void PlaneGeometry::Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const { // pt2d_mm is measured from the origin of the world geometry (at least it called form BaseRendere::Mouse...Event) Point3D pt3d_units; pt3d_units[0] = pt2d_mm[0] / (GetExtentInMM(0) / GetExtent(0)); pt3d_units[1] = pt2d_mm[1] / (GetExtentInMM(1) / GetExtent(1)); pt3d_units[2] = 0; // pt3d_units is a continuous index. We divided it with the Scale Factor (= spacing in x and y) to convert it from mm // to index units. // pt3d_mm = GetIndexToWorldTransform()->TransformPoint(pt3d_units); // now we convert the 3d index to a 3D world point in mm. We could have used IndexToWorld as well as // GetITW->Transform... } void PlaneGeometry::SetSizeInUnits(mitk::ScalarType width, mitk::ScalarType height) { ScalarType bounds[6] = {0, width, 0, height, 0, 1}; ScalarType extent, newextentInMM; if (GetExtent(0) > 0) { extent = GetExtent(0); if (width > extent) newextentInMM = GetExtentInMM(0) / width * extent; else newextentInMM = GetExtentInMM(0) * extent / width; SetExtentInMM(0, newextentInMM); } if (GetExtent(1) > 0) { extent = GetExtent(1); if (width > extent) newextentInMM = GetExtentInMM(1) / height * extent; else newextentInMM = GetExtentInMM(1) * extent / height; SetExtentInMM(1, newextentInMM); } SetBounds(bounds); } bool PlaneGeometry::Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const { assert(this->IsBoundingBoxNull() == false); Point3D pt3d_units; Superclass::WorldToIndex(pt3d_mm, pt3d_units); pt3d_units[2] = 0; projectedPt3d_mm = GetIndexToWorldTransform()->TransformPoint(pt3d_units); return this->GetBoundingBox()->IsInside(pt3d_units); } bool PlaneGeometry::Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { assert(this->IsBoundingBoxNull() == false); Vector3D vec3d_units; Superclass::WorldToIndex(vec3d_mm, vec3d_units); vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); return true; } bool PlaneGeometry::Project(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { MITK_WARN << "Deprecated function! Call Project(vec3D,vec3D) instead."; assert(this->IsBoundingBoxNull() == false); Vector3D vec3d_units; Superclass::WorldToIndex(atPt3d_mm, vec3d_mm, vec3d_units); vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); Point3D pt3d_units; Superclass::WorldToIndex(atPt3d_mm, pt3d_units); return this->GetBoundingBox()->IsInside(pt3d_units); } bool PlaneGeometry::Map(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const { Point2D pt2d_mm_start, pt2d_mm_end; Point3D pt3d_mm_end; bool inside = Map(atPt3d_mm, pt2d_mm_start); pt3d_mm_end = atPt3d_mm + vec3d_mm; inside &= Map(pt3d_mm_end, pt2d_mm_end); vec2d_mm = pt2d_mm_end - pt2d_mm_start; return inside; } void PlaneGeometry::Map(const mitk::Point2D & /*atPt2d_mm*/, const mitk::Vector2D & /*vec2d_mm*/, mitk::Vector3D & /*vec3d_mm*/) const { //@todo implement parallel to the other Map method! assert(false); } void PlaneGeometry::SetReferenceGeometry(const mitk::BaseGeometry *geometry) { m_ReferenceGeometry = geometry; } const mitk::BaseGeometry *PlaneGeometry::GetReferenceGeometry() const { return m_ReferenceGeometry; } bool PlaneGeometry::HasReferenceGeometry() const { return (m_ReferenceGeometry != nullptr); } } // namespace diff --git a/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp b/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp index 6e23ef32d9..d03779a6a1 100644 --- a/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp +++ b/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp @@ -1,962 +1,960 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include "mitkSlicedGeometry3D.h" #include "mitkAbstractTransformGeometry.h" #include "mitkApplyTransformMatrixOperation.h" #include "mitkInteractionConst.h" #include "mitkPlaneGeometry.h" #include "mitkPlaneOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkRotationOperation.h" #include "mitkSliceNavigationController.h" const mitk::ScalarType PI = 3.14159265359; mitk::SlicedGeometry3D::SlicedGeometry3D() : m_EvenlySpaced(true), m_Slices(0), m_ReferenceGeometry(nullptr), m_SliceNavigationController(nullptr) { m_DirectionVector.Fill(0); this->InitializeSlicedGeometry(m_Slices); } mitk::SlicedGeometry3D::SlicedGeometry3D(const SlicedGeometry3D &other) : Superclass(other), m_EvenlySpaced(other.m_EvenlySpaced), m_Slices(other.m_Slices), m_ReferenceGeometry(other.m_ReferenceGeometry), m_SliceNavigationController(other.m_SliceNavigationController) { m_DirectionVector.Fill(0); SetSpacing(other.GetSpacing()); SetDirectionVector(other.GetDirectionVector()); if (m_EvenlySpaced) { assert(!other.m_PlaneGeometries.empty() && "This may happen when you use one of the old Initialize methods, which had a bool parameter that is implicitly casted to the number of slices now."); PlaneGeometry::Pointer geometry = other.m_PlaneGeometries[0]->Clone(); assert(geometry.IsNotNull()); SetPlaneGeometry(geometry, 0); } else { unsigned int s; for (s = 0; s < other.m_Slices; ++s) { if (other.m_PlaneGeometries[s].IsNull()) { assert(other.m_EvenlySpaced); m_PlaneGeometries[s] = nullptr; } else { PlaneGeometry *geometry2D = other.m_PlaneGeometries[s]->Clone(); assert(geometry2D != nullptr); SetPlaneGeometry(geometry2D, s); } } } } mitk::SlicedGeometry3D::~SlicedGeometry3D() { } mitk::PlaneGeometry *mitk::SlicedGeometry3D::GetPlaneGeometry(int s) const { mitk::PlaneGeometry::Pointer geometry2D = nullptr; if (this->IsValidSlice(s)) { geometry2D = m_PlaneGeometries[s]; // If (a) m_EvenlySpaced==true, (b) we don't have a PlaneGeometry stored // for the requested slice, and (c) the first slice (s=0) // is a PlaneGeometry instance, then we calculate the geometry of the // requested as the plane of the first slice shifted by m_Spacing[2]*s // in the direction of m_DirectionVector. if ((m_EvenlySpaced) && (geometry2D.IsNull())) { PlaneGeometry *firstSlice = m_PlaneGeometries[0]; if (firstSlice != nullptr && dynamic_cast(m_PlaneGeometries[0].GetPointer()) == nullptr) { if ((m_DirectionVector[0] == 0.0) && (m_DirectionVector[1] == 0.0) && (m_DirectionVector[2] == 0.0)) { m_DirectionVector = firstSlice->GetNormal(); m_DirectionVector.Normalize(); } Vector3D direction; direction = m_DirectionVector * this->GetSpacing()[2]; mitk::PlaneGeometry::Pointer requestedslice; requestedslice = static_cast(firstSlice->Clone().GetPointer()); requestedslice->SetOrigin(requestedslice->GetOrigin() + direction * s); geometry2D = requestedslice; m_PlaneGeometries[s] = geometry2D; } } return geometry2D; } else { return nullptr; } } const mitk::BoundingBox *mitk::SlicedGeometry3D::GetBoundingBox() const { assert(this->IsBoundingBoxNull() == false); return Superclass::GetBoundingBox(); } bool mitk::SlicedGeometry3D::SetPlaneGeometry(mitk::PlaneGeometry *geometry2D, int s) { if (this->IsValidSlice(s)) { m_PlaneGeometries[s] = geometry2D; m_PlaneGeometries[s]->SetReferenceGeometry(m_ReferenceGeometry); return true; } return false; } void mitk::SlicedGeometry3D::InitializeSlicedGeometry(unsigned int slices) { Superclass::Initialize(); m_Slices = slices; PlaneGeometry::Pointer gnull = nullptr; m_PlaneGeometries.assign(m_Slices, gnull); Vector3D spacing; spacing.Fill(1.0); this->SetSpacing(spacing); m_DirectionVector.Fill(0); } void mitk::SlicedGeometry3D::InitializeEvenlySpaced(mitk::PlaneGeometry *geometry2D, unsigned int slices) { assert(geometry2D != nullptr); this->InitializeEvenlySpaced(geometry2D, geometry2D->GetExtentInMM(2) / geometry2D->GetExtent(2), slices); } void mitk::SlicedGeometry3D::InitializeEvenlySpaced(mitk::PlaneGeometry *geometry2D, mitk::ScalarType zSpacing, unsigned int slices) { assert(geometry2D != nullptr); assert(geometry2D->GetExtent(0) > 0); assert(geometry2D->GetExtent(1) > 0); geometry2D->Register(); Superclass::Initialize(); m_Slices = slices; BoundingBox::BoundsArrayType bounds = geometry2D->GetBounds(); bounds[4] = 0; bounds[5] = slices; // clear and reserve PlaneGeometry::Pointer gnull = nullptr; m_PlaneGeometries.assign(m_Slices, gnull); Vector3D directionVector = geometry2D->GetAxisVector(2); directionVector.Normalize(); directionVector *= zSpacing; // Normally we should use the following four lines to create a copy of // the transform contained in geometry2D, because it may not be changed // by us. But we know that SetSpacing creates a new transform without // changing the old (coming from geometry2D), so we can use the fifth // line instead. We check this at (**). // // AffineTransform3D::Pointer transform = AffineTransform3D::New(); // transform->SetMatrix(geometry2D->GetIndexToWorldTransform()->GetMatrix()); // transform->SetOffset(geometry2D->GetIndexToWorldTransform()->GetOffset()); // SetIndexToWorldTransform(transform); this->SetIndexToWorldTransform(geometry2D->GetIndexToWorldTransform()); mitk::Vector3D spacing; FillVector3D(spacing, geometry2D->GetExtentInMM(0) / bounds[1], geometry2D->GetExtentInMM(1) / bounds[3], zSpacing); this->SetDirectionVector(directionVector); this->SetBounds(bounds); this->SetPlaneGeometry(geometry2D, 0); this->SetSpacing(spacing, true); this->SetEvenlySpaced(); // this->SetTimeBounds( geometry2D->GetTimeBounds() ); assert(this->GetIndexToWorldTransform() != geometry2D->GetIndexToWorldTransform()); // (**) see above. this->SetFrameOfReferenceID(geometry2D->GetFrameOfReferenceID()); this->SetImageGeometry(geometry2D->GetImageGeometry()); geometry2D->UnRegister(); } void mitk::SlicedGeometry3D::InitializePlanes(const mitk::BaseGeometry *geometry3D, mitk::AnatomicalPlane orientation, bool top, bool frontside, bool rotated) { m_ReferenceGeometry = geometry3D; PlaneGeometry::Pointer planeGeometry = mitk::PlaneGeometry::New(); planeGeometry->InitializeStandardPlane(geometry3D, top, orientation, frontside, rotated); int worldAxis = orientation == AnatomicalPlane::Sagittal ? 0 : orientation == AnatomicalPlane::Coronal ? 1 : 2; - // Inspired by: - // http://www.na-mic.org/Wiki/index.php/Coordinate_System_Conversion_Between_ITK_and_Slicer3 + int axes[3]; + geometry3D->MapAxesToOrientations(axes); + int axis = axes[worldAxis]; - mitk::AffineTransform3D::MatrixType matrix = geometry3D->GetIndexToWorldTransform()->GetMatrix(); - matrix.GetVnlMatrix().normalize_columns(); - mitk::AffineTransform3D::MatrixType::InternalMatrixType inverseMatrix = matrix.GetTranspose(); - - int dominantAxis = planeGeometry->CalculateDominantAxes(inverseMatrix).at(worldAxis); - ScalarType viewSpacing = geometry3D->GetSpacing()[dominantAxis]; - - /// Although the double value returned by GetExtent() holds a round number, - /// you need to add 0.5 to safely convert it to unsigned it. I have seen a - /// case when the result was less by one without this. - auto slices = static_cast(geometry3D->GetExtent(dominantAxis) + 0.5); - if ( slices == 0 && geometry3D->GetExtent(dominantAxis) > 0) { - // require at least one slice if there is _some_ extent - slices = 1; + ScalarType viewSpacing = geometry3D->GetSpacing()[axis]; + unsigned int slices = static_cast(geometry3D->GetExtent(axis) + 0.5); + + if (slices == 0 && geometry3D->GetExtent(axis) > 0) + { + // require at least one slice if there is _some_ extent + slices = 1; } #ifndef NDEBUG - int upDirection = itk::Function::Sign(inverseMatrix[dominantAxis][worldAxis]); + auto matrix = geometry3D->GetIndexToWorldTransform()->GetMatrix(); + matrix.GetVnlMatrix().normalize_columns(); + auto inverseMatrix = matrix.GetInverse(); + + int upDirection = itk::Function::Sign(inverseMatrix[axis][worldAxis]); /// The normal vector of an imaginary plane that points from the world origin (bottom left back /// corner or the world, with the lowest physical coordinates) towards the inside of the volume, /// along the renderer axis. Length is the slice thickness. - Vector3D worldPlaneNormal = inverseMatrix.get_row(dominantAxis) * (upDirection * viewSpacing); + Vector3D worldPlaneNormal = inverseMatrix.get_row(axis) * (upDirection * viewSpacing); /// The normal of the standard plane geometry just created. Vector3D standardPlaneNormal = planeGeometry->GetNormal(); /// The standard plane must be parallel to the 'world plane'. The normal of the standard plane /// must point against the world plane if and only if 'top' is 'false'. The length of the /// standard plane normal must be equal to the slice thickness. assert((standardPlaneNormal - (top ? 1.0 : -1.0) * worldPlaneNormal).GetSquaredNorm() < 0.000001); #endif this->InitializeEvenlySpaced(planeGeometry, viewSpacing, slices); #ifndef NDEBUG /// The standard plane normal and the z axis vector of the sliced geometry must point in /// the same direction. Vector3D zAxisVector = this->GetAxisVector(2); Vector3D upscaledStandardPlaneNormal = standardPlaneNormal; upscaledStandardPlaneNormal *= slices; assert((zAxisVector - upscaledStandardPlaneNormal).GetSquaredNorm() < 0.000001); /// You can use this test is to check the handedness of the coordinate system of the current /// geometry. In principle, you can use either left- or right-handed coordinate systems, but /// you normally want it to be consistent, that is the handedness should be the same across /// the renderers of the same viewer. // ScalarType det = vnl_det(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix()); // MITK_DEBUG << "world axis: " << worldAxis << (det > 0 ? " ; right-handed" : " ; left-handed"); #endif } void mitk::SlicedGeometry3D::ReinitializePlanes(const Point3D ¢er, const Point3D &referencePoint) { // Need a reference frame to align the rotated planes if (!m_ReferenceGeometry) { return; } // Get first plane of plane stack PlaneGeometry *firstPlane = m_PlaneGeometries[0]; // If plane stack is empty, exit if (!firstPlane || dynamic_cast(firstPlane)) { return; } // Calculate the "directed" spacing when taking the plane (defined by its axes // vectors and normal) as the reference coordinate frame. // // This is done by calculating the radius of the ellipsoid defined by the // original volume spacing axes, in the direction of the respective axis of the // reference frame. mitk::Vector3D axis0 = firstPlane->GetAxisVector(0); mitk::Vector3D axis1 = firstPlane->GetAxisVector(1); mitk::Vector3D normal = firstPlane->GetNormal(); normal.Normalize(); Vector3D spacing; spacing[0] = this->CalculateSpacing(axis0); spacing[1] = this->CalculateSpacing(axis1); spacing[2] = this->CalculateSpacing(normal); Superclass::SetSpacing(spacing); // Now we need to calculate the number of slices in the plane's normal // direction, so that the entire volume is covered. This is done by first // calculating the dot product between the volume diagonal (the maximum // distance inside the volume) and the normal, and dividing this value by // the directed spacing calculated above. ScalarType directedExtent = std::abs(m_ReferenceGeometry->GetExtentInMM(0) * normal[0]) + std::abs(m_ReferenceGeometry->GetExtentInMM(1) * normal[1]) + std::abs(m_ReferenceGeometry->GetExtentInMM(2) * normal[2]); if (directedExtent >= spacing[2]) { m_Slices = static_cast(directedExtent / spacing[2] + 0.5); } else { m_Slices = 1; } // The origin of our "first plane" needs to be adapted to this new extent. // To achieve this, we first calculate the current distance to the volume's // center, and then shift the origin in the direction of the normal by the // difference between this distance and half of the new extent. double centerOfRotationDistance = firstPlane->SignedDistanceFromPlane(center); if (centerOfRotationDistance > 0) { firstPlane->SetOrigin(firstPlane->GetOrigin() + normal * (centerOfRotationDistance - directedExtent / 2.0)); m_DirectionVector = normal; } else { firstPlane->SetOrigin(firstPlane->GetOrigin() + normal * (directedExtent / 2.0 + centerOfRotationDistance)); m_DirectionVector = -normal; } // Now we adjust this distance according with respect to the given reference // point: we need to make sure that the point is touched by one slice of the // new slice stack. double referencePointDistance = firstPlane->SignedDistanceFromPlane(referencePoint); auto referencePointSlice = static_cast(referencePointDistance / spacing[2]); double alignmentValue = referencePointDistance / spacing[2] - referencePointSlice; firstPlane->SetOrigin(firstPlane->GetOrigin() + normal * alignmentValue * spacing[2]); // Finally, we can clear the previous geometry stack and initialize it with // our re-initialized "first plane". m_PlaneGeometries.assign(m_Slices, PlaneGeometry::Pointer(nullptr)); if (m_Slices > 0) { m_PlaneGeometries[0] = firstPlane; } // Reinitialize SNC with new number of slices m_SliceNavigationController->GetStepper()->SetSteps(m_Slices); this->Modified(); } double mitk::SlicedGeometry3D::CalculateSpacing(const mitk::Vector3D &d) const { // Need the spacing of the underlying dataset / geometry if (!m_ReferenceGeometry) { return 1.0; } const mitk::Vector3D &spacing = m_ReferenceGeometry->GetSpacing(); return SlicedGeometry3D::CalculateSpacing(spacing, d); } double mitk::SlicedGeometry3D::CalculateSpacing(const mitk::Vector3D &spacing, const mitk::Vector3D &d) { // The following can be derived from the ellipsoid equation // // 1 = x^2/a^2 + y^2/b^2 + z^2/c^2 // // where (a,b,c) = spacing of original volume (ellipsoid radii) // and (x,y,z) = scaled coordinates of vector d (according to ellipsoid) // double scaling = d[0] * d[0] / (spacing[0] * spacing[0]) + d[1] * d[1] / (spacing[1] * spacing[1]) + d[2] * d[2] / (spacing[2] * spacing[2]); scaling = sqrt(scaling); return (sqrt(d[0] * d[0] + d[1] * d[1] + d[2] * d[2]) / scaling); } mitk::Vector3D mitk::SlicedGeometry3D::AdjustNormal(const mitk::Vector3D &normal) const { TransformType::Pointer inverse = TransformType::New(); m_ReferenceGeometry->GetIndexToWorldTransform()->GetInverse(inverse); Vector3D transformedNormal = inverse->TransformVector(normal); transformedNormal.Normalize(); return transformedNormal; } void mitk::SlicedGeometry3D::SetImageGeometry(const bool isAnImageGeometry) { Superclass::SetImageGeometry(isAnImageGeometry); unsigned int s; for (s = 0; s < m_Slices; ++s) { mitk::BaseGeometry *geometry = m_PlaneGeometries[s]; if (geometry != nullptr) { geometry->SetImageGeometry(isAnImageGeometry); } } } void mitk::SlicedGeometry3D::ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry) { unsigned int s; for (s = 0; s < m_Slices; ++s) { mitk::BaseGeometry *geometry = m_PlaneGeometries[s]; if (geometry != nullptr) { geometry->ChangeImageGeometryConsideringOriginOffset(isAnImageGeometry); } } Superclass::ChangeImageGeometryConsideringOriginOffset(isAnImageGeometry); } bool mitk::SlicedGeometry3D::IsValidSlice(int s) const { return ((s >= 0) && (s < (int)m_Slices)); } const mitk::BaseGeometry *mitk::SlicedGeometry3D::GetReferenceGeometry() const { return m_ReferenceGeometry; } void mitk::SlicedGeometry3D::SetReferenceGeometry(const BaseGeometry *referenceGeometry) { m_ReferenceGeometry = referenceGeometry; std::vector::iterator it; for (it = m_PlaneGeometries.begin(); it != m_PlaneGeometries.end(); ++it) { (*it)->SetReferenceGeometry(referenceGeometry); } } bool mitk::SlicedGeometry3D::HasReferenceGeometry() const { return ( m_ReferenceGeometry != nullptr ); } void mitk::SlicedGeometry3D::PreSetSpacing(const mitk::Vector3D &aSpacing) { bool hasEvenlySpacedPlaneGeometry = false; mitk::Point3D origin; mitk::Vector3D rightDV, bottomDV; BoundingBox::BoundsArrayType bounds; // Check for valid spacing if (!(aSpacing[0] > 0 && aSpacing[1] > 0 && aSpacing[2] > 0)) { mitkThrow() << "You try to set a spacing with at least one element equal or " "smaller to \"0\". This might lead to a crash during rendering. Please double" " check your data!"; } // In case of evenly-spaced data: re-initialize instances of PlaneGeometry, // since the spacing influences them if ((m_EvenlySpaced) && (m_PlaneGeometries.size() > 0)) { const PlaneGeometry *planeGeometry = m_PlaneGeometries[0]; if (planeGeometry && !dynamic_cast(planeGeometry)) { this->WorldToIndex(planeGeometry->GetOrigin(), origin); this->WorldToIndex(planeGeometry->GetAxisVector(0), rightDV); this->WorldToIndex(planeGeometry->GetAxisVector(1), bottomDV); bounds = planeGeometry->GetBounds(); hasEvenlySpacedPlaneGeometry = true; } } BaseGeometry::_SetSpacing(aSpacing); mitk::PlaneGeometry::Pointer firstGeometry; // In case of evenly-spaced data: re-initialize instances of PlaneGeometry, // since the spacing influences them if (hasEvenlySpacedPlaneGeometry) { // create planeGeometry according to new spacing this->IndexToWorld(origin, origin); this->IndexToWorld(rightDV, rightDV); this->IndexToWorld(bottomDV, bottomDV); mitk::PlaneGeometry::Pointer planeGeometry = mitk::PlaneGeometry::New(); planeGeometry->SetImageGeometry(this->GetImageGeometry()); planeGeometry->SetReferenceGeometry(m_ReferenceGeometry); // Store spacing, as Initialize... needs a pointer mitk::Vector3D lokalSpacing = this->GetSpacing(); planeGeometry->InitializeStandardPlane(rightDV.GetVnlVector(), bottomDV.GetVnlVector(), &lokalSpacing); planeGeometry->SetOrigin(origin); planeGeometry->SetBounds(bounds); firstGeometry = planeGeometry; } else if ((m_EvenlySpaced) && (m_PlaneGeometries.size() > 0)) { firstGeometry = m_PlaneGeometries[0].GetPointer(); } // clear and reserve PlaneGeometry::Pointer gnull = nullptr; m_PlaneGeometries.assign(m_Slices, gnull); if (m_Slices > 0) { m_PlaneGeometries[0] = firstGeometry; } this->Modified(); } void mitk::SlicedGeometry3D::SetSliceNavigationController(SliceNavigationController *snc) { m_SliceNavigationController = snc; } mitk::SliceNavigationController *mitk::SlicedGeometry3D::GetSliceNavigationController() { return m_SliceNavigationController; } void mitk::SlicedGeometry3D::SetEvenlySpaced(bool on) { if (m_EvenlySpaced != on) { m_EvenlySpaced = on; this->Modified(); } } void mitk::SlicedGeometry3D::SetDirectionVector(const mitk::Vector3D &directionVector) { Vector3D newDir = directionVector; newDir.Normalize(); if (newDir != m_DirectionVector) { m_DirectionVector = newDir; this->Modified(); } } // void // mitk::SlicedGeometry3D::SetTimeBounds( const mitk::TimeBounds& timebounds ) //{ // Superclass::SetTimeBounds( timebounds ); // // unsigned int s; // for ( s = 0; s < m_Slices; ++s ) // { // if(m_Geometry2Ds[s].IsNotNull()) // { // m_Geometry2Ds[s]->SetTimeBounds( timebounds ); // } // } // m_TimeBounds = timebounds; //} itk::LightObject::Pointer mitk::SlicedGeometry3D::InternalClone() const { Self::Pointer newGeometry = new SlicedGeometry3D(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } void mitk::SlicedGeometry3D::PrintSelf(std::ostream &os, itk::Indent indent) const { Superclass::PrintSelf(os, indent); os << indent << " EvenlySpaced: " << m_EvenlySpaced << std::endl; if (m_EvenlySpaced) { os << indent << " DirectionVector: " << m_DirectionVector << std::endl; } os << indent << " Slices: " << m_Slices << std::endl; os << std::endl; os << indent << " GetPlaneGeometry(0): "; if (this->GetPlaneGeometry(0) == nullptr) { os << "nullptr" << std::endl; } else { this->GetPlaneGeometry(0)->Print(os, indent); } } void mitk::SlicedGeometry3D::ExecuteOperation(Operation *operation) { PlaneGeometry::Pointer geometry2D; ApplyTransformMatrixOperation *applyMatrixOp; Point3D center; switch (operation->GetOperationType()) { case OpNOTHING: break; case OpROTATE: if (m_EvenlySpaced) { // Need a reference frame to align the rotation if (m_ReferenceGeometry) { // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // Save first slice PlaneGeometry::Pointer geometry2D = m_PlaneGeometries[0]; auto *rotOp = dynamic_cast(operation); // Generate a RotationOperation using the dataset center instead of // the supplied rotation center. This is necessary so that the rotated // zero-plane does not shift away. The supplied center is instead used // to adjust the slice stack afterwards. Point3D center = m_ReferenceGeometry->GetCenter(); RotationOperation centeredRotation( rotOp->GetOperationType(), center, rotOp->GetVectorOfRotation(), rotOp->GetAngleOfRotation()); // Rotate first slice geometry2D->ExecuteOperation(¢eredRotation); // Clear the slice stack and adjust it according to the center of // the dataset and the supplied rotation center (see documentation of // ReinitializePlanes) this->ReinitializePlanes(center, rotOp->GetCenterOfRotation()); geometry2D->SetSpacing(this->GetSpacing()); if (m_SliceNavigationController) { m_SliceNavigationController->SelectSliceByPoint(rotOp->GetCenterOfRotation()); m_SliceNavigationController->AdjustSliceStepperRange(); } BaseGeometry::ExecuteOperation(¢eredRotation); } else { // we also have to consider the case, that there is no reference geometry available. if (m_PlaneGeometries.size() > 0) { // Reach through to all slices in my container for (auto iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { // Test for empty slices, which can happen if evenly spaced geometry if ((*iter).IsNotNull()) { (*iter)->ExecuteOperation(operation); } } // rotate overall geometry auto *rotOp = dynamic_cast(operation); BaseGeometry::ExecuteOperation(rotOp); } } } else { // Reach through to all slices for (auto iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpORIENT: if (m_EvenlySpaced) { // get operation data auto *planeOp = dynamic_cast(operation); // Get first slice PlaneGeometry::Pointer planeGeometry = m_PlaneGeometries[0]; // Need a PlaneGeometry, a PlaneOperation and a reference frame to // carry out the re-orientation. If not all available, stop here if (!m_ReferenceGeometry || (!planeGeometry || dynamic_cast(planeGeometry.GetPointer())) || !planeOp) { break; } // General Behavior: // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // // 1st Step: Reorient Normal Vector of first plane // Point3D center = planeOp->GetPoint(); // m_ReferenceGeometry->GetCenter(); mitk::Vector3D currentNormal = planeGeometry->GetNormal(); mitk::Vector3D newNormal; if (planeOp->AreAxisDefined()) { // If planeOp was defined by one centerpoint and two axis vectors newNormal = CrossProduct(planeOp->GetAxisVec0(), planeOp->GetAxisVec1()); } else { // If planeOp was defined by one centerpoint and one normal vector newNormal = planeOp->GetNormal(); } // Get Rotation axis und angle currentNormal.Normalize(); newNormal.Normalize(); ScalarType rotationAngle = angle(currentNormal.GetVnlVector(), newNormal.GetVnlVector()); rotationAngle *= 180.0 / vnl_math::pi; // from rad to deg Vector3D rotationAxis = itk::CrossProduct(currentNormal, newNormal); if (std::abs(rotationAngle - 180) < mitk::eps) { // current Normal and desired normal are not linear independent!!(e.g 1,0,0 and -1,0,0). // Rotation Axis should be ANY vector that is 90� to current Normal mitk::Vector3D helpNormal; helpNormal = currentNormal; helpNormal[0] += 1; helpNormal[1] -= 1; helpNormal[2] += 1; helpNormal.Normalize(); rotationAxis = itk::CrossProduct(helpNormal, currentNormal); } RotationOperation centeredRotation(mitk::OpROTATE, center, rotationAxis, rotationAngle); // Rotate first slice planeGeometry->ExecuteOperation(¢eredRotation); // Reinitialize planes and select slice, if my rotations are all done. if (!planeOp->AreAxisDefined()) { // Clear the slice stack and adjust it according to the center of // rotation and plane position (see documentation of ReinitializePlanes) this->ReinitializePlanes(center, planeOp->GetPoint()); planeGeometry->SetSpacing(this->GetSpacing()); if (m_SliceNavigationController) { m_SliceNavigationController->SelectSliceByPoint(planeOp->GetPoint()); m_SliceNavigationController->AdjustSliceStepperRange(); } } // Also apply rotation on the slicedGeometry - Geometry3D (Bounding geometry) BaseGeometry::ExecuteOperation(¢eredRotation); // // 2nd step. If axis vectors were defined, rotate the plane around its normal to fit these // if (planeOp->AreAxisDefined()) { mitk::Vector3D vecAxixNew = planeOp->GetAxisVec0(); vecAxixNew.Normalize(); mitk::Vector3D VecAxisCurr = planeGeometry->GetAxisVector(0); VecAxisCurr.Normalize(); ScalarType rotationAngle = angle(VecAxisCurr.GetVnlVector(), vecAxixNew.GetVnlVector()); rotationAngle = rotationAngle * 180 / PI; // Rad to Deg // we rotate around the normal of the plane, but we do not know, if we need to rotate clockwise // or anti-clockwise. So we rotate around the crossproduct of old and new Axisvector. // Since both axis vectors lie in the plane, the crossproduct is the planes normal or the negative planes // normal rotationAxis = itk::CrossProduct(VecAxisCurr, vecAxixNew); if (std::abs(rotationAngle - 180) < mitk::eps) { // current axisVec and desired axisVec are not linear independent!!(e.g 1,0,0 and -1,0,0). // Rotation Axis can be just plane Normal. (have to rotate by 180�) rotationAxis = newNormal; } // Perform Rotation mitk::RotationOperation op(mitk::OpROTATE, center, rotationAxis, rotationAngle); planeGeometry->ExecuteOperation(&op); // Apply changes on first slice to whole slice stack this->ReinitializePlanes(center, planeOp->GetPoint()); planeGeometry->SetSpacing(this->GetSpacing()); if (m_SliceNavigationController) { m_SliceNavigationController->SelectSliceByPoint(planeOp->GetPoint()); m_SliceNavigationController->AdjustSliceStepperRange(); } // Also apply rotation on the slicedGeometry - Geometry3D (Bounding geometry) BaseGeometry::ExecuteOperation(&op); } } else { // Reach through to all slices for (auto iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpRESTOREPLANEPOSITION: if (m_EvenlySpaced) { // Save first slice PlaneGeometry::Pointer planeGeometry = m_PlaneGeometries[0]; auto *restorePlaneOp = dynamic_cast(operation); // Need a PlaneGeometry, a PlaneOperation and a reference frame to // carry out the re-orientation if (m_ReferenceGeometry && (planeGeometry && dynamic_cast(planeGeometry.GetPointer()) == nullptr) && restorePlaneOp) { // Clear all generated geometries and then rotate only the first slice. // The other slices will be re-generated on demand // Rotate first slice planeGeometry->ExecuteOperation(restorePlaneOp); m_DirectionVector = restorePlaneOp->GetDirectionVector(); double centerOfRotationDistance = planeGeometry->SignedDistanceFromPlane(m_ReferenceGeometry->GetCenter()); if (centerOfRotationDistance <= 0) { m_DirectionVector = -m_DirectionVector; } Vector3D spacing = restorePlaneOp->GetSpacing(); Superclass::SetSpacing(spacing); // /*Now we need to calculate the number of slices in the plane's normal // direction, so that the entire volume is covered. This is done by first // calculating the dot product between the volume diagonal (the maximum // distance inside the volume) and the normal, and dividing this value by // the directed spacing calculated above.*/ ScalarType directedExtent = std::abs(m_ReferenceGeometry->GetExtentInMM(0) * m_DirectionVector[0]) + std::abs(m_ReferenceGeometry->GetExtentInMM(1) * m_DirectionVector[1]) + std::abs(m_ReferenceGeometry->GetExtentInMM(2) * m_DirectionVector[2]); if (directedExtent >= spacing[2]) { m_Slices = static_cast(directedExtent / spacing[2] + 0.5); } else { m_Slices = 1; } m_PlaneGeometries.assign(m_Slices, PlaneGeometry::Pointer(nullptr)); if (m_Slices > 0) { m_PlaneGeometries[0] = planeGeometry; } m_SliceNavigationController->GetStepper()->SetSteps(m_Slices); this->Modified(); // End Reinitialization if (m_SliceNavigationController) { m_SliceNavigationController->GetStepper()->SetPos(restorePlaneOp->GetPos()); m_SliceNavigationController->AdjustSliceStepperRange(); } BaseGeometry::ExecuteOperation(restorePlaneOp); } } else { // Reach through to all slices for (auto iter = m_PlaneGeometries.begin(); iter != m_PlaneGeometries.end(); ++iter) { (*iter)->ExecuteOperation(operation); } } break; case OpAPPLYTRANSFORMMATRIX: // Clear all generated geometries and then transform only the first slice. // The other slices will be re-generated on demand // Save first slice geometry2D = m_PlaneGeometries[0]; applyMatrixOp = dynamic_cast(operation); // Apply transformation to first plane geometry2D->ExecuteOperation(applyMatrixOp); // Generate a ApplyTransformMatrixOperation using the dataset center instead of // the supplied rotation center. The supplied center is instead used to adjust the // slice stack afterwards (see OpROTATE). center = m_ReferenceGeometry->GetCenter(); // Clear the slice stack and adjust it according to the center of // the dataset and the supplied rotation center (see documentation of // ReinitializePlanes) this->ReinitializePlanes(center, applyMatrixOp->GetReferencePoint()); BaseGeometry::ExecuteOperation(applyMatrixOp); break; default: // let handle by base class if we don't do anything BaseGeometry::ExecuteOperation(operation); } this->Modified(); } diff --git a/Modules/Core/test/mitkPlaneGeometryTest.cpp b/Modules/Core/test/mitkPlaneGeometryTest.cpp index e64ebc6e26..737222fc05 100644 --- a/Modules/Core/test/mitkPlaneGeometryTest.cpp +++ b/Modules/Core/test/mitkPlaneGeometryTest.cpp @@ -1,1093 +1,1084 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkAffineTransform3D.h" #include "mitkBaseGeometry.h" #include "mitkGeometry3D.h" #include "mitkInteractionConst.h" #include "mitkLine.h" #include "mitkPlaneGeometry.h" #include "mitkRotationOperation.h" #include "mitkSlicedGeometry3D.h" #include "mitkThinPlateSplineCurvedGeometry.h" #include #include #include #include #include #include #include #include static const mitk::ScalarType testEps = 1E-9; // the epsilon used in this test == at least float precision. class mitkPlaneGeometryTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkPlaneGeometryTestSuite); MITK_TEST(TestInitializeStandardPlane); MITK_TEST(TestProjectPointOntoPlane); MITK_TEST(TestPlaneGeometryCloning); MITK_TEST(TestInheritance); MITK_TEST(TestSetExtendInMM); MITK_TEST(TestRotate); MITK_TEST(TestClone); MITK_TEST(TestPlaneComparison); MITK_TEST(TestAxialInitialization); MITK_TEST(TestCoronalInitialization); MITK_TEST(TestSagittalInitialization); MITK_TEST(TestLefthandedCoordinateSystem); - MITK_TEST(TestDominantAxesError); MITK_TEST(TestCheckRotationMatrix); // Currently commented out, see See bug 15990 // MITK_TEST(testPlaneGeometryInitializeOrder); MITK_TEST(TestIntersectionPoint); MITK_TEST(TestCase1210); CPPUNIT_TEST_SUITE_END(); private: // private test members that are initialized by setUp() mitk::PlaneGeometry::Pointer planegeometry; mitk::Point3D origin; mitk::Vector3D right, bottom, normal, spacing; mitk::ScalarType width, height; mitk::ScalarType widthInMM, heightInMM, thicknessInMM; public: void setUp() override { planegeometry = mitk::PlaneGeometry::New(); width = 100; widthInMM = width; height = 200; heightInMM = height; thicknessInMM = 1.0; mitk::FillVector3D(origin, 4.5, 7.3, 11.2); mitk::FillVector3D(right, widthInMM, 0, 0); mitk::FillVector3D(bottom, 0, heightInMM, 0); mitk::FillVector3D(normal, 0, 0, thicknessInMM); mitk::FillVector3D(spacing, 1.0, 1.0, thicknessInMM); planegeometry->InitializeStandardPlane(right, bottom); planegeometry->SetOrigin(origin); planegeometry->SetSpacing(spacing); } void tearDown() override {} // This test verifies inheritance behaviour, this test will fail if the behaviour changes in the future void TestInheritance() { mitk::PlaneGeometry::Pointer plane = mitk::PlaneGeometry::New(); mitk::Geometry3D::Pointer g3d = dynamic_cast(plane.GetPointer()); CPPUNIT_ASSERT_MESSAGE("Planegeometry should not be castable to Geometry 3D", g3d.IsNull()); mitk::BaseGeometry::Pointer base = dynamic_cast(plane.GetPointer()); CPPUNIT_ASSERT_MESSAGE("Planegeometry should be castable to BaseGeometry", base.IsNotNull()); g3d = mitk::Geometry3D::New(); base = dynamic_cast(g3d.GetPointer()); CPPUNIT_ASSERT_MESSAGE("Geometry3D should be castable to BaseGeometry", base.IsNotNull()); mitk::SlicedGeometry3D::Pointer sliced = mitk::SlicedGeometry3D::New(); g3d = dynamic_cast(sliced.GetPointer()); CPPUNIT_ASSERT_MESSAGE("SlicedGeometry3D should not be castable to Geometry3D", g3d.IsNull()); mitk::ThinPlateSplineCurvedGeometry::Pointer thin = mitk::ThinPlateSplineCurvedGeometry::New(); plane = dynamic_cast(thin.GetPointer()); CPPUNIT_ASSERT_MESSAGE("AbstractTransformGeometry should be castable to PlaneGeometry", plane.IsNotNull()); plane = mitk::PlaneGeometry::New(); mitk::AbstractTransformGeometry::Pointer atg = dynamic_cast(plane.GetPointer()); CPPUNIT_ASSERT_MESSAGE("PlaneGeometry should not be castable to AbstractTransofrmGeometry", atg.IsNull()); } - void TestDominantAxesError() - { - auto image = mitk::IOUtil::Load(GetTestDataFilePath("NotQuiteARotationMatrix.nrrd")); - auto matrix = image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().transpose(); - std::vector< int > axes = mitk::PlaneGeometry::CalculateDominantAxes(matrix); - CPPUNIT_ASSERT_MESSAGE("Domiant axes cannot be determined in this dataset. Output should be default ordering.", axes.at(0)==0 && axes.at(1)==1 && axes.at(2)==2); - } - void TestCheckRotationMatrix() { auto image = mitk::IOUtil::Load(GetTestDataFilePath("NotQuiteARotationMatrix.nrrd")); bool is_rotation = mitk::PlaneGeometry::CheckRotationMatrix(image->GetGeometry()->GetIndexToWorldTransform(), 1e-8); CPPUNIT_ASSERT_MESSAGE("Since the test data matrix is not quite a rotation matrix, this should be detected.", !is_rotation); } void TestLefthandedCoordinateSystem() { /** * @brief This method tests InitializeStandardPlane() and IndexToWorld() * with a left-handed coordinate orientation or indexToWorldMatrix. * * Of course this test does not use standard Parameters, which are right-handed. * See also discussion of bug #11477: https://phabricator.mitk.org/T11477 */ planegeometry = mitk::PlaneGeometry::New(); width = 100; widthInMM = 5; height = 200; heightInMM = 3; thicknessInMM = 1.0; mitk::FillVector3D(right, widthInMM, 0, 0); mitk::FillVector3D(bottom, 0, heightInMM, 0); // This one negative sign results in lefthanded coordinate orientation and det(matrix) < 0. mitk::FillVector3D(normal, 0, 0, -thicknessInMM); mitk::AffineTransform3D::Pointer transform = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix; mitk::AffineTransform3D::MatrixType::InternalMatrixType &vnl_matrix = matrix.GetVnlMatrix(); vnl_matrix.set_column(0, right); vnl_matrix.set_column(1, bottom); vnl_matrix.set_column(2, normal); // making sure that we didn't screw up this special test case or else fail deadly: assert(vnl_determinant(vnl_matrix) < 0.0); transform->SetIdentity(); transform->SetMatrix(matrix); planegeometry->InitializeStandardPlane(width, height, transform); // Crux of the matter. CPPUNIT_ASSERT_MESSAGE( "Testing if IndexToWorldMatrix is correct after InitializeStandardPlane( width, height, transform ) ", mitk::MatrixEqualElementWise(planegeometry->GetIndexToWorldTransform()->GetMatrix(), matrix)); mitk::Point3D p_index; p_index[0] = 10.; p_index[1] = 10.; p_index[2] = 0.; mitk::Point3D p_world; mitk::Point3D p_expectedResult; p_expectedResult[0] = 50.; p_expectedResult[1] = 30.; p_expectedResult[2] = 0.; ((mitk::BaseGeometry::Pointer)planegeometry)->IndexToWorld(p_index, p_world); // Crux of the matter. CPPUNIT_ASSERT_MESSAGE("Testing if IndexToWorld(a,b) function works correctly with lefthanded matrix ", mitk::Equal(p_world, p_expectedResult, testEps)); } // See bug 1210 // Test does not use standard Parameters void TestCase1210() { mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); mitk::Point3D origin; mitk::Vector3D right, down, spacing; mitk::FillVector3D(origin, 4.5, 7.3, 11.2); mitk::FillVector3D(right, 1.015625, 1.015625, 1.1999969482421875); mitk::FillVector3D(down, 1.4012984643248170709237295832899161312802619418765e-45, 0, 0); mitk::FillVector3D(spacing, 0, 1.4713633875410579244699160624544119378442750389703e-43, 9.2806360452222355258639080851310540729807238879469e-32); std::cout << "Testing InitializeStandardPlane(rightVector, downVector, spacing = nullptr): " << std::endl; CPPUNIT_ASSERT_NO_THROW(planegeometry->InitializeStandardPlane(right, down, &spacing)); /* std::cout << "Testing width, height and thickness (in units): "; if((mitk::Equal(planegeometry->GetExtent(0),width)==false) || (mitk::Equal(planegeometry->GetExtent(1),height)==false) || (mitk::Equal(planegeometry->GetExtent(2),1)==false) ) { std::cout<<"[FAILED]"<GetExtentInMM(0),widthInMM)==false) || (mitk::Equal(planegeometry->GetExtentInMM(1),heightInMM)==false) || (mitk::Equal(planegeometry->GetExtentInMM(2),thicknessInMM)==false) ) { std::cout<<"[FAILED]"< 0. * */ // Test does not use standard Parameters void TestIntersectionPoint() { // init plane with its parameter mitk::PlaneGeometry::Pointer myPlaneGeometry = mitk::PlaneGeometry::New(); mitk::Point3D origin; origin[0] = 0.0; origin[1] = 2.0; origin[2] = 0.0; mitk::Vector3D normal; normal[0] = 0.0; normal[1] = 1.0; normal[2] = 0.0; myPlaneGeometry->InitializePlane(origin, normal); // generate points and line for intersection testing // point distance of given line > 1 mitk::Point3D pointP1; pointP1[0] = 2.0; pointP1[1] = 1.0; pointP1[2] = 0.0; mitk::Point3D pointP2; pointP2[0] = 2.0; pointP2[1] = 4.0; pointP2[2] = 0.0; mitk::Vector3D lineDirection; lineDirection[0] = pointP2[0] - pointP1[0]; lineDirection[1] = pointP2[1] - pointP1[1]; lineDirection[2] = pointP2[2] - pointP1[2]; mitk::Line3D xingline(pointP1, lineDirection); mitk::Point3D calcXingPoint; myPlaneGeometry->IntersectionPoint(xingline, calcXingPoint); // point distance of given line < 1 mitk::Point3D pointP3; pointP3[0] = 2.0; pointP3[1] = 2.2; pointP3[2] = 0.0; mitk::Point3D pointP4; pointP4[0] = 2.0; pointP4[1] = 1.7; pointP4[2] = 0.0; mitk::Vector3D lineDirection2; lineDirection2[0] = pointP4[0] - pointP3[0]; lineDirection2[1] = pointP4[1] - pointP3[1]; lineDirection2[2] = pointP4[2] - pointP3[2]; mitk::Line3D xingline2(pointP3, lineDirection2); mitk::Point3D calcXingPoint2; myPlaneGeometry->IntersectionPoint(xingline2, calcXingPoint2); // intersection points must be the same CPPUNIT_ASSERT_MESSAGE("Failed to calculate Intersection Point", calcXingPoint == calcXingPoint2); } /** * @brief This method tests method ProjectPointOntoPlane. * * See also bug #3409. */ // Test does not use standard Parameters void TestProjectPointOntoPlane() { mitk::PlaneGeometry::Pointer myPlaneGeometry = mitk::PlaneGeometry::New(); // create normal mitk::Vector3D normal; normal[0] = 0.0; normal[1] = 0.0; normal[2] = 1.0; // create origin mitk::Point3D origin; origin[0] = -27.582859; origin[1] = 50; origin[2] = 200.27742; // initialize plane geometry myPlaneGeometry->InitializePlane(origin, normal); // output to describe the test std::cout << "Testing PlaneGeometry according to bug #3409" << std::endl; std::cout << "Our normal is: " << normal << std::endl; std::cout << "So ALL projected points should have exactly the same z-value!" << std::endl; // create a number of points mitk::Point3D myPoints[5]; myPoints[0][0] = -27.582859; myPoints[0][1] = 50.00; myPoints[0][2] = 200.27742; myPoints[1][0] = -26.58662; myPoints[1][1] = 50.00; myPoints[1][2] = 200.19026; myPoints[2][0] = -26.58662; myPoints[2][1] = 50.00; myPoints[2][2] = 200.33124; myPoints[3][0] = 104.58662; myPoints[3][1] = 452.12313; myPoints[3][2] = 866.41236; myPoints[4][0] = -207.58662; myPoints[4][1] = 312.00; myPoints[4][2] = -300.12346; // project points onto plane mitk::Point3D myProjectedPoints[5]; for (unsigned int i = 0; i < 5; ++i) { myProjectedPoints[i] = myPlaneGeometry->ProjectPointOntoPlane(myPoints[i]); } // compare z-values with z-value of plane (should be equal) bool allPointsOnPlane = true; for (auto &myProjectedPoint : myProjectedPoints) { if (fabs(myProjectedPoint[2] - origin[2]) > mitk::sqrteps) { allPointsOnPlane = false; } } CPPUNIT_ASSERT_MESSAGE("All points lie not on the same plane", allPointsOnPlane); } void TestPlaneGeometryCloning() { mitk::PlaneGeometry::Pointer geometry2D = createPlaneGeometry(); try { mitk::PlaneGeometry::Pointer clone = geometry2D->Clone(); itk::Matrix matrix = clone->GetIndexToWorldTransform()->GetMatrix(); CPPUNIT_ASSERT_MESSAGE("Test if matrix element exists...", matrix[0][0] == 31); double origin = geometry2D->GetOrigin()[0]; CPPUNIT_ASSERT_MESSAGE("First Point of origin as expected...", mitk::Equal(origin, 8)); double spacing = geometry2D->GetSpacing()[0]; CPPUNIT_ASSERT_MESSAGE("First Point of spacing as expected...", mitk::Equal(spacing, 31)); } catch (...) { CPPUNIT_FAIL("Error during access on a member of cloned geometry"); } // direction [row] [column] MITK_TEST_OUTPUT(<< "Casting a rotated 2D ITK Image to a MITK Image and check if Geometry is still same"); } void TestPlaneGeometryInitializeOrder() { mitk::Vector3D mySpacing; mySpacing[0] = 31; mySpacing[1] = 0.1; mySpacing[2] = 5.4; mitk::Point3D myOrigin; myOrigin[0] = 8; myOrigin[1] = 9; myOrigin[2] = 10; mitk::AffineTransform3D::Pointer myTransform = mitk::AffineTransform3D::New(); itk::Matrix transMatrix; transMatrix.Fill(0); transMatrix[0][0] = 1; transMatrix[1][1] = 2; transMatrix[2][2] = 4; myTransform->SetMatrix(transMatrix); mitk::PlaneGeometry::Pointer geometry2D1 = mitk::PlaneGeometry::New(); geometry2D1->SetIndexToWorldTransform(myTransform); geometry2D1->SetSpacing(mySpacing); geometry2D1->SetOrigin(myOrigin); mitk::PlaneGeometry::Pointer geometry2D2 = mitk::PlaneGeometry::New(); geometry2D2->SetSpacing(mySpacing); geometry2D2->SetOrigin(myOrigin); geometry2D2->SetIndexToWorldTransform(myTransform); mitk::PlaneGeometry::Pointer geometry2D3 = mitk::PlaneGeometry::New(); geometry2D3->SetIndexToWorldTransform(myTransform); geometry2D3->SetSpacing(mySpacing); geometry2D3->SetOrigin(myOrigin); geometry2D3->SetIndexToWorldTransform(myTransform); CPPUNIT_ASSERT_MESSAGE("Origin of Geometry 1 matches that of Geometry 2.", mitk::Equal(geometry2D1->GetOrigin(), geometry2D2->GetOrigin())); CPPUNIT_ASSERT_MESSAGE("Origin of Geometry 1 match those of Geometry 3.", mitk::Equal(geometry2D1->GetOrigin(), geometry2D3->GetOrigin())); CPPUNIT_ASSERT_MESSAGE("Origin of Geometry 2 match those of Geometry 3.", mitk::Equal(geometry2D2->GetOrigin(), geometry2D3->GetOrigin())); CPPUNIT_ASSERT_MESSAGE("Spacing of Geometry 1 match those of Geometry 2.", mitk::Equal(geometry2D1->GetSpacing(), geometry2D2->GetSpacing())); CPPUNIT_ASSERT_MESSAGE("Spacing of Geometry 1 match those of Geometry 3.", mitk::Equal(geometry2D1->GetSpacing(), geometry2D3->GetSpacing())); CPPUNIT_ASSERT_MESSAGE("Spacing of Geometry 2 match those of Geometry 3.", mitk::Equal(geometry2D2->GetSpacing(), geometry2D3->GetSpacing())); CPPUNIT_ASSERT_MESSAGE("Transformation of Geometry 1 match those of Geometry 2.", compareMatrix(geometry2D1->GetIndexToWorldTransform()->GetMatrix(), geometry2D2->GetIndexToWorldTransform()->GetMatrix())); CPPUNIT_ASSERT_MESSAGE("Transformation of Geometry 1 match those of Geometry 3.", compareMatrix(geometry2D1->GetIndexToWorldTransform()->GetMatrix(), geometry2D3->GetIndexToWorldTransform()->GetMatrix())); CPPUNIT_ASSERT_MESSAGE("Transformation of Geometry 2 match those of Geometry 3.", compareMatrix(geometry2D2->GetIndexToWorldTransform()->GetMatrix(), geometry2D3->GetIndexToWorldTransform()->GetMatrix())); } void TestInitializeStandardPlane() { CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: width", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: height", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: depth", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: width in mm", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: heght in mm", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: depth in mm", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: AxisVectorRight", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: AxisVectorBottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: AxisVectorNormal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); mitk::Vector3D spacing; thicknessInMM = 1.5; normal.Normalize(); normal *= thicknessInMM; mitk::FillVector3D(spacing, 1.0, 1.0, thicknessInMM); planegeometry->InitializeStandardPlane(right.GetVnlVector(), bottom.GetVnlVector(), &spacing); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: width", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: height", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: depth", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: width in mm", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: height in mm", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: depth in mm", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: AxisVectorRight", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: AxisVectorBottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: AxisVectorNormal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); ; } void TestSetExtendInMM() { normal.Normalize(); normal *= thicknessInMM; planegeometry->SetExtentInMM(2, thicknessInMM); CPPUNIT_ASSERT_MESSAGE("Testing SetExtentInMM(2, ...), querying by GetExtentInMM(2): ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing SetExtentInMM(2, ...), querying by GetAxisVector(2) and comparing to normal: ", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); planegeometry->SetOrigin(origin); CPPUNIT_ASSERT_MESSAGE("Testing SetOrigin", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() after SetOrigin: Right", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() after SetOrigin: Bottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() after SetOrigin: Normal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestRotate() { // Changing the IndexToWorldTransform to a rotated version by SetIndexToWorldTransform() (keep origin): mitk::AffineTransform3D::Pointer transform = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = planegeometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix(); mitk::VnlVector axis(3); mitk::FillVector3D(axis, 1.0, 1.0, 1.0); axis.normalize(); vnl_quaternion rotation(axis, 0.223); vnlmatrix = rotation.rotation_matrix_transpose() * vnlmatrix; mitk::Matrix3D matrix; matrix = vnlmatrix; transform->SetMatrix(matrix); transform->SetOffset(planegeometry->GetIndexToWorldTransform()->GetOffset()); right.SetVnlVector(rotation.rotation_matrix_transpose() * right.GetVnlVector()); bottom.SetVnlVector(rotation.rotation_matrix_transpose() * bottom.GetVnlVector()); normal.SetVnlVector(rotation.rotation_matrix_transpose() * normal.GetVnlVector()); planegeometry->SetIndexToWorldTransform(transform); // The origin changed,because m_Origin=m_IndexToWorldTransform->GetOffset()+GetAxisVector(2)*0.5 // and the AxisVector changes due to the rotation. In other words: the rotation was done around // the corner of the box, not around the planes origin. Now change it to a rotation around // the origin, simply by re-setting the origin to the original one: planegeometry->SetOrigin(origin); CPPUNIT_ASSERT_MESSAGE("Testing whether SetIndexToWorldTransform kept origin: ", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); mitk::Point2D point; point[0] = 4; point[1] = 3; mitk::Point2D dummy; planegeometry->WorldToIndex(point, dummy); planegeometry->IndexToWorld(dummy, dummy); CPPUNIT_ASSERT_MESSAGE("Testing consistency of index and world coordinates.", dummy == point); CPPUNIT_ASSERT_MESSAGE("Testing width of rotated version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height of rotated version: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness of rotated version: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of rotated version: right ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of rotated version: bottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of rotated version: normal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(0).GetNorm(), planegeometry->GetExtentInMM(0), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(1).GetNorm(), planegeometry->GetExtentInMM(1), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(2).GetNorm(), planegeometry->GetExtentInMM(2), testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); width *= 2; height *= 3; planegeometry->SetSizeInUnits(width, height); CPPUNIT_ASSERT_MESSAGE("Testing SetSizeInUnits() of rotated version: ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing SetSizeInUnits() of rotated version: ", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing SetSizeInUnits() of rotated version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of version with changed size in units: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of version with changed size in units: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of version with changed size in units: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of version with changed size in units: right ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of version with changed size in units: bottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of version with changed size in units: normal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(0).GetNorm(), planegeometry->GetExtentInMM(0), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(1).GetNorm(), planegeometry->GetExtentInMM(1), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(2).GetNorm(), planegeometry->GetExtentInMM(2), testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestClone() { mitk::PlaneGeometry::Pointer clonedplanegeometry = dynamic_cast(planegeometry->Clone().GetPointer()); // Cave: Statement below is negated! CPPUNIT_ASSERT_MESSAGE("Testing Clone(): ", !((clonedplanegeometry.IsNull()) || (clonedplanegeometry->GetReferenceCount() != 1))); CPPUNIT_ASSERT_MESSAGE("Testing origin of cloned version: ", mitk::Equal(clonedplanegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in units) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in units) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing extent (in units) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of cloned version: right", mitk::Equal(clonedplanegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of cloned version: bottom", mitk::Equal(clonedplanegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of cloned version: normal", mitk::Equal(clonedplanegeometry->GetAxisVector(2), normal, testEps)); mappingTests2D(clonedplanegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestSagittalInitialization() { mitk::Point3D cornerpoint0 = planegeometry->GetCornerPoint(0); mitk::PlaneGeometry::Pointer clonedplanegeometry = planegeometry->Clone(); // Testing InitializeStandardPlane(clonedplanegeometry, anatomicalplane = Sagittal, zPosition = 0, frontside=true): planegeometry->InitializeStandardPlane(clonedplanegeometry, mitk::AnatomicalPlane::Sagittal); mitk::Vector3D newright, newbottom, newnormal; mitk::ScalarType newthicknessInMM; newright = bottom; newthicknessInMM = widthInMM / width * 1.0; // extent in normal direction is 1; newnormal = right; newnormal.Normalize(); newnormal *= newthicknessInMM; newbottom = normal; newbottom.Normalize(); newbottom *= thicknessInMM; CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of sagittally initialized version:", mitk::Equal(planegeometry->GetCornerPoint(0), cornerpoint0, testEps)); // ok, corner was fine, so we can dare to believe the origin is ok. origin = planegeometry->GetOrigin(); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of sagittally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of sagittally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of sagittally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of sagittally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of sagittally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of sagittally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), newthicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of sagittally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of sagittally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of sagittally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), newnormal, testEps)); mappingTests2D(planegeometry, height, 1, heightInMM, thicknessInMM, origin, newright, newbottom); // set origin back to the one of the axial slice: origin = clonedplanegeometry->GetOrigin(); // Testing backside initialization: InitializeStandardPlane(clonedplanegeometry, anatomicalplane = Axial, zPosition // = 0, frontside=false, rotated=true): planegeometry->InitializeStandardPlane(clonedplanegeometry, mitk::AnatomicalPlane::Axial, 0, false, true); mitk::Point3D backsideorigin; backsideorigin = origin + clonedplanegeometry->GetAxisVector(1); //+clonedplanegeometry->GetAxisVector(2); CPPUNIT_ASSERT_MESSAGE("Testing origin of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetOrigin(), backsideorigin, testEps)); mitk::Point3D backsidecornerpoint0; backsidecornerpoint0 = cornerpoint0 + clonedplanegeometry->GetAxisVector(1); //+clonedplanegeometry->GetAxisVector(2); CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of sagittally initialized version: ", mitk::Equal(planegeometry->GetCornerPoint(0), backsidecornerpoint0, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of backsidedly, axially initialized version " "(should be same as in mm due to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of backsidedly, axially initialized version " "(should be same as in mm due to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of backsidedly, axially initialized version " "(should be same as in mm due to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), -bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, backsideorigin, right, -bottom); } void TestCoronalInitialization() { mitk::Point3D cornerpoint0 = planegeometry->GetCornerPoint(0); mitk::PlaneGeometry::Pointer clonedplanegeometry = dynamic_cast(planegeometry->Clone().GetPointer()); //-------- mitk::Vector3D newright, newbottom, newnormal; mitk::ScalarType newthicknessInMM; // Testing InitializeStandardPlane(clonedplanegeometry, anatomicalplane = Coronal, zPosition = 0, frontside=true) planegeometry->InitializeStandardPlane(clonedplanegeometry, mitk::AnatomicalPlane::Coronal); newright = right; newbottom = normal; newbottom.Normalize(); newbottom *= thicknessInMM; newthicknessInMM = heightInMM / height * 1.0 /*extent in normal direction is 1*/; newnormal = -bottom; newnormal.Normalize(); newnormal *= newthicknessInMM; CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of coronally initialized version: ", mitk::Equal(planegeometry->GetCornerPoint(0), cornerpoint0, testEps)); // ok, corner was fine, so we can dare to believe the origin is ok. origin = planegeometry->GetOrigin(); CPPUNIT_ASSERT_MESSAGE("Testing width (in units) of coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in units) of coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in units) of coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), newthicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), -newnormal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, width, 1, widthInMM, thicknessInMM, origin, newright, newbottom); // Changing plane to in-plane unit spacing using SetSizeInUnits: planegeometry->SetSizeInUnits(planegeometry->GetExtentInMM(0), planegeometry->GetExtentInMM(1)); CPPUNIT_ASSERT_MESSAGE("Testing origin of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), newthicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), -newnormal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, widthInMM, thicknessInMM, widthInMM, thicknessInMM, origin, newright, newbottom); // Changing plane to unit spacing also in normal direction using SetExtentInMM(2, 1.0): planegeometry->SetExtentInMM(2, 1.0); newnormal.Normalize(); CPPUNIT_ASSERT_MESSAGE("Testing origin of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), 1.0, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, coronally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), -newnormal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, widthInMM, thicknessInMM, widthInMM, thicknessInMM, origin, newright, newbottom); } void TestAxialInitialization() { mitk::Point3D cornerpoint0 = planegeometry->GetCornerPoint(0); // Clone, move, rotate and test for 'IsParallel' and 'IsOnPlane' mitk::PlaneGeometry::Pointer clonedplanegeometry = dynamic_cast(planegeometry->Clone().GetPointer()); CPPUNIT_ASSERT_MESSAGE("Testing Clone(): ", !((clonedplanegeometry.IsNull()) || (clonedplanegeometry->GetReferenceCount() != 1))); std::cout << "Testing InitializeStandardPlane(clonedplanegeometry, anatomicalplane = Axial, zPosition = 0, " "frontside=true): " << std::endl; planegeometry->InitializeStandardPlane(clonedplanegeometry); CPPUNIT_ASSERT_MESSAGE("Testing origin of axially initialized version: ", mitk::Equal(planegeometry->GetOrigin(), origin)); CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of axially initialized version: ", mitk::Equal(planegeometry->GetCornerPoint(0), cornerpoint0)); CPPUNIT_ASSERT_MESSAGE("Testing width (in units) of axially initialized version (should be same as in mm due to " "unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in units) of axially initialized version (should be same as in mm due to " "unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in units) of axially initialized version (should be same as in mm due " "to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestPlaneComparison() { // Clone, move, rotate and test for 'IsParallel' and 'IsOnPlane' mitk::PlaneGeometry::Pointer clonedplanegeometry2 = dynamic_cast(planegeometry->Clone().GetPointer()); CPPUNIT_ASSERT_MESSAGE("Testing Clone(): ", !((clonedplanegeometry2.IsNull()) || (clonedplanegeometry2->GetReferenceCount() != 1))); CPPUNIT_ASSERT_MESSAGE("Testing whether original and clone are at the same position", clonedplanegeometry2->IsOnPlane(planegeometry.GetPointer())); CPPUNIT_ASSERT_MESSAGE(" Asserting that origin is on the plane cloned plane:", clonedplanegeometry2->IsOnPlane(origin)); mitk::VnlVector newaxis(3); mitk::FillVector3D(newaxis, 1.0, 1.0, 1.0); newaxis.normalize(); vnl_quaternion rotation2(newaxis, 0.0); mitk::Vector3D clonednormal = clonedplanegeometry2->GetNormal(); mitk::Point3D clonedorigin = clonedplanegeometry2->GetOrigin(); auto planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), 180.0); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE(" Asserting that a flipped plane is still on the original plane: ", clonedplanegeometry2->IsOnPlane(planegeometry.GetPointer())); clonedorigin += clonednormal; clonedplanegeometry2->SetOrigin(clonedorigin); CPPUNIT_ASSERT_MESSAGE("Testing if the translated (cloned, flipped) plane is parallel to its origin plane: ", clonedplanegeometry2->IsParallel(planegeometry)); delete planerot; planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), 0.5); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE("Testing if a non-parallel plane gets recognized as not parallel [rotation +0.5 degree] : ", !clonedplanegeometry2->IsParallel(planegeometry)); delete planerot; planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), -1.0); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE("Testing if a non-parallel plane gets recognized as not parallel [rotation -0.5 degree] : ", !clonedplanegeometry2->IsParallel(planegeometry)); delete planerot; planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), 360.5); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE("Testing if a non-parallel plane gets recognized as parallel [rotation 360 degree] : ", clonedplanegeometry2->IsParallel(planegeometry)); } private: // helper Methods for the Tests mitk::PlaneGeometry::Pointer createPlaneGeometry() { mitk::Vector3D mySpacing; mySpacing[0] = 31; mySpacing[1] = 0.1; mySpacing[2] = 5.4; mitk::Point3D myOrigin; myOrigin[0] = 8; myOrigin[1] = 9; myOrigin[2] = 10; mitk::AffineTransform3D::Pointer myTransform = mitk::AffineTransform3D::New(); itk::Matrix transMatrix; transMatrix.Fill(0); transMatrix[0][0] = 1; transMatrix[1][1] = 2; transMatrix[2][2] = 4; myTransform->SetMatrix(transMatrix); mitk::PlaneGeometry::Pointer geometry2D = mitk::PlaneGeometry::New(); geometry2D->SetIndexToWorldTransform(myTransform); geometry2D->SetSpacing(mySpacing); geometry2D->SetOrigin(myOrigin); return geometry2D; } bool compareMatrix(itk::Matrix left, itk::Matrix right) { bool equal = true; for (int i = 0; i < 3; ++i) for (int j = 0; j < 3; ++j) equal &= mitk::Equal(left[i][j], right[i][j]); return equal; } /** * This function tests for correct mapping and is called several times from other tests **/ void mappingTests2D(const mitk::PlaneGeometry *planegeometry, const mitk::ScalarType &width, const mitk::ScalarType &height, const mitk::ScalarType &widthInMM, const mitk::ScalarType &heightInMM, const mitk::Point3D &origin, const mitk::Vector3D &right, const mitk::Vector3D &bottom) { std::cout << "Testing mapping Map(pt2d_mm(x=widthInMM/2.3,y=heightInMM/2.5), pt3d_mm) and compare with expected: "; mitk::Point2D pt2d_mm; mitk::Point3D pt3d_mm, expected_pt3d_mm; pt2d_mm[0] = widthInMM / 2.3; pt2d_mm[1] = heightInMM / 2.5; expected_pt3d_mm = origin + right * (pt2d_mm[0] / right.GetNorm()) + bottom * (pt2d_mm[1] / bottom.GetNorm()); planegeometry->Map(pt2d_mm, pt3d_mm); CPPUNIT_ASSERT_MESSAGE( "Testing mapping Map(pt2d_mm(x=widthInMM/2.3,y=heightInMM/2.5), pt3d_mm) and compare with expected", mitk::Equal(pt3d_mm, expected_pt3d_mm, testEps)); std::cout << "Testing mapping Map(pt3d_mm, pt2d_mm) and compare with expected: "; mitk::Point2D testpt2d_mm; planegeometry->Map(pt3d_mm, testpt2d_mm); std::cout << std::setprecision(12) << "Expected pt2d_mm " << pt2d_mm << std::endl; std::cout << std::setprecision(12) << "Result testpt2d_mm " << testpt2d_mm << std::endl; std::cout << std::setprecision(12) << "10*mitk::eps " << 10 * mitk::eps << std::endl; // This eps is temporarily set to 10*mitk::eps. See bug #15037 for details. CPPUNIT_ASSERT_MESSAGE("Testing mapping Map(pt3d_mm, pt2d_mm) and compare with expected", mitk::Equal(pt2d_mm, testpt2d_mm, 10 * mitk::eps)); std::cout << "Testing IndexToWorld(pt2d_units, pt2d_mm) and compare with expected: "; mitk::Point2D pt2d_units; pt2d_units[0] = width / 2.0; pt2d_units[1] = height / 2.0; pt2d_mm[0] = widthInMM / 2.0; pt2d_mm[1] = heightInMM / 2.0; planegeometry->IndexToWorld(pt2d_units, testpt2d_mm); std::cout << std::setprecision(12) << "Expected pt2d_mm " << pt2d_mm << std::endl; std::cout << std::setprecision(12) << "Result testpt2d_mm " << testpt2d_mm << std::endl; std::cout << std::setprecision(12) << "10*mitk::eps " << 10 * mitk::eps << std::endl; // This eps is temporarily set to 10*mitk::eps. See bug #15037 for details. CPPUNIT_ASSERT_MESSAGE("Testing IndexToWorld(pt2d_units, pt2d_mm) and compare with expected: ", mitk::Equal(pt2d_mm, testpt2d_mm, 10 * mitk::eps)); std::cout << "Testing WorldToIndex(pt2d_mm, pt2d_units) and compare with expected: "; mitk::Point2D testpt2d_units; planegeometry->WorldToIndex(pt2d_mm, testpt2d_units); std::cout << std::setprecision(12) << "Expected pt2d_units " << pt2d_units << std::endl; std::cout << std::setprecision(12) << "Result testpt2d_units " << testpt2d_units << std::endl; std::cout << std::setprecision(12) << "10*mitk::eps " << 10 * mitk::eps << std::endl; // This eps is temporarily set to 10*mitk::eps. See bug #15037 for details. CPPUNIT_ASSERT_MESSAGE("Testing WorldToIndex(pt2d_mm, pt2d_units) and compare with expected:", mitk::Equal(pt2d_units, testpt2d_units, 10 * mitk::eps)); } }; MITK_TEST_SUITE_REGISTRATION(mitkPlaneGeometry) diff --git a/Modules/CppMicroServices/CMakeLists.txt b/Modules/CppMicroServices/CMakeLists.txt index 4a7d9ca897..4a026cf4e3 100644 --- a/Modules/CppMicroServices/CMakeLists.txt +++ b/Modules/CppMicroServices/CMakeLists.txt @@ -1,440 +1,438 @@ project(CppMicroServices) set(${PROJECT_NAME}_MAJOR_VERSION 2) set(${PROJECT_NAME}_MINOR_VERSION 99) set(${PROJECT_NAME}_PATCH_VERSION 0) set(${PROJECT_NAME}_VERSION ${${PROJECT_NAME}_MAJOR_VERSION}.${${PROJECT_NAME}_MINOR_VERSION}.${${PROJECT_NAME}_PATCH_VERSION}) -cmake_minimum_required(VERSION 2.8.12) -cmake_policy(VERSION 2.8.12) -cmake_policy(SET CMP0017 NEW) +cmake_minimum_required(VERSION ${MITK_CMAKE_MINIMUM_REQUIRED_VERSION}) #----------------------------------------------------------------------------- # Update CMake module path #------------------------------------------------------------------------------ set(US_CMAKE_DIR ${PROJECT_SOURCE_DIR}/cmake) set(CMAKE_MODULE_PATH ${US_CMAKE_DIR} ${CMAKE_MODULE_PATH} ) #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- include(CMakeParseArguments) include(CMakePackageConfigHelpers) include(CheckCXXSourceCompiles) include(usFunctionAddResources) include(usFunctionEmbedResources) include(usFunctionGetResourceSource) include(usFunctionCheckResourceLinking) include(usFunctionCheckCompilerFlags) include(usFunctionGetGccVersion) include(usFunctionGenerateModuleInit) include(usMacroCreateModule) if(US_BUILD_TESTING) include(usFunctionCompileSnippets) endif() #----------------------------------------------------------------------------- # Init output directories #----------------------------------------------------------------------------- set(US_ARCHIVE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib") set(US_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib") set(US_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") foreach(_type ARCHIVE LIBRARY RUNTIME) if(NOT CMAKE_${_type}_OUTPUT_DIRECTORY) set(CMAKE_${_type}_OUTPUT_DIRECTORY ${US_${_type}_OUTPUT_DIRECTORY}) endif() endforeach() #----------------------------------------------------------------------------- # Set a default build type if none was specified #----------------------------------------------------------------------------- if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) message(STATUS "Setting build type to 'Debug' as none was specified.") set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE) # Set the possible values of build type for cmake-gui set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") endif() #----------------------------------------------------------------------------- # CMake options #----------------------------------------------------------------------------- function(us_cache_var _var_name _var_default _var_type _var_help) set(_advanced 0) set(_force) foreach(_argn ${ARGN}) if(_argn STREQUAL ADVANCED) set(_advanced 1) elseif(_argn STREQUAL FORCE) set(_force FORCE) endif() endforeach() if(US_IS_EMBEDDED) if(NOT DEFINED ${_var_name} OR _force) set(${_var_name} ${_var_default} PARENT_SCOPE) endif() else() set(${_var_name} ${_var_default} CACHE ${_var_type} "${_var_help}" ${_force}) if(_advanced) mark_as_advanced(${_var_name}) endif() endif() endfunction() # Determine if we are being build inside a larger project if(NOT DEFINED US_IS_EMBEDDED) if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME) set(US_IS_EMBEDDED 0) else() set(US_IS_EMBEDDED 1) endif() endif() # Determine the name of the install component for "SDK" artifacts. # The default is "sdk" if(NOT DEFINED US_SDK_INSTALL_COMPONENT) set(US_SDK_INSTALL_COMPONENT COMPONENT sdk) elseif(US_SDK_INSTALL_COMPONENT) set(US_SDK_INSTALL_COMPONENT COMPONENT ${US_SDK_INSTALL_COMPONENT}) endif() us_cache_var(US_ENABLE_AUTOLOADING_SUPPORT OFF BOOL "Enable module auto-loading support") us_cache_var(US_ENABLE_THREADING_SUPPORT OFF BOOL "Enable threading support") us_cache_var(US_ENABLE_DEBUG_OUTPUT OFF BOOL "Enable debug messages" ADVANCED) us_cache_var(US_BUILD_SHARED_LIBS ON BOOL "Build shared libraries") us_cache_var(US_BUILD_TESTING OFF BOOL "Build tests") us_cache_var(US_BUILD_EXAMPLES OFF BOOL "Build example projects") if(US_BUILD_TESTING) enable_testing() endif() if(WIN32 AND NOT CYGWIN) set(default_runtime_install_dir bin/) set(default_library_install_dir bin/) set(default_archive_install_dir lib/) set(default_header_install_dir include/) set(default_auxiliary_install_dir share/) else() set(default_runtime_install_dir bin/) set(default_library_install_dir lib/${PROJECT_NAME}) set(default_archive_install_dir lib/${PROJECT_NAME}) set(default_header_install_dir include/${PROJECT_NAME}) set(default_auxiliary_install_dir share/${PROJECT_NAME}) endif() us_cache_var(RUNTIME_INSTALL_DIR ${default_runtime_install_dir} STRING "Relative install location for binaries" ADVANCED) us_cache_var(LIBRARY_INSTALL_DIR ${default_library_install_dir} STRING "Relative install location for libraries" ADVANCED) us_cache_var(ARCHIVE_INSTALL_DIR ${default_archive_install_dir} STRING "Relative install location for archives" ADVANCED) us_cache_var(HEADER_INSTALL_DIR ${default_header_install_dir} STRING "Relative install location for headers" ADVANCED) us_cache_var(AUXILIARY_INSTALL_DIR ${default_auxiliary_install_dir} STRING "Relative install location for auxiliary files" ADVANCED) set(AUXILIARY_CMAKE_INSTALL_DIR ${AUXILIARY_INSTALL_DIR}/cmake) us_cache_var(US_NAMESPACE "us" STRING "The namespace for the C++ Micro Services symbols") set(BUILD_SHARED_LIBS ${US_BUILD_SHARED_LIBS}) set(US_MODULE_INIT_TEMPLATE "${US_CMAKE_DIR}/usModuleInit.cpp" CACHE INTERNAL "The module initialization template code") set(US_RESOURCE_RC_TEMPLATE "${US_CMAKE_DIR}/us_resources.rc.in" CACHE INTERNAL "The Windows RC resource template") set(US_CMAKE_RESOURCE_DEPENDENCIES_CPP "${US_CMAKE_DIR}/usCMakeResourceDependencies.cpp" CACHE INTERNAL "The dummy resource dependencies code") #----------------------------------------------------------------------------- # US C/CXX Flags #----------------------------------------------------------------------------- if(US_IS_EMBEDDED) set(CMAKE_C_FLAGS) set(CMAKE_C_FLAGS_RELEASE) set(CMAKE_C_FLAGS_DEBUG) set(CMAKE_CXX_FLAGS) set(CMAKE_CXX_FLAGS_RELEASE) set(CMAKE_CXX_FLAGS_DEBUG) set(CMAKE_LINK_FLAGS) set(CMAKE_LINK_FLAGS_RELEASE) set(CMAKE_LINK_FLAGS_DEBUG) endif() # Set C++ compiler flags if(NOT MSVC) foreach(_cxxflag -Werror -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -Woverloaded-virtual -Wnon-virtual-dtor -Wstrict-null-sentinel -Wsign-promo -fdiagnostics-show-option -Wno-error=deprecated-copy -Wno-error=implicit-int-float-conversion) usFunctionCheckCompilerFlags(${_cxxflag} US_CXX_FLAGS) endforeach() endif() set(US_HAVE_VISIBILITY_ATTRIBUTE 0) usFunctionCheckCompilerFlags("-fvisibility=hidden -fvisibility-inlines-hidden" _have_visibility) if(_have_visibility) set(US_HAVE_VISIBILITY_ATTRIBUTE 1) endif() if(CMAKE_COMPILER_IS_GNUCXX) usFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION) if(${GCC_VERSION} VERSION_LESS "4.0.0") message(FATAL_ERROR "gcc version ${GCC_VERSION} not supported. Please use gcc >= 4.") endif() # With older versions of gcc the flag -fstack-protector-all requires an extra dependency to libssp.so. # If the gcc version is lower than 4.4.0 and the build type is Release let's not include the flag. if(${GCC_VERSION} VERSION_GREATER "4.4.0" OR (CMAKE_BUILD_TYPE STREQUAL "Debug" AND ${GCC_VERSION} VERSION_LESS "4.4.0")) usFunctionCheckCompilerFlags("-fstack-protector-all" US_CXX_FLAGS) endif() # Enable visibility support (only for gcc >= 4.5) # We only support hidden visibility with gcc for now. # # Clang has troubles with correctly marking template declarations and explicit template # instantiations as exported across shared library boundaries. Specifically, comparing # type_info objects from STL types does not work (used in us::Any::Type() == typeid(std::string)) # which could be related to the default visibility of STL types declared in libstdc++ and/or libc++ # but also to using RTLD_LOCAL or RTLD_GLOBAL when loading shared libraries via dlopen(). # if(_have_visibility AND NOT ${GCC_VERSION} VERSION_LESS "4.5") set(US_CXX_FLAGS "${US_CXX_FLAGS} ${_have_visibility}") else() set(US_GCC_RTTI_WORKAROUND_NEEDED 1) endif() usFunctionCheckCompilerFlags("-O1 -D_FORTIFY_SOURCE=2" _fortify_source_flag) if(_fortify_source_flag) set(US_CXX_FLAGS_RELEASE "${US_CXX_FLAGS_RELEASE} -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=2") endif() endif() if(MSVC) set(US_CXX_FLAGS "/MP /WX /wd4180 /wd4996 /wd4251 /wd4503 ${US_CXX_FLAGS}") endif() set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${US_CXX_FLAGS}") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${US_CXX_FLAGS_RELEASE}") set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${US_C_FLAGS}") set(CMAKE_C_FLAGS_REALEASE "${CMAKE_C_FLAGS_RELEASE} ${US_C_FLAGS_RELEASE}") #----------------------------------------------------------------------------- # US Link Flags #----------------------------------------------------------------------------- set(US_LINK_FLAGS ) if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE) foreach(_linkflag -Wl,--no-undefined) set(_add_flag) usFunctionCheckCompilerFlags("${_linkflag}" _add_flag) if(_add_flag) set(US_LINK_FLAGS "${US_LINK_FLAGS} ${_linkflag}") endif() endforeach() endif() usFunctionCheckResourceLinking() #----------------------------------------------------------------------------- # US Header Checks #----------------------------------------------------------------------------- include(CheckIncludeFileCXX) include(CheckCXXSourceCompiles) CHECK_INCLUDE_FILE_CXX(cxxabi.h US_HAVE_CXXABI_H) CHECK_INCLUDE_FILE_CXX(stdint.h US_HAVE_STDINT_H) CHECK_INCLUDE_FILE_CXX(tr1/unordered_map US_HAVE_TR1_UNORDERED_MAP_H) CHECK_INCLUDE_FILE_CXX(tr1/unordered_set US_HAVE_TR1_UNORDERED_SET_H) CHECK_INCLUDE_FILE_CXX(tr1/functional US_HAVE_TR1_FUNCTIONAL_H) CHECK_INCLUDE_FILE_CXX(unordered_map US_HAVE_UNORDERED_MAP_H) CHECK_INCLUDE_FILE_CXX(unordered_set US_HAVE_UNORDERED_SET_H) CHECK_INCLUDE_FILE_CXX(functional US_HAVE_FUNCTIONAL_H) if(US_HAVE_UNORDERED_MAP_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_map m; return 0; }" US_HAVE_TR1_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_map m; return 0; }" US_HAVE_STD_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::hash(); return 0; }" US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::hash(); return 0; }" US_HAVE_STD_HASH) if(US_HAVE_STD_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_CLASS) elseif(US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_CLASS) endif() elseif(US_HAVE_TR1_UNORDERED_MAP_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_map m; return 0; }" US_HAVE_TR1_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_map m; return 0; }" US_HAVE_STD_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::hash(); return 0; }" US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::hash(); return 0; }" US_HAVE_STD_HASH) if(US_HAVE_STD_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_CLASS) elseif(US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_CLASS) endif() else() message(SEND_ERROR "The header file \"unordered_map\" is not available.") endif() if(NOT (US_HAVE_TR1_UNORDERED_MAP OR US_HAVE_STD_UNORDERED_MAP)) message(SEND_ERROR "The \"unordered_map\" type is not available.") endif() if(US_HAVE_UNORDERED_SET_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_set s; return 0; }" US_HAVE_TR1_UNORDERED_SET) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_set s; return 0; }" US_HAVE_STD_UNORDERED_SET) elseif(US_HAVE_TR1_UNORDERED_SET_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_set s; return 0; }" US_HAVE_TR1_UNORDERED_SET) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_set s; return 0; }" US_HAVE_STD_UNORDERED_SET) else() message(SEND_ERROR "The header file \"unordered_set\" is not available.") endif() if(NOT (US_HAVE_TR1_UNORDERED_SET OR US_HAVE_STD_UNORDERED_SET)) message(SEND_ERROR "The \"unordered_set\" type is not available.") endif() if(NOT (US_HAVE_FUNCTIONAL_H OR US_HAVE_TR1_FUNCTIONAL_H)) message(SEND_ERROR "The header file \"functional\" is not available.") endif() if(US_HAVE_FUNCTIONAL_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::function f(main); return 0; }" US_HAVE_TR1_FUNCTION) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::function f(main); return 0; }" US_HAVE_STD_FUNCTION) endif() if((NOT (US_HAVE_STD_FUNCTION OR US_HAVE_TR1_FUNCTION)) AND US_HAVE_TR1_FUNCTIONAL_H) unset(US_HAVE_TR1_FUNCTION CACHE) unset(US_HAVE_STD_FUNCTION CACHE) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::function f(main); return 0; }" US_HAVE_TR1_FUNCTION) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::function f(main); return 0; }" US_HAVE_STD_FUNCTION) endif() if(NOT (US_HAVE_STD_FUNCTION OR US_HAVE_TR1_FUNCTION)) message(SEND_ERROR "The \"function\" type is not available.") endif() #----------------------------------------------------------------------------- # Source directory #----------------------------------------------------------------------------- set(US_INCLUDE_DIRS ${PROJECT_SOURCE_DIR}/third_party ${PROJECT_BINARY_DIR}/include) # Configure CppMicroServicesConfig.cmake for the build tree. # The file is used in sub-directories. set(PACKAGE_CONFIG_INCLUDE_DIR ${US_INCLUDE_DIRS}) set(PACKAGE_CONFIG_RUNTIME_DIR ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) set(PACKAGE_CONFIG_CMAKE_DIR ${US_CMAKE_DIR}) set(US_RCC_EXECUTABLE_NAME usResourceCompiler CACHE INTERNAL "The target name of the usResourceCompiler executable.") configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}Config.cmake.in ${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake @ONLY ) set(us_global_config_h_file "${PROJECT_BINARY_DIR}/include/usGlobalConfig.h") configure_file(${US_CMAKE_DIR}/usGlobalConfig.h.in ${us_global_config_h_file}) include_directories(${US_INCLUDE_DIRS}) add_subdirectory(tools) add_subdirectory(core) #----------------------------------------------------------------------------- # Documentation #----------------------------------------------------------------------------- add_subdirectory(doc) #----------------------------------------------------------------------------- # Last configuration and install steps #----------------------------------------------------------------------------- # Version information configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}ConfigVersion.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake @ONLY ) export(TARGETS ${US_RCC_EXECUTABLE_NAME} FILE ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Targets.cmake) if(NOT US_NO_INSTALL) install(EXPORT ${PROJECT_NAME}Targets FILE ${PROJECT_NAME}Targets.cmake DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR}) set(_install_cmake_scripts ${US_MODULE_INIT_TEMPLATE} ${US_CMAKE_RESOURCE_DEPENDENCIES_CPP} ${US_CMAKE_DIR}/usFunctionGenerateModuleInit.cmake ${US_CMAKE_DIR}/usFunctionAddResources.cmake ${US_CMAKE_DIR}/usFunctionEmbedResources.cmake ${US_CMAKE_DIR}/usFunctionGetResourceSource.cmake ${US_CMAKE_DIR}/usFunctionCheckResourceLinking.cmake ${US_CMAKE_DIR}/usFunctionCheckCompilerFlags.cmake ) install(FILES ${_install_cmake_scripts} DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR}) install(FILES ${us_global_config_h_file} DESTINATION ${HEADER_INSTALL_DIR}) # Configure CppMicroServicesConfig.cmake for the install tree set(CONFIG_INCLUDE_DIR ${HEADER_INSTALL_DIR}) set(CONFIG_RUNTIME_DIR ${RUNTIME_INSTALL_DIR}) set(CONFIG_CMAKE_DIR ${AUXILIARY_CMAKE_INSTALL_DIR}) configure_package_config_file( ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}Config.cmake.in ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${PROJECT_NAME}Config.cmake INSTALL_DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR} PATH_VARS CONFIG_INCLUDE_DIR CONFIG_RUNTIME_DIR CONFIG_CMAKE_DIR NO_SET_AND_CHECK_MACRO NO_CHECK_REQUIRED_COMPONENTS_MACRO ) install(FILES ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${PROJECT_NAME}Config.cmake ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR} ${US_SDK_INSTALL_COMPONENT} ) endif() diff --git a/Modules/ModelFit/autoload/Models/mitkModelFitModelsActivator.cpp b/Modules/ModelFit/autoload/Models/mitkModelFitModelsActivator.cpp index 6c62aaf983..c9688f320c 100644 --- a/Modules/ModelFit/autoload/Models/mitkModelFitModelsActivator.cpp +++ b/Modules/ModelFit/autoload/Models/mitkModelFitModelsActivator.cpp @@ -1,64 +1,68 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include //general models #include "mitkGenericParamModelFactory.h" #include "mitkLinearModelFactory.h" -#include "mitkT2DecayModelFactory.h" +#include "mitkExponentialDecayModelFactory.h" #include "mitkExpDecayOffsetModelFactory.h" #include "mitkExponentialSaturationModelFactory.h" +#include "mitkTwoStepLinearModelFactory.h" +#include "mitkThreeStepLinearModelFactory.h" namespace mitk { /* * This is the module activator for the IO aspects of the "ModelFit" module. */ class ModelFitModelsActivator : public us::ModuleActivator { public: template void RegisterProvider(us::ModuleContext* context) { auto provider = new TProvider(); provider->RegisterService(context); m_RegisteredProviders.push_back(std::unique_ptr(provider)); } void Load(us::ModuleContext* context) override { m_RegisteredProviders.clear(); RegisterProvider >(context); RegisterProvider >(context); - RegisterProvider >(context); + RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); + RegisterProvider >(context); + RegisterProvider >(context); } void Unload(us::ModuleContext* ) override { } private: std::vector > m_RegisteredProviders; }; } US_EXPORT_MODULE_ACTIVATOR(mitk::ModelFitModelsActivator) diff --git a/Modules/ModelFit/files.cmake b/Modules/ModelFit/files.cmake index 97c70eaeb0..2749ab3b99 100644 --- a/Modules/ModelFit/files.cmake +++ b/Modules/ModelFit/files.cmake @@ -1,82 +1,88 @@ file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") set(CPP_FILES Common/mitkExtractTimeGrid.cpp Common/mitkTimeGridHelper.cpp Common/mitkMaskedDynamicImageStatisticsGenerator.cpp Common/mitkModelFitConstants.cpp Common/mitkModelFitParameter.cpp Common/mitkModelFitCmdAppsHelper.cpp Common/mitkParameterFitImageGeneratorBase.cpp Common/mitkPixelBasedParameterFitImageGenerator.cpp Common/mitkROIBasedParameterFitImageGenerator.cpp Common/mitkModelFitInfo.cpp Common/mitkModelFitStaticParameterMap.cpp Common/mitkModelGenerator.cpp Common/mitkModelFitResultHelper.cpp Common/mitkScalarListLookupTable.cpp Common/mitkScalarListLookupTableProperty.cpp Common/mitkScalarListLookupTablePropertySerializer.cpp Common/mitkIModelFitProvider.cpp Common/mitkModelFitParameterValueExtraction.cpp Common/mitkBinaryImageToLabelSetImageFilter.cpp Common/mitkFormulaParser.cpp Common/mitkFresnel.cpp Common/mitkModelFitPlotDataHelper.cpp Common/mitkModelSignalImageGenerator.cpp Common/mitkModelFitResultRelationRule.cpp Functors/mitkSimpleFunctorBase.cpp Functors/mitkSimpleFunctorPolicy.cpp Functors/mitkChiSquareFitCostFunction.cpp Functors/mitkReducedChiSquareFitCostFunction.cpp Functors/mitkConstraintCheckerBase.cpp Functors/mitkSimpleBarrierConstraintChecker.cpp Functors/mitkSquaredDifferencesFitCostFunction.cpp Functors/mitkSumOfSquaredDifferencesFitCostFunction.cpp Functors/mitkMVConstrainedCostFunctionDecorator.cpp Functors/mitkMVModelFitCostFunction.cpp Functors/mitkNormalizedSumOfSquaredDifferencesFitCostFunction.cpp Functors/mitkSVModelFitCostFunction.cpp Functors/mitkModelFitFunctorBase.cpp Functors/mitkLevenbergMarquardtModelFitFunctor.cpp Functors/mitkDummyModelFitFunctor.cpp Functors/mitkModelFitInfoSignalGenerationFunctor.cpp Functors/mitkIndexedValueFunctorPolicy.cpp Functors/mitkModelDataGenerationFunctor.cpp Models/mitkModelBase.cpp Models/mitkModelFactoryBase.cpp Models/mitkModelParameterizerBase.cpp Models/mitkLinearModel.cpp Models/mitkLinearModelFactory.cpp Models/mitkInitialParameterizationDelegateBase.cpp Models/mitkImageBasedParameterizationDelegate.cpp Models/mitkGenericParamModel.cpp Models/mitkGenericParamModelFactory.cpp Models/mitkGenericParamModelParameterizer.cpp Models/mitkValueBasedParameterizationDelegate.cpp - Models/mitkT2DecayModel.cpp - Models/mitkT2DecayModelFactory.cpp - Models/mitkT2DecayModelParameterizer.cpp + Models/mitkExponentialDecayModel.cpp + Models/mitkExponentialDecayModelFactory.cpp + Models/mitkExponentialDecayModelParameterizer.cpp Models/mitkExponentialSaturationModel.cpp Models/mitkExponentialSaturationModelFactory.cpp Models/mitkExponentialSaturationModelParameterizer.cpp Models/mitkExpDecayOffsetModel.cpp Models/mitkExpDecayOffsetModelFactory.cpp Models/mitkExpDecayOffsetModelParameterizer.cpp + Models/mitkTwoStepLinearModel.cpp + Models/mitkTwoStepLinearModelFactory.cpp + Models/mitkTwoStepLinearModelParameterizer.cpp + Models/mitkThreeStepLinearModel.cpp + Models/mitkThreeStepLinearModelFactory.cpp + Models/mitkThreeStepLinearModelParameterizer.cpp TestingHelper/mitkTestModel.cpp TestingHelper/mitkTestModelFactory.cpp ) set(TPP_FILES include/itkMultiOutputNaryFunctorImageFilter.tpp include/itkMaskedStatisticsImageFilter.hxx include/itkMaskedNaryStatisticsImageFilter.hxx include/mitkModelFitProviderBase.tpp ) set(HXX_FILES ) set(MOC_H_FILES ) diff --git a/Modules/ModelFit/include/mitkExpDecayOffsetModel.h b/Modules/ModelFit/include/mitkExpDecayOffsetModel.h index 33d286984b..e9b779f3bf 100644 --- a/Modules/ModelFit/include/mitkExpDecayOffsetModel.h +++ b/Modules/ModelFit/include/mitkExpDecayOffsetModel.h @@ -1,87 +1,129 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkExpDecayOffsetModel_h #define mitkExpDecayOffsetModel_h #include "mitkModelBase.h" #include "MitkModelFitExports.h" namespace mitk { /** @class ExpDecayOffsetModel * @brief Implementation of a general exponential decay model with offset, - * following the function: f(x) = a * exp(-1.0 * x * b) + c. + * following the function: y(x) = y-intercept * exp(-rate*x) + baseline. */ class MITKMODELFIT_EXPORT ExpDecayOffsetModel : public mitk::ModelBase { public: typedef ExpDecayOffsetModel Self; typedef mitk::ModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; typedef Superclass::ParameterNameType ParameterNameType; typedef Superclass::ParametersSizeType ParametersSizeType; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(ExpDecayOffsetModel, ModelBase); - std::string GetModelDisplayName() const override; + static const std::string NAME_PARAMETER_y0; + static const std::string NAME_PARAMETER_k; + static const std::string NAME_PARAMETER_y_bl; - std::string GetModelType() const override; + static const unsigned int NUMBER_OF_PARAMETERS; - FunctionStringType GetFunctionString() const override; + static const std::string UNIT_PARAMETER_y0; + static const std::string UNIT_PARAMETER_k; + static const std::string UNIT_PARAMETER_y_bl; - std::string GetXName() const override; + static const unsigned int POSITION_PARAMETER_y0; + static const unsigned int POSITION_PARAMETER_k; + static const unsigned int POSITION_PARAMETER_y_bl; + + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + static const std::string FUNCTION_STRING; + + static const std::string X_NAME; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; + ParamterUnitMapType GetParameterUnits() const override; + ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; + std::string GetModelDisplayName() const override; + + std::string GetModelType() const override; + + FunctionStringType GetFunctionString() const override; + + std::string GetXName() const override; + + std::string GetXAxisName() const override; + + std::string GetXAxisUnit() const override; + + std::string GetYAxisName() const override; + + std::string GetYAxisUnit() const override; + protected: ExpDecayOffsetModel() {}; ~ExpDecayOffsetModel() override {}; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; private: //No copy constructor allowed ExpDecayOffsetModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/ModelFit/include/mitkT2DecayModel.h b/Modules/ModelFit/include/mitkExponentialDecayModel.h similarity index 54% rename from Modules/ModelFit/include/mitkT2DecayModel.h rename to Modules/ModelFit/include/mitkExponentialDecayModel.h index 7bb5f48409..60797f420b 100644 --- a/Modules/ModelFit/include/mitkT2DecayModel.h +++ b/Modules/ModelFit/include/mitkExponentialDecayModel.h @@ -1,95 +1,142 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef mitkT2DecayModel_h -#define mitkT2DecayModel_h +#ifndef mitkExponentialDecayModel_h +#define mitkExponentialDecayModel_h #include "mitkModelBase.h" #include "MitkModelFitExports.h" namespace mitk { - /** @class T2DecayModel - * @brief Simple model of the MR T2 signal decay. This corresponds to an exponential decay in the form of: - * f(t) = M0 * exp(-t/T2) with T2 being the transverse / spin-spin relaxation time. The derived parameter R2 - * is calculated from T2 by inversion. + /** @class ExponentialDecayModel + * @brief Simple model of exponential decay in the form of: + * y(x) = y-intercept * exp(-x/lambda) with lambda being the decay constant. */ - class MITKMODELFIT_EXPORT T2DecayModel : public mitk::ModelBase + class MITKMODELFIT_EXPORT ExponentialDecayModel : public mitk::ModelBase { public: - typedef T2DecayModel Self; + typedef ExponentialDecayModel Self; typedef mitk::ModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; typedef Superclass::ParameterNameType ParameterNameType; typedef Superclass::ParametersSizeType ParametersSizeType; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ - itkTypeMacro(T2DecayModel, ModelBase); + itkTypeMacro(ExponentialDecayModel, ModelBase); - std::string GetModelDisplayName() const override; - std::string GetModelType() const override; + static const std::string NAME_PARAMETER_y0; + static const std::string NAME_PARAMETER_lambda; - FunctionStringType GetFunctionString() const override; + static const unsigned int NUMBER_OF_PARAMETERS; - std::string GetXName() const override; + static const std::string UNIT_PARAMETER_y0; + static const std::string UNIT_PARAMETER_lambda; + + static const unsigned int POSITION_PARAMETER_y0; + static const unsigned int POSITION_PARAMETER_lambda; + + static const std::string NAME_DERIVED_PARAMETER_k; + + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; + + static const std::string UNIT_DERIVED_PARAMETER_k; + + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + static const std::string FUNCTION_STRING; + + static const std::string X_NAME; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; + ParamterUnitMapType GetParameterUnits() const override; + + ParameterNamesType GetDerivedParameterNames() const override; + + ParametersSizeType GetNumberOfDerivedParameters() const override; + + ParamterUnitMapType GetDerivedParameterUnits() const override; + ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; - DerivedParametersSizeType GetNumberOfDerivedParameters() const override; + std::string GetModelDisplayName() const override; + + std::string GetModelType() const override; + + FunctionStringType GetFunctionString() const override; + + std::string GetXName() const override; + + std::string GetXAxisName() const override; + + std::string GetXAxisUnit() const override; + + std::string GetYAxisName() const override; - DerivedParameterNamesType GetDerivedParameterNames() const override; + std::string GetYAxisUnit() const override; mitk::ModelBase::DerivedParameterMapType ComputeDerivedParameters( const mitk::ModelBase::ParametersType ¶meters) const; protected: - T2DecayModel() {}; - ~T2DecayModel() override {}; + ExponentialDecayModel() {}; + ~ExponentialDecayModel() override {}; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; private: //No copy constructor allowed - T2DecayModel(const Self& source); + ExponentialDecayModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/ModelFit/include/mitkT2DecayModelFactory.h b/Modules/ModelFit/include/mitkExponentialDecayModelFactory.h similarity index 66% rename from Modules/ModelFit/include/mitkT2DecayModelFactory.h rename to Modules/ModelFit/include/mitkExponentialDecayModelFactory.h index c3553fe9c1..2a7c1ded12 100644 --- a/Modules/ModelFit/include/mitkT2DecayModelFactory.h +++ b/Modules/ModelFit/include/mitkExponentialDecayModelFactory.h @@ -1,53 +1,53 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef mitkT2DecayModelFactory_h -#define mitkT2DecayModelFactory_h +#ifndef mitkExponentialDecayModelFactory_h +#define mitkExponentialDecayModelFactory_h #include #include "mitkConcreteModelFactoryBase.h" -#include "mitkT2DecayModel.h" +#include "mitkExponentialDecayModel.h" #include "MitkModelFitExports.h" namespace mitk { - class MITKMODELFIT_EXPORT T2DecayModelFactory : public ConcreteModelFactoryBase + class MITKMODELFIT_EXPORT ExponentialDecayModelFactory : public ConcreteModelFactoryBase { public: - mitkClassMacroItkParent(T2DecayModelFactory, ConcreteModelFactoryBase); + mitkClassMacroItkParent(ExponentialDecayModelFactory, ConcreteModelFactoryBase); itkFactorylessNewMacro(Self); ParametersType GetDefaultInitialParameterization() const override; ConstraintCheckerBase::Pointer CreateDefaultConstraints() const override; protected: ModelParameterizerBase::Pointer DoCreateParameterizer(const modelFit::ModelFitInfo* fit) const override; - T2DecayModelFactory(); + ExponentialDecayModelFactory(); - ~T2DecayModelFactory() override; + ~ExponentialDecayModelFactory() override; private: //No copy constructor allowed - T2DecayModelFactory(const Self& source); + ExponentialDecayModelFactory(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/ModelFit/include/mitkT2DecayModelParameterizer.h b/Modules/ModelFit/include/mitkExponentialDecayModelParameterizer.h similarity index 66% rename from Modules/ModelFit/include/mitkT2DecayModelParameterizer.h rename to Modules/ModelFit/include/mitkExponentialDecayModelParameterizer.h index 3f4fe5e092..2606384594 100644 --- a/Modules/ModelFit/include/mitkT2DecayModelParameterizer.h +++ b/Modules/ModelFit/include/mitkExponentialDecayModelParameterizer.h @@ -1,63 +1,63 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef mitkT2DecayModelParameterizer_h -#define mitkT2DecayModelParameterizer_h +#ifndef mitkExponentialDecayModelParameterizer_h +#define mitkExponentialDecayModelParameterizer_h #include "mitkConcreteModelParameterizerBase.h" -#include "mitkT2DecayModel.h" +#include "mitkExponentialDecayModel.h" #include "MitkModelFitExports.h" namespace mitk { - class MITKMODELFIT_EXPORT T2DecayModelParameterizer : public - mitk::ConcreteModelParameterizerBase + class MITKMODELFIT_EXPORT ExponentialDecayModelParameterizer : public + mitk::ConcreteModelParameterizerBase { public: - typedef T2DecayModelParameterizer Self; - typedef mitk::ConcreteModelParameterizerBase Superclass; + typedef ExponentialDecayModelParameterizer Self; + typedef mitk::ConcreteModelParameterizerBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; - itkTypeMacro(T2DecayModelParameterizer, - mitk::ConcreteModelParameterizerBase); + itkTypeMacro(ExponentialDecayModelParameterizer, + mitk::ConcreteModelParameterizerBase); itkFactorylessNewMacro(Self); typedef Superclass::ModelBaseType ModelBaseType; typedef Superclass::ModelBasePointer ModelBasePointer; typedef Superclass::ModelType ModelType; typedef ModelType::Pointer ModelPointer; typedef Superclass::StaticParameterValueType StaticParameterValueType; typedef Superclass::StaticParameterValuesType StaticParameterValuesType; typedef Superclass::StaticParameterMapType StaticParameterMapType; typedef Superclass::IndexType IndexType; ParametersType GetDefaultInitialParameterization() const override; protected: - T2DecayModelParameterizer(); + ExponentialDecayModelParameterizer(); - ~T2DecayModelParameterizer() override; + ~ExponentialDecayModelParameterizer() override; private: //No copy constructor allowed - T2DecayModelParameterizer(const Self& source); + ExponentialDecayModelParameterizer(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/ModelFit/include/mitkExponentialSaturationModel.h b/Modules/ModelFit/include/mitkExponentialSaturationModel.h index 7072660796..daba982745 100644 --- a/Modules/ModelFit/include/mitkExponentialSaturationModel.h +++ b/Modules/ModelFit/include/mitkExponentialSaturationModel.h @@ -1,86 +1,132 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __MITK_EXPONENTIAL_SATURATION_MODEL_H_ #define __MITK_EXPONENTIAL_SATURATION_MODEL_H_ #include "mitkModelBase.h" #include "MitkModelFitExports.h" namespace mitk { /** @class ExponentialSaturationModel - * @brief This genric model has the form: if x Pointer; typedef itk::SmartPointer< const Self > ConstPointer; typedef Superclass::ParameterNameType ParameterNameType; typedef Superclass::ParametersSizeType ParametersSizeType; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(ExponentialSaturationModel, ModelBase); - std::string GetModelDisplayName() const override; + static const std::string NAME_PARAMETER_BAT; + static const std::string NAME_PARAMETER_y_bl; + static const std::string NAME_PARAMETER_y_fin; + static const std::string NAME_PARAMETER_k; - std::string GetModelType() const override; + static const unsigned int NUMBER_OF_PARAMETERS; - FunctionStringType GetFunctionString() const override; + static const std::string UNIT_PARAMETER_BAT; + static const std::string UNIT_PARAMETER_y_bl; + static const std::string UNIT_PARAMETER_y_fin; + static const std::string UNIT_PARAMETER_k; - std::string GetXName() const override; + static const unsigned int POSITION_PARAMETER_BAT; + static const unsigned int POSITION_PARAMETER_y_bl; + static const unsigned int POSITION_PARAMETER_y_fin; + static const unsigned int POSITION_PARAMETER_k; + + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + static const std::string FUNCTION_STRING; + + static const std::string X_NAME; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; + ParamterUnitMapType GetParameterUnits() const override; + ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; + std::string GetModelDisplayName() const override; + + std::string GetModelType() const override; + + FunctionStringType GetFunctionString() const override; + + std::string GetXName() const override; + + std::string GetXAxisName() const override; + + std::string GetXAxisUnit() const override; + + std::string GetYAxisName() const override; + + std::string GetYAxisUnit() const override; + + protected: ExponentialSaturationModel() {}; ~ExponentialSaturationModel() override {}; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; private: //No copy constructor allowed ExponentialSaturationModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/ModelFit/include/mitkLinearModel.h b/Modules/ModelFit/include/mitkLinearModel.h index fe12b0d16b..e10578f78d 100644 --- a/Modules/ModelFit/include/mitkLinearModel.h +++ b/Modules/ModelFit/include/mitkLinearModel.h @@ -1,89 +1,138 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkLinearModel_h #define mitkLinearModel_h #include "mitkModelBase.h" #include "MitkModelFitExports.h" namespace mitk { class MITKMODELFIT_EXPORT LinearModel : public mitk::ModelBase { public: typedef LinearModel Self; typedef mitk::ModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; typedef Superclass::ParameterNameType ParameterNameType; typedef Superclass::ParametersSizeType ParametersSizeType; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(LinearModel, ModelBase); - std::string GetModelDisplayName() const override; + static const std::string NAME_PARAMETER_y0; + static const std::string NAME_PARAMETER_b; - std::string GetModelType() const override; + static const unsigned int NUMBER_OF_PARAMETERS; - FunctionStringType GetFunctionString() const override; + static const std::string UNIT_PARAMETER_y0; + static const std::string UNIT_PARAMETER_b; + + static const unsigned int POSITION_PARAMETER_y0; + static const unsigned int POSITION_PARAMETER_b; + + static const std::string NAME_DERIVED_PARAMETER_x_intercept; + + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; + + static const std::string UNIT_DERIVED_PARAMETER_x_intercept; + + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + static const std::string FUNCTION_STRING; + + static const std::string X_NAME; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; - std::string GetXName() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; + ParamterUnitMapType GetParameterUnits() const override; + + ParameterNamesType GetDerivedParameterNames() const override; + + ParametersSizeType GetNumberOfDerivedParameters() const override; + + ParamterUnitMapType GetDerivedParameterUnits() const override; + ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; - ParameterNamesType GetDerivedParameterNames() const override; + std::string GetModelDisplayName() const override; + + std::string GetModelType() const override; + + FunctionStringType GetFunctionString() const override; + + std::string GetXName() const override; + + std::string GetXAxisName() const override; + + std::string GetXAxisUnit() const override; + + std::string GetYAxisName() const override; + + std::string GetYAxisUnit() const override; - ParametersSizeType GetNumberOfDerivedParameters() const override; protected: LinearModel() {}; ~LinearModel() override {}; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& parameters) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; private: //No copy constructor allowed LinearModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkThreeStepLinearModel.h b/Modules/ModelFit/include/mitkThreeStepLinearModel.h similarity index 61% rename from Modules/Pharmacokinetics/include/mitkThreeStepLinearModel.h rename to Modules/ModelFit/include/mitkThreeStepLinearModel.h index bdfc6a7cff..144c14f081 100644 --- a/Modules/Pharmacokinetics/include/mitkThreeStepLinearModel.h +++ b/Modules/ModelFit/include/mitkThreeStepLinearModel.h @@ -1,125 +1,160 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkThreeStepLinearModel_h #define mitkThreeStepLinearModel_h #include "mitkModelBase.h" -#include "MitkPharmacokineticsExports.h" +#include "MitkModelFitExports.h" namespace mitk { - class MITKPHARMACOKINETICS_EXPORT ThreeStepLinearModel : public mitk::ModelBase + class MITKMODELFIT_EXPORT ThreeStepLinearModel : public mitk::ModelBase { public: typedef ThreeStepLinearModel Self; typedef mitk::ModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; typedef Superclass::ParameterNameType ParameterNameType; typedef Superclass::ParametersSizeType ParametersSizeType; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(ThreeStepLinearModel, ModelBase); - static const std::string MODEL_DISPLAY_NAME; - static const std::string NAME_PARAMETER_s0; - static const std::string NAME_PARAMETER_t1; - static const std::string NAME_PARAMETER_t2; - static const std::string NAME_PARAMETER_a1; - static const std::string NAME_PARAMETER_a2; + static const std::string NAME_PARAMETER_y_bl; + static const std::string NAME_PARAMETER_x0; + static const std::string NAME_PARAMETER_x1; + static const std::string NAME_PARAMETER_b0; static const std::string NAME_PARAMETER_b1; - static const std::string NAME_PARAMETER_b2; - static const std::string UNIT_PARAMETER_s0; - static const std::string UNIT_PARAMETER_t1; - static const std::string UNIT_PARAMETER_t2; - static const std::string UNIT_PARAMETER_a1; - static const std::string UNIT_PARAMETER_a2; + static const unsigned int NUMBER_OF_PARAMETERS; + + static const std::string UNIT_PARAMETER_y_bl; + static const std::string UNIT_PARAMETER_x0; + static const std::string UNIT_PARAMETER_x1; + static const std::string UNIT_PARAMETER_b0; static const std::string UNIT_PARAMETER_b1; - static const std::string UNIT_PARAMETER_b2; - static const unsigned int POSITION_PARAMETER_s0; - static const unsigned int POSITION_PARAMETER_t1; - static const unsigned int POSITION_PARAMETER_t2; - static const unsigned int POSITION_PARAMETER_a1; - static const unsigned int POSITION_PARAMETER_a2; + static const unsigned int POSITION_PARAMETER_y_bl; + static const unsigned int POSITION_PARAMETER_x0; + static const unsigned int POSITION_PARAMETER_x1; + static const unsigned int POSITION_PARAMETER_b0; static const unsigned int POSITION_PARAMETER_b1; - static const unsigned int POSITION_PARAMETER_b2; - static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string NAME_DERIVED_PARAMETER_auc; + static const std::string NAME_DERIVED_PARAMETER_x_fin; + static const std::string NAME_DERIVED_PARAMETER_y_fin; + static const std::string NAME_DERIVED_PARAMETER_y_max; + static const std::string NAME_DERIVED_PARAMETER_y1; + static const std::string NAME_DERIVED_PARAMETER_y2; - std::string GetModelDisplayName() const override; + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; - std::string GetModelType() const override; + static const std::string UNIT_DERIVED_PARAMETER_auc; + static const std::string UNIT_DERIVED_PARAMETER_x_fin; + static const std::string UNIT_DERIVED_PARAMETER_y_fin; + static const std::string UNIT_DERIVED_PARAMETER_y_max; + static const std::string UNIT_DERIVED_PARAMETER_y1; + static const std::string UNIT_DERIVED_PARAMETER_y2; - FunctionStringType GetFunctionString() const override; + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; - std::string GetXName() const override; + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + static const std::string FUNCTION_STRING; + + static const std::string X_NAME; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; + ParameterNamesType GetDerivedParameterNames() const override; + + ParametersSizeType GetNumberOfDerivedParameters() const override; + + ParamterUnitMapType GetDerivedParameterUnits() const override; + ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; - ParameterNamesType GetDerivedParameterNames() const override; + std::string GetModelDisplayName() const override; - ParametersSizeType GetNumberOfDerivedParameters() const override; + std::string GetModelType() const override; - ParamterUnitMapType GetDerivedParameterUnits() const override; + FunctionStringType GetFunctionString() const override; + + std::string GetXName() const override; + + std::string GetXAxisName() const override; + + std::string GetXAxisUnit() const override; + + std::string GetYAxisName() const override; + + std::string GetYAxisUnit() const override; protected: ThreeStepLinearModel() {}; ~ThreeStepLinearModel() override{}; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& parameters) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; static double ComputeSignalFromParameters(double x, double s0, double t1, double t2, double a1, double a2, double b1, double b2); private: //No copy constructor allowed ThreeStepLinearModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkThreeStepLinearModelFactory.h b/Modules/ModelFit/include/mitkThreeStepLinearModelFactory.h similarity index 89% rename from Modules/Pharmacokinetics/include/mitkThreeStepLinearModelFactory.h rename to Modules/ModelFit/include/mitkThreeStepLinearModelFactory.h index 9ea1d756a4..8d844f5abe 100644 --- a/Modules/Pharmacokinetics/include/mitkThreeStepLinearModelFactory.h +++ b/Modules/ModelFit/include/mitkThreeStepLinearModelFactory.h @@ -1,55 +1,55 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkThreeStepLinearModelFactory_h #define mitkThreeStepLinearModelFactory_h #include #include "mitkConcreteModelFactoryBase.h" #include "mitkThreeStepLinearModel.h" #include "mitkThreeStepLinearModelParameterizer.h" -#include "MitkPharmacokineticsExports.h" +#include "MitkModelFitExports.h" namespace mitk { - class MITKPHARMACOKINETICS_EXPORT ThreeStepLinearModelFactory : public ConcreteModelFactoryBase + class MITKMODELFIT_EXPORT ThreeStepLinearModelFactory : public ConcreteModelFactoryBase { public: mitkClassMacroItkParent(ThreeStepLinearModelFactory, ConcreteModelFactoryBase); itkFactorylessNewMacro(Self); /** This function returns the default parameterization (e.g. initial parametrization for fitting) defined by the model developer for for the given model.*/ ParametersType GetDefaultInitialParameterization() const override; protected: ModelParameterizerBase::Pointer DoCreateParameterizer(const modelFit::ModelFitInfo* fit) const override; ThreeStepLinearModelFactory(); ~ThreeStepLinearModelFactory() override; private: //No copy constructor allowed ThreeStepLinearModelFactory(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkThreeStepLinearModelParameterizer.h b/Modules/ModelFit/include/mitkThreeStepLinearModelParameterizer.h similarity index 96% rename from Modules/Pharmacokinetics/include/mitkThreeStepLinearModelParameterizer.h rename to Modules/ModelFit/include/mitkThreeStepLinearModelParameterizer.h index d5dfcd1571..e03e3d8751 100644 --- a/Modules/Pharmacokinetics/include/mitkThreeStepLinearModelParameterizer.h +++ b/Modules/ModelFit/include/mitkThreeStepLinearModelParameterizer.h @@ -1,62 +1,62 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkThreeStepLinearModelParameterizer_h #define mitkThreeStepLinearModelParameterizer_h #include "mitkConcreteModelParameterizerBase.h" #include "mitkThreeStepLinearModel.h" namespace mitk { -class MITKPHARMACOKINETICS_EXPORT ThreeStepLinearModelParameterizer : public +class MITKMODELFIT_EXPORT ThreeStepLinearModelParameterizer : public mitk::ConcreteModelParameterizerBase { public: typedef ThreeStepLinearModelParameterizer Self; typedef mitk::ConcreteModelParameterizerBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; itkTypeMacro(ThreeStepLinearModelParameterizer, ConcreteModelParameterizerBase); itkFactorylessNewMacro(Self); typedef Superclass::ModelBaseType ModelBaseType; typedef Superclass::ModelBasePointer ModelBasePointer; typedef Superclass::ModelType ModelType; typedef Superclass::ModelPointer ModelPointer; typedef Superclass::StaticParameterValueType StaticParameterValueType; typedef Superclass::StaticParameterValuesType StaticParameterValuesType; typedef Superclass::StaticParameterMapType StaticParameterMapType; typedef Superclass::IndexType IndexType; /** This function returns the default parameterization (e.g. initial parametrization for fitting) defined by the model developer for for the given model.*/ ParametersType GetDefaultInitialParameterization() const override; protected: ThreeStepLinearModelParameterizer(){}; ~ThreeStepLinearModelParameterizer() override{}; private: //No copy constructor allowed ThreeStepLinearModelParameterizer(const Self& source); void operator=(const Self&); //purposely not implemented };} #endif diff --git a/Modules/ModelFit/include/mitkTwoStepLinearModel.h b/Modules/ModelFit/include/mitkTwoStepLinearModel.h new file mode 100644 index 0000000000..8e93819089 --- /dev/null +++ b/Modules/ModelFit/include/mitkTwoStepLinearModel.h @@ -0,0 +1,153 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef mitkTwoStepLinearModel_h +#define mitkTwoStepLinearModel_h + +#include "mitkModelBase.h" + +#include "MitkModelFitExports.h" + +namespace mitk +{ + + class MITKMODELFIT_EXPORT TwoStepLinearModel : public mitk::ModelBase + { + + public: + typedef TwoStepLinearModel Self; + typedef mitk::ModelBase Superclass; + typedef itk::SmartPointer< Self > Pointer; + typedef itk::SmartPointer< const Self > ConstPointer; + + typedef Superclass::ParameterNameType ParameterNameType; + typedef Superclass::ParametersSizeType ParametersSizeType; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(TwoStepLinearModel, ModelBase) + + static const std::string NAME_PARAMETER_y0; + static const std::string NAME_PARAMETER_x0; + static const std::string NAME_PARAMETER_b0; + static const std::string NAME_PARAMETER_b1; + + static const unsigned int NUMBER_OF_PARAMETERS; + + static const std::string UNIT_PARAMETER_y0; + static const std::string UNIT_PARAMETER_x0; + static const std::string UNIT_PARAMETER_b0; + static const std::string UNIT_PARAMETER_b1; + + static const unsigned int POSITION_PARAMETER_y0; + static const unsigned int POSITION_PARAMETER_x0; + static const unsigned int POSITION_PARAMETER_b0; + static const unsigned int POSITION_PARAMETER_b1; + + static const std::string NAME_DERIVED_PARAMETER_auc; + static const std::string NAME_DERIVED_PARAMETER_y_fin; + static const std::string NAME_DERIVED_PARAMETER_y_max; + static const std::string NAME_DERIVED_PARAMETER_y1; + + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; + + static const std::string UNIT_DERIVED_PARAMETER_auc; + static const std::string UNIT_DERIVED_PARAMETER_y_fin; + static const std::string UNIT_DERIVED_PARAMETER_y_max; + static const std::string UNIT_DERIVED_PARAMETER_y1; + + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + static const std::string FUNCTION_STRING; + + static const std::string X_NAME; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; + + + ParameterNamesType GetParameterNames() const override; + + ParametersSizeType GetNumberOfParameters() const override; + + ParamterUnitMapType GetParameterUnits() const override; + + ParameterNamesType GetDerivedParameterNames() const override; + + ParametersSizeType GetNumberOfDerivedParameters() const override; + + ParamterUnitMapType GetDerivedParameterUnits() const override; + + ParameterNamesType GetStaticParameterNames() const override; + + ParametersSizeType GetNumberOfStaticParameters() const override; + + std::string GetModelDisplayName() const override; + + std::string GetModelType() const override; + + FunctionStringType GetFunctionString() const override; + + std::string GetXName() const override; + + std::string GetXAxisName() const override; + + std::string GetXAxisUnit() const override; + + std::string GetYAxisName() const override; + + std::string GetYAxisUnit() const override; + + + protected: + TwoStepLinearModel() {}; + virtual ~TwoStepLinearModel(){}; + + + /** + * Actual implementation of the clone method. This method should be reimplemeted + * in subclasses to clone the extra required parameters. + */ + virtual itk::LightObject::Pointer InternalClone() const; + + virtual ModelResultType ComputeModelfunction(const ParametersType& parameters) const; + virtual DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& + parameters) const; + + virtual void SetStaticParameter(const ParameterNameType& name, + const StaticParameterValuesType& values); + virtual StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const; + + static double ComputeSignalFromParameters(double x, double t, double a1, double a2, double b1, double b2); + + private: + + //No copy constructor allowed + TwoStepLinearModel(const Self& source); + void operator=(const Self&); //purposely not implemented + }; +} + + +#endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelFactory.h b/Modules/ModelFit/include/mitkTwoStepLinearModelFactory.h similarity index 89% rename from Modules/Pharmacokinetics/include/mitkTwoStepLinearModelFactory.h rename to Modules/ModelFit/include/mitkTwoStepLinearModelFactory.h index fd13df6575..a4166b4278 100644 --- a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelFactory.h +++ b/Modules/ModelFit/include/mitkTwoStepLinearModelFactory.h @@ -1,55 +1,55 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkTwoStepLinearModelFactory_h #define mitkTwoStepLinearModelFactory_h #include #include "mitkConcreteModelFactoryBase.h" #include "mitkTwoStepLinearModel.h" #include "mitkTwoStepLinearModelParameterizer.h" -#include "MitkPharmacokineticsExports.h" +#include "MitkModelFitExports.h" namespace mitk { - class MITKPHARMACOKINETICS_EXPORT TwoStepLinearModelFactory : public ConcreteModelFactoryBase + class MITKMODELFIT_EXPORT TwoStepLinearModelFactory : public ConcreteModelFactoryBase { public: mitkClassMacroItkParent(TwoStepLinearModelFactory, ConcreteModelFactoryBase); itkFactorylessNewMacro(Self); /** This function returns the default parameterization (e.g. initial parametrization for fitting) defined by the model developer for for the given model.*/ virtual ParametersType GetDefaultInitialParameterization() const; protected: virtual ModelParameterizerBase::Pointer DoCreateParameterizer(const modelFit::ModelFitInfo* fit) const; TwoStepLinearModelFactory(); virtual ~TwoStepLinearModelFactory(); private: //No copy constructor allowed TwoStepLinearModelFactory(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelParameterizer.h b/Modules/ModelFit/include/mitkTwoStepLinearModelParameterizer.h similarity index 96% rename from Modules/Pharmacokinetics/include/mitkTwoStepLinearModelParameterizer.h rename to Modules/ModelFit/include/mitkTwoStepLinearModelParameterizer.h index 588fe4b08b..9beda06309 100644 --- a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelParameterizer.h +++ b/Modules/ModelFit/include/mitkTwoStepLinearModelParameterizer.h @@ -1,63 +1,63 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkTwoStepLinearModelParameterizer_h #define mitkTwoStepLinearModelParameterizer_h #include "mitkConcreteModelParameterizerBase.h" #include "mitkTwoStepLinearModel.h" namespace mitk { -class MITKPHARMACOKINETICS_EXPORT TwoStepLinearModelParameterizer : public +class MITKMODELFIT_EXPORT TwoStepLinearModelParameterizer : public mitk::ConcreteModelParameterizerBase { public: typedef TwoStepLinearModelParameterizer Self; typedef mitk::ConcreteModelParameterizerBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; itkTypeMacro(TwoStepLinearModelParameterizer, ConcreteModelParameterizerBase); itkFactorylessNewMacro(Self); typedef typename Superclass::ModelBaseType ModelBaseType; typedef typename Superclass::ModelBasePointer ModelBasePointer; typedef typename Superclass::ModelType ModelType; typedef typename Superclass::ModelPointer ModelPointer; typedef typename Superclass::StaticParameterValueType StaticParameterValueType; typedef typename Superclass::StaticParameterValuesType StaticParameterValuesType; typedef typename Superclass::StaticParameterMapType StaticParameterMapType; typedef typename Superclass::IndexType IndexType; /** This function returns the default parameterization (e.g. initial parametrization for fitting) defined by the model developer for for the given model.*/ virtual ParametersType GetDefaultInitialParameterization() const; protected: TwoStepLinearModelParameterizer(){}; virtual ~TwoStepLinearModelParameterizer(){}; private: //No copy constructor allowed TwoStepLinearModelParameterizer(const Self& source); void operator=(const Self&); //purposely not implemented };} #endif diff --git a/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp b/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp index 306bc796ad..ee293b11e4 100644 --- a/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp +++ b/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp @@ -1,275 +1,275 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "itkCommand.h" #include "itkMultiOutputNaryFunctorImageFilter.h" #include "mitkPixelBasedParameterFitImageGenerator.h" #include "mitkImageTimeSelector.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkModelFitFunctorPolicy.h" #include "mitkExtractTimeGrid.h" void mitk::PixelBasedParameterFitImageGenerator:: onFitProgressEvent(::itk::Object* caller, const ::itk::EventObject& /*eventObject*/) { - this->InvokeEvent(::itk::ProgressEvent()); auto* process = dynamic_cast(caller); if (process) { this->m_Progress = process->GetProgress(); } + this->InvokeEvent(::itk::ProgressEvent()); }; template void mitk::PixelBasedParameterFitImageGenerator::DoPrepareMask(itk::Image* image) { m_InternalMask = dynamic_cast(image); if (m_InternalMask.IsNull()) { MITK_INFO << "Parameter Fit Generator. Need to cast mask for parameter fit."; using InputImageType = itk::Image; using CastFilterType = itk::CastImageFilter< InputImageType, InternalMaskType >; typename CastFilterType::Pointer spImageCaster = CastFilterType::New(); spImageCaster->SetInput(image); m_InternalMask = spImageCaster->GetOutput(); spImageCaster->Update(); } } template mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType StoreResultImages( mitk::ModelFitFunctorBase::ParameterNamesType ¶mNames, itk::ImageSource* source, mitk::ModelFitFunctorBase::ParameterNamesType::size_type startPos, mitk::ModelFitFunctorBase::ParameterNamesType::size_type& endPos ) { mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType result; for (mitk::ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < paramNames.size(); ++j) { if (source->GetNumberOfOutputs() < startPos+j) { mitkThrow() << "Error while generating fitted parameter images. Number of sources is too low and does not match expected parameter number. Output size: "<< source->GetNumberOfOutputs()<<"; number of param names: "<GetOutput(startPos+j); mitk::CastToMitkImage(outputImg, paramImage); result.insert(std::make_pair(paramNames[j],paramImage)); } endPos = startPos + paramNames.size(); return result; } template void mitk::PixelBasedParameterFitImageGenerator::DoParameterFit(itk::Image* /*image*/) { using InputFrameImageType = itk::Image; using ParameterImageType = itk::Image; using FitFilterType = itk::MultiOutputNaryFunctorImageFilter; typename FitFilterType::Pointer fitFilter = FitFilterType::New(); typename ::itk::MemberCommand::Pointer spProgressCommand = ::itk::MemberCommand::New(); spProgressCommand->SetCallbackFunction(this, &Self::onFitProgressEvent); fitFilter->AddObserver(::itk::ProgressEvent(), spProgressCommand); //add the time frames to the fit filter mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(this->m_DynamicImage); std::vector frameCache; for (unsigned int i = 0; i < this->m_DynamicImage->GetTimeSteps(); ++i) { typename InputFrameImageType::Pointer frameImage; imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); Image::Pointer frameMITKImage = imageTimeSelector->GetOutput(); frameCache.push_back(frameMITKImage); mitk::CastToItkImage(frameMITKImage, frameImage); fitFilter->SetInput(i,frameImage); } ModelBaseType::TimeGridType timeGrid = ExtractTimeGrid(m_DynamicImage); if (m_TimeGridByParameterizer) { if (timeGrid.GetSize() != m_ModelParameterizer->GetDefaultTimeGrid().GetSize()) { mitkThrow() << "Cannot do fitting. Filter is set to use default time grid of the parameterizer, but grid size does not match the number of input image frames. Grid size: " << m_ModelParameterizer->GetDefaultTimeGrid().GetSize() << "; frame count: " << timeGrid.GetSize(); } } else { this->m_ModelParameterizer->SetDefaultTimeGrid(timeGrid); } ModelFitFunctorPolicy functor; functor.SetModelFitFunctor(this->m_FitFunctor); functor.SetModelParameterizer(this->m_ModelParameterizer); fitFilter->SetFunctor(functor); if (this->m_InternalMask.IsNotNull()) { fitFilter->SetMask(this->m_InternalMask); } //generate the fits fitFilter->Update(); //convert the outputs into mitk images and fill the parameter image map ModelBaseType::Pointer refModel = this->m_ModelParameterizer->GenerateParameterizedModel(); ModelFitFunctorBase::ParameterNamesType paramNames = refModel->GetParameterNames(); ModelFitFunctorBase::ParameterNamesType derivedParamNames = refModel->GetDerivedParameterNames(); ModelFitFunctorBase::ParameterNamesType criterionNames = this->m_FitFunctor->GetCriterionNames(); ModelFitFunctorBase::ParameterNamesType evaluationParamNames = this->m_FitFunctor->GetEvaluationParameterNames(); ModelFitFunctorBase::ParameterNamesType debugParamNames = this->m_FitFunctor->GetDebugParameterNames(); if (fitFilter->GetNumberOfOutputs() != (paramNames.size() + derivedParamNames.size() + criterionNames.size() + evaluationParamNames.size() + debugParamNames.size())) { mitkThrow() << "Error while generating fitted parameter images. Fit filter output size does not match expected parameter number. Output size: "<< fitFilter->GetNumberOfOutputs(); } ModelFitFunctorBase::ParameterNamesType::size_type resultPos = 0; this->m_TempResultMap = StoreResultImages(paramNames,fitFilter,resultPos, resultPos); this->m_TempDerivedResultMap = StoreResultImages(derivedParamNames,fitFilter,resultPos, resultPos); this->m_TempCriterionResultMap = StoreResultImages(criterionNames,fitFilter,resultPos, resultPos); this->m_TempEvaluationResultMap = StoreResultImages(evaluationParamNames,fitFilter,resultPos, resultPos); //also add debug params (if generated) to the evaluation result map mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType debugMap = StoreResultImages(debugParamNames, fitFilter, resultPos, resultPos); this->m_TempEvaluationResultMap.insert(debugMap.begin(), debugMap.end()); } bool mitk::PixelBasedParameterFitImageGenerator::HasOutdatedResult() const { bool result = Superclass::HasOutdatedResult(); if (m_ModelParameterizer.IsNotNull()) { if (m_ModelParameterizer->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_FitFunctor.IsNotNull()) { if (m_FitFunctor->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_DynamicImage.IsNotNull()) { if (m_DynamicImage->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_Mask.IsNotNull()) { if (m_Mask->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } return result; }; void mitk::PixelBasedParameterFitImageGenerator::CheckValidInputs() const { Superclass::CheckValidInputs(); if (m_DynamicImage.IsNull()) { mitkThrow() << "Cannot generate fitted parameter images. Input dynamic image is not set."; } }; void mitk::PixelBasedParameterFitImageGenerator::DoFitAndGetResults(ParameterImageMapType& parameterImages, ParameterImageMapType& derivedParameterImages, ParameterImageMapType& criterionImages, ParameterImageMapType& evaluationParameterImages) { this->m_Progress = 0; if(this->m_Mask.IsNotNull()) { AccessFixedDimensionByItk(m_Mask, mitk::PixelBasedParameterFitImageGenerator::DoPrepareMask, 3); } else { this->m_InternalMask = nullptr; } AccessFixedDimensionByItk(m_DynamicImage, mitk::PixelBasedParameterFitImageGenerator::DoParameterFit, 4); parameterImages = this->m_TempResultMap; derivedParameterImages = this->m_TempDerivedResultMap; criterionImages = this->m_TempCriterionResultMap; evaluationParameterImages = this->m_TempEvaluationResultMap; }; double mitk::PixelBasedParameterFitImageGenerator::GetProgress() const { return m_Progress; }; mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetParameterNames() const { ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(); return parameterizedModel->GetParameterNames(); } mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetDerivedParameterNames() const { ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(); return parameterizedModel->GetDerivedParameterNames(); } mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetCriterionNames() const { return this->m_FitFunctor->GetCriterionNames(); } mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetEvaluationParameterNames() const { auto evals = this->m_FitFunctor->GetEvaluationParameterNames(); auto debugs = this->m_FitFunctor->GetDebugParameterNames(); evals.insert(evals.end(), debugs.begin(), debugs.end()); return evals; } diff --git a/Modules/ModelFit/src/Common/mitkROIBasedParameterFitImageGenerator.cpp b/Modules/ModelFit/src/Common/mitkROIBasedParameterFitImageGenerator.cpp index 78fcf960fe..9cb6ff5928 100644 --- a/Modules/ModelFit/src/Common/mitkROIBasedParameterFitImageGenerator.cpp +++ b/Modules/ModelFit/src/Common/mitkROIBasedParameterFitImageGenerator.cpp @@ -1,264 +1,264 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "itkChangeInformationImageFilter.h" #include "mitkROIBasedParameterFitImageGenerator.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" void mitk::ROIBasedParameterFitImageGenerator:: onFitProgressEvent(::itk::Object* caller, const ::itk::EventObject& /*eventObject*/) { - this->InvokeEvent(::itk::ProgressEvent()); itk::ProcessObject* process = dynamic_cast(caller); if (process) { this->m_Progress = process->GetProgress(); } + this->InvokeEvent(::itk::ProgressEvent()); }; template void mitk::ROIBasedParameterFitImageGenerator::DoImageGeneration(itk::Image* image, double value) { typedef itk::Image MaskType; typedef itk::Image ParameterImageType; typedef itk::ChangeInformationImageFilter< ParameterImageType > OutputImageInformationFilterType; typename OutputImageInformationFilterType::Pointer copyGeoInfoFilter = OutputImageInformationFilterType::New(); typename ParameterImageType::Pointer paramImg = ParameterImageType::New(); copyGeoInfoFilter->ChangeDirectionOn(); copyGeoInfoFilter->SetOutputDirection(image->GetDirection()); copyGeoInfoFilter->ChangeOriginOn(); copyGeoInfoFilter->SetOutputOrigin(image->GetOrigin()); copyGeoInfoFilter->ChangeSpacingOn(); copyGeoInfoFilter->SetOutputSpacing(image->GetSpacing()); copyGeoInfoFilter->SetInput(paramImg); copyGeoInfoFilter->Update(); paramImg = copyGeoInfoFilter->GetOutput(); paramImg->SetRegions(image->GetLargestPossibleRegion()); paramImg->Allocate(); paramImg->FillBuffer(0.0); typedef itk::ImageRegionConstIterator MaskIteratorType; typedef itk::ImageRegionIterator ImageIteratorType; MaskIteratorType maskItr(image, image->GetLargestPossibleRegion()); ImageIteratorType imgItr(paramImg, image->GetLargestPossibleRegion()); maskItr.GoToBegin(); imgItr.GoToBegin(); while (!maskItr.IsAtEnd()) { if (maskItr.Get() > 0.0) { imgItr.Set(value); } ++maskItr; ++imgItr; } m_TempResultImage = Image::New(); mitk::CastToMitkImage(paramImg, m_TempResultImage); } bool mitk::ROIBasedParameterFitImageGenerator::HasOutdatedResult() const { bool result = Superclass::HasOutdatedResult(); if (m_ModelParameterizer.IsNotNull()) { if (m_ModelParameterizer->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_Mask.IsNotNull()) { if (m_Mask->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_FitFunctor.IsNotNull()) { if (m_FitFunctor->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } return result; }; void mitk::ROIBasedParameterFitImageGenerator::CheckValidInputs() const { Superclass::CheckValidInputs(); if (m_Mask.IsNull()) { mitkThrow() << "Cannot generate fitted parameter images. Input mask is not set."; } if (m_Signal.Size() != m_TimeGrid.Size()) { mitkThrow() << "Cannot generate fitted parameter images. Signal and TimeGrid do not match."; } }; void mitk::ROIBasedParameterFitImageGenerator::DoFitAndGetResults(ParameterImageMapType& parameterImages, ParameterImageMapType& derivedParameterImages, ParameterImageMapType& criterionImages, ParameterImageMapType& evaluationParameterImages) { this->m_Progress = 0; //fit the signal ModelParameterizerBase::IndexType index; index.Fill(0); this->m_ModelParameterizer->SetDefaultTimeGrid(m_TimeGrid); ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(index); ParameterizerType::ParametersType initialParameters = m_ModelParameterizer->GetInitialParameterization(index); ModelFitFunctorBase::InputPixelArrayType inputValues; for (SignalType::const_iterator pos = m_Signal.begin(); pos != m_Signal.end(); ++pos) { inputValues.push_back(*pos); } ModelFitFunctorBase::OutputPixelArrayType fitResult = m_FitFunctor->Compute(inputValues, parameterizedModel, initialParameters); //generate the results maps ParameterImageMapType tempResultMap; ParameterImageMapType tempDerivedResultMap; ParameterImageMapType tempEvaluationResultMap; ParameterImageMapType tempCriterionResultMap; ModelFitFunctorBase::ParameterNamesType paramNames = parameterizedModel->GetParameterNames(); ModelFitFunctorBase::ParameterNamesType derivedParamNames = parameterizedModel->GetDerivedParameterNames(); ModelFitFunctorBase::ParameterNamesType criterionNames = this->m_FitFunctor->GetCriterionNames(); ModelFitFunctorBase::ParameterNamesType evaluationParamNames = this->m_FitFunctor->GetEvaluationParameterNames(); ModelFitFunctorBase::ParameterNamesType debugParamNames = this->m_FitFunctor->GetDebugParameterNames(); if (fitResult.size() != (paramNames.size() + derivedParamNames.size() + criterionNames.size() + evaluationParamNames.size() + debugParamNames.size())) { mitkThrow() << "Error while generating fitted parameter images. Fit functor output size does not match expected parameter number. Output size: " << fitResult.size(); } for (ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < paramNames.size(); ++j) { ModelFitFunctorBase::OutputPixelArrayType::value_type value = fitResult[j]; AccessByItk_n(m_Mask, mitk::ROIBasedParameterFitImageGenerator::DoImageGeneration, (value)); tempResultMap.insert(std::make_pair(paramNames[j], m_TempResultImage)); } ModelFitFunctorBase::ParameterNamesType::size_type offset = paramNames.size(); for (ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < derivedParamNames.size(); ++j) { ModelFitFunctorBase::OutputPixelArrayType::value_type value = fitResult[j + offset]; AccessByItk_n(m_Mask, mitk::ROIBasedParameterFitImageGenerator::DoImageGeneration, (value)); tempDerivedResultMap.insert(std::make_pair(derivedParamNames[j], m_TempResultImage)); } offset += derivedParamNames.size(); for (ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < criterionNames.size(); ++j) { ModelFitFunctorBase::OutputPixelArrayType::value_type value = fitResult[j + offset]; AccessByItk_n(m_Mask, mitk::ROIBasedParameterFitImageGenerator::DoImageGeneration, (value)); tempCriterionResultMap.insert(std::make_pair(criterionNames[j], m_TempResultImage)); } offset += criterionNames.size(); for (ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < evaluationParamNames.size(); ++j) { ModelFitFunctorBase::OutputPixelArrayType::value_type value = fitResult[j + offset]; AccessByItk_n(m_Mask, mitk::ROIBasedParameterFitImageGenerator::DoImageGeneration, (value)); tempEvaluationResultMap.insert(std::make_pair(evaluationParamNames[j], m_TempResultImage)); } offset += evaluationParamNames.size(); for (ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < debugParamNames.size(); ++j) { //add debug params (if they are generated to the evaluation result map ModelFitFunctorBase::OutputPixelArrayType::value_type value = fitResult[j + offset]; AccessByItk_n(m_Mask, mitk::ROIBasedParameterFitImageGenerator::DoImageGeneration, (value)); tempEvaluationResultMap.insert(std::make_pair(debugParamNames[j], m_TempResultImage)); } parameterImages = tempResultMap; derivedParameterImages = tempDerivedResultMap; criterionImages = tempCriterionResultMap; evaluationParameterImages = tempEvaluationResultMap; }; double mitk::ROIBasedParameterFitImageGenerator::GetProgress() const { return m_Progress; }; mitk::ROIBasedParameterFitImageGenerator::ParameterNamesType mitk::ROIBasedParameterFitImageGenerator::GetParameterNames() const { ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(); return parameterizedModel->GetParameterNames(); } mitk::ROIBasedParameterFitImageGenerator::ParameterNamesType mitk::ROIBasedParameterFitImageGenerator::GetDerivedParameterNames() const { ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(); return parameterizedModel->GetDerivedParameterNames(); } mitk::ROIBasedParameterFitImageGenerator::ParameterNamesType mitk::ROIBasedParameterFitImageGenerator::GetCriterionNames() const { return this->m_FitFunctor->GetCriterionNames(); } mitk::ROIBasedParameterFitImageGenerator::ParameterNamesType mitk::ROIBasedParameterFitImageGenerator::GetEvaluationParameterNames() const { auto evals = this->m_FitFunctor->GetEvaluationParameterNames(); auto debugs = this->m_FitFunctor->GetDebugParameterNames(); evals.insert(evals.end(), debugs.begin(), debugs.end()); return evals; } diff --git a/Modules/ModelFit/src/Models/mitkExpDecayOffsetModel.cpp b/Modules/ModelFit/src/Models/mitkExpDecayOffsetModel.cpp index 4b9a687d65..19e19a1597 100644 --- a/Modules/ModelFit/src/Models/mitkExpDecayOffsetModel.cpp +++ b/Modules/ModelFit/src/Models/mitkExpDecayOffsetModel.cpp @@ -1,101 +1,167 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkExpDecayOffsetModel.h" + +const std::string mitk::ExpDecayOffsetModel::NAME_PARAMETER_y0 = "y-intercept"; +const std::string mitk::ExpDecayOffsetModel::NAME_PARAMETER_k = "rate"; +const std::string mitk::ExpDecayOffsetModel::NAME_PARAMETER_y_bl = "baseline"; + +const unsigned int mitk::ExpDecayOffsetModel::NUMBER_OF_PARAMETERS = 3; + +const std::string mitk::ExpDecayOffsetModel::UNIT_PARAMETER_y0 = "[unit of y]"; +const std::string mitk::ExpDecayOffsetModel::UNIT_PARAMETER_k = "1/[unit of x]"; +const std::string mitk::ExpDecayOffsetModel::UNIT_PARAMETER_y_bl = "[unit of y]"; + +const unsigned int mitk::ExpDecayOffsetModel::POSITION_PARAMETER_y0 = 0; +const unsigned int mitk::ExpDecayOffsetModel::POSITION_PARAMETER_k = 1; +const unsigned int mitk::ExpDecayOffsetModel::POSITION_PARAMETER_y_bl = 2; + +const unsigned int mitk::ExpDecayOffsetModel::NUMBER_OF_STATIC_PARAMETERS = 0; + +const std::string mitk::ExpDecayOffsetModel::MODEL_DISPLAY_NAME = "Exponential Decay Offset Model"; + +const std::string mitk::ExpDecayOffsetModel::MODEL_TYPE = "Generic"; + +const std::string mitk::ExpDecayOffsetModel::FUNCTION_STRING = "y(x) = y-intercept * exp(-rate*x) + baseline"; + +const std::string mitk::ExpDecayOffsetModel::X_NAME = "x"; + +const std::string mitk::ExpDecayOffsetModel::X_AXIS_NAME = "X"; + +const std::string mitk::ExpDecayOffsetModel::X_AXIS_UNIT = "unit of x"; + +const std::string mitk::ExpDecayOffsetModel::Y_AXIS_NAME = "Y"; + +const std::string mitk::ExpDecayOffsetModel::Y_AXIS_UNIT = "unit of y"; + +/////////// + std::string mitk::ExpDecayOffsetModel::GetModelDisplayName() const { - return "Exponential Decay Offset Model"; + return MODEL_DISPLAY_NAME; }; std::string mitk::ExpDecayOffsetModel::GetModelType() const { - return "Generic"; + return MODEL_TYPE; }; mitk::ExpDecayOffsetModel::FunctionStringType mitk::ExpDecayOffsetModel::GetFunctionString() const { - return "a*exp(-1.0*x*b)+c"; + return FUNCTION_STRING; }; std::string mitk::ExpDecayOffsetModel::GetXName() const { - return "x"; + return X_NAME; }; +std::string mitk::ExpDecayOffsetModel::GetXAxisName() const +{ + return X_AXIS_NAME; +}; + +std::string mitk::ExpDecayOffsetModel::GetXAxisUnit() const +{ + return X_AXIS_UNIT; +} + +std::string mitk::ExpDecayOffsetModel::GetYAxisName() const +{ + return Y_AXIS_NAME; +}; + +std::string mitk::ExpDecayOffsetModel::GetYAxisUnit() const +{ + return Y_AXIS_UNIT; +} + mitk::ExpDecayOffsetModel::ParameterNamesType mitk::ExpDecayOffsetModel::GetParameterNames() const { ParameterNamesType result; - result.push_back("a"); - result.push_back("b"); - result.push_back("c"); + result.push_back(NAME_PARAMETER_y0); + result.push_back(NAME_PARAMETER_k); + result.push_back(NAME_PARAMETER_y_bl); return result; }; +mitk::ExpDecayOffsetModel::ParamterUnitMapType mitk::ExpDecayOffsetModel::GetParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_PARAMETER_y0, UNIT_PARAMETER_y0)); + result.insert(std::make_pair(NAME_PARAMETER_k, UNIT_PARAMETER_k)); + result.insert(std::make_pair(NAME_PARAMETER_y_bl, UNIT_PARAMETER_y_bl)); + + return result; +} + mitk::ExpDecayOffsetModel::ParametersSizeType mitk::ExpDecayOffsetModel::GetNumberOfParameters() const { - return 3; + return NUMBER_OF_PARAMETERS; }; mitk::ExpDecayOffsetModel::ModelResultType mitk::ExpDecayOffsetModel::ComputeModelfunction(const ParametersType& parameters) const { ModelResultType signal(m_TimeGrid.GetSize()); const auto timeGridEnd = m_TimeGrid.end(); ModelResultType::iterator signalPos = signal.begin(); for (auto gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd; ++gridPos, ++signalPos) { *signalPos = parameters[0] * exp(-1.0 * (*gridPos) * parameters[1]) + parameters[2]; } return signal; }; mitk::ExpDecayOffsetModel::ParameterNamesType mitk::ExpDecayOffsetModel::GetStaticParameterNames() const { return {}; } mitk::ExpDecayOffsetModel::ParametersSizeType mitk::ExpDecayOffsetModel::GetNumberOfStaticParameters() const { - return 0; + return NUMBER_OF_STATIC_PARAMETERS; } void mitk::ExpDecayOffsetModel::SetStaticParameter(const ParameterNameType& /*name*/, const StaticParameterValuesType& /*values*/) { //do nothing }; mitk::ExpDecayOffsetModel::StaticParameterValuesType mitk::ExpDecayOffsetModel::GetStaticParameterValue( const ParameterNameType& /*name*/) const { StaticParameterValuesType result; //do nothing return result; }; itk::LightObject::Pointer mitk::ExpDecayOffsetModel::InternalClone() const { ExpDecayOffsetModel::Pointer newClone = ExpDecayOffsetModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; diff --git a/Modules/ModelFit/src/Models/mitkExponentialDecayModel.cpp b/Modules/ModelFit/src/Models/mitkExponentialDecayModel.cpp new file mode 100644 index 0000000000..ca96684b30 --- /dev/null +++ b/Modules/ModelFit/src/Models/mitkExponentialDecayModel.cpp @@ -0,0 +1,208 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkExponentialDecayModel.h" +#include "mitkNumericConstants.h" + +const std::string mitk::ExponentialDecayModel::NAME_PARAMETER_y0 = "y-intercept"; +const std::string mitk::ExponentialDecayModel::NAME_PARAMETER_lambda = "lambda"; + +const unsigned int mitk::ExponentialDecayModel::NUMBER_OF_PARAMETERS = 2; + +const std::string mitk::ExponentialDecayModel::UNIT_PARAMETER_y0 = "[unit of y]"; +const std::string mitk::ExponentialDecayModel::UNIT_PARAMETER_lambda = "[unit of x]"; + +const unsigned int mitk::ExponentialDecayModel::POSITION_PARAMETER_y0 = 0; +const unsigned int mitk::ExponentialDecayModel::POSITION_PARAMETER_lambda = 1; + +const std::string mitk::ExponentialDecayModel::NAME_DERIVED_PARAMETER_k = "rate"; + +const unsigned int mitk::ExponentialDecayModel::NUMBER_OF_DERIVED_PARAMETERS = 1; + +const std::string mitk::ExponentialDecayModel::UNIT_DERIVED_PARAMETER_k = "1/[unit of x]"; + +const unsigned int mitk::ExponentialDecayModel::NUMBER_OF_STATIC_PARAMETERS = 0; + +const std::string mitk::ExponentialDecayModel::MODEL_DISPLAY_NAME = "Exponential Decay Model"; + +const std::string mitk::ExponentialDecayModel::MODEL_TYPE = "Generic"; + +const std::string mitk::ExponentialDecayModel::FUNCTION_STRING = "y(x) = y-intercept * exp(-x/lambda)"; + +const std::string mitk::ExponentialDecayModel::X_NAME = "x"; + +const std::string mitk::ExponentialDecayModel::X_AXIS_NAME = "X"; + +const std::string mitk::ExponentialDecayModel::X_AXIS_UNIT = "unit of x"; + +const std::string mitk::ExponentialDecayModel::Y_AXIS_NAME = "Y"; + +const std::string mitk::ExponentialDecayModel::Y_AXIS_UNIT = "unit of y"; + + +std::string mitk::ExponentialDecayModel::GetModelDisplayName() const +{ + return MODEL_DISPLAY_NAME; +}; + +std::string mitk::ExponentialDecayModel::GetModelType() const +{ + return MODEL_TYPE; +}; + +mitk::ExponentialDecayModel::FunctionStringType mitk::ExponentialDecayModel::GetFunctionString() const +{ + return FUNCTION_STRING; +}; + +std::string mitk::ExponentialDecayModel::GetXName() const +{ + return X_NAME; +}; + +std::string mitk::ExponentialDecayModel::GetXAxisName() const +{ + return X_AXIS_NAME; +}; + +std::string mitk::ExponentialDecayModel::GetXAxisUnit() const +{ + return X_AXIS_UNIT; +} + +std::string mitk::ExponentialDecayModel::GetYAxisName() const +{ + return Y_AXIS_NAME; +}; + +std::string mitk::ExponentialDecayModel::GetYAxisUnit() const +{ + return Y_AXIS_UNIT; +} + +mitk::ExponentialDecayModel::ParameterNamesType +mitk::ExponentialDecayModel::GetParameterNames() const +{ + ParameterNamesType result; + result.push_back(NAME_PARAMETER_y0); + result.push_back(NAME_PARAMETER_lambda); + return result; +}; + +mitk::ExponentialDecayModel::ParamterUnitMapType mitk::ExponentialDecayModel::GetParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_PARAMETER_y0, UNIT_PARAMETER_y0)); + result.insert(std::make_pair(NAME_PARAMETER_lambda, UNIT_PARAMETER_lambda)); + + return result; +} + +mitk::ExponentialDecayModel::ParametersSizeType +mitk::ExponentialDecayModel::GetNumberOfParameters() const +{ + return NUMBER_OF_PARAMETERS; +}; + +mitk::ExponentialDecayModel::ParameterNamesType +mitk::ExponentialDecayModel::GetDerivedParameterNames() const +{ + ParameterNamesType result; + result.push_back(NAME_DERIVED_PARAMETER_k); + return result; +}; + +mitk::ExponentialDecayModel::ParametersSizeType +mitk::ExponentialDecayModel::GetNumberOfDerivedParameters() const +{ + return NUMBER_OF_DERIVED_PARAMETERS; +}; + +mitk::ExponentialDecayModel::ParamterUnitMapType mitk::ExponentialDecayModel::GetDerivedParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_k, UNIT_DERIVED_PARAMETER_k)); + + return result; +}; + +mitk::ExponentialDecayModel::ModelResultType +mitk::ExponentialDecayModel::ComputeModelfunction(const ParametersType& parameters) const +{ + double y0 = parameters[POSITION_PARAMETER_y0]; + double lambda = parameters[POSITION_PARAMETER_lambda]; + + ModelResultType signal(m_TimeGrid.GetSize()); + + ModelResultType::iterator signalPos = signal.begin(); + + for (const auto& gridPos : m_TimeGrid) + { + *signalPos = y0 * exp(-1.0 * gridPos/ lambda); + ++signalPos; + } + + return signal; +}; + +mitk::ExponentialDecayModel::ParameterNamesType mitk::ExponentialDecayModel::GetStaticParameterNames() const +{ + ParameterNamesType result; + + return result; +} + +mitk::ExponentialDecayModel::ParametersSizeType mitk::ExponentialDecayModel::GetNumberOfStaticParameters() const +{ + return NUMBER_OF_STATIC_PARAMETERS; +} + +void mitk::ExponentialDecayModel::SetStaticParameter(const ParameterNameType& /*name*/, + const StaticParameterValuesType& /*values*/) +{ + //do nothing +}; + +mitk::ExponentialDecayModel::StaticParameterValuesType mitk::ExponentialDecayModel::GetStaticParameterValue( + const ParameterNameType& /*name*/) const +{ + StaticParameterValuesType result; + + //do nothing + + return result; +}; + + +mitk::ModelBase::DerivedParameterMapType mitk::ExponentialDecayModel::ComputeDerivedParameters( + const mitk::ModelBase::ParametersType ¶meters) const +{ + DerivedParameterMapType result; + + //Model Parameters + double lambda = parameters[POSITION_PARAMETER_lambda]; + + double k = 1.0 / (lambda + mitk::eps); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_k, k)); + return result; +}; + +itk::LightObject::Pointer mitk::ExponentialDecayModel::InternalClone() const +{ + ExponentialDecayModel::Pointer newClone = ExponentialDecayModel::New(); + + newClone->SetTimeGrid(this->m_TimeGrid); + + return newClone.GetPointer(); +}; diff --git a/Modules/ModelFit/src/Models/mitkT2DecayModelFactory.cpp b/Modules/ModelFit/src/Models/mitkExponentialDecayModelFactory.cpp similarity index 53% rename from Modules/ModelFit/src/Models/mitkT2DecayModelFactory.cpp rename to Modules/ModelFit/src/Models/mitkExponentialDecayModelFactory.cpp index 8e843c4dea..a2ab3a559a 100644 --- a/Modules/ModelFit/src/Models/mitkT2DecayModelFactory.cpp +++ b/Modules/ModelFit/src/Models/mitkExponentialDecayModelFactory.cpp @@ -1,45 +1,45 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#include "mitkT2DecayModelFactory.h" -#include "mitkT2DecayModelParameterizer.h" +#include "mitkExponentialDecayModelFactory.h" +#include "mitkExponentialDecayModelParameterizer.h" #include "mitkSimpleBarrierConstraintChecker.h" -mitk::T2DecayModelFactory::T2DecayModelFactory() +mitk::ExponentialDecayModelFactory::ExponentialDecayModelFactory() { }; -mitk::T2DecayModelFactory::~T2DecayModelFactory() +mitk::ExponentialDecayModelFactory::~ExponentialDecayModelFactory() { }; mitk::ModelParameterizerBase::ParametersType -mitk::T2DecayModelFactory::GetDefaultInitialParameterization() const +mitk::ExponentialDecayModelFactory::GetDefaultInitialParameterization() const { - return T2DecayModelParameterizer::New()->GetDefaultInitialParameterization(); + return ExponentialDecayModelParameterizer::New()->GetDefaultInitialParameterization(); }; -mitk::ConstraintCheckerBase::Pointer mitk::T2DecayModelFactory::CreateDefaultConstraints() const +mitk::ConstraintCheckerBase::Pointer mitk::ExponentialDecayModelFactory::CreateDefaultConstraints() const { mitk::SimpleBarrierConstraintChecker::Pointer constraints = SimpleBarrierConstraintChecker::New(); constraints->SetLowerBarrier(0, 0, 0); constraints->SetLowerBarrier(1, 0, 0); return constraints.GetPointer(); }; -mitk::ModelParameterizerBase::Pointer mitk::T2DecayModelFactory::DoCreateParameterizer( +mitk::ModelParameterizerBase::Pointer mitk::ExponentialDecayModelFactory::DoCreateParameterizer( const modelFit::ModelFitInfo* /*fit*/) const { - return T2DecayModelParameterizer::New().GetPointer(); + return ExponentialDecayModelParameterizer::New().GetPointer(); }; diff --git a/Modules/ModelFit/src/Models/mitkT2DecayModelParameterizer.cpp b/Modules/ModelFit/src/Models/mitkExponentialDecayModelParameterizer.cpp similarity index 53% rename from Modules/ModelFit/src/Models/mitkT2DecayModelParameterizer.cpp rename to Modules/ModelFit/src/Models/mitkExponentialDecayModelParameterizer.cpp index 890c5e25b1..f5d2e364d0 100644 --- a/Modules/ModelFit/src/Models/mitkT2DecayModelParameterizer.cpp +++ b/Modules/ModelFit/src/Models/mitkExponentialDecayModelParameterizer.cpp @@ -1,32 +1,32 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#include "mitkT2DecayModelParameterizer.h" +#include "mitkExponentialDecayModelParameterizer.h" -mitk::T2DecayModelParameterizer::ParametersType -mitk::T2DecayModelParameterizer::GetDefaultInitialParameterization() const +mitk::ExponentialDecayModelParameterizer::ParametersType +mitk::ExponentialDecayModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(2); - initialParameters[0] = 10; //M0 - initialParameters[1] = 1000; //T2 + initialParameters[0] = 10; //y0 + initialParameters[1] = 1000; //lambda return initialParameters; }; -mitk::T2DecayModelParameterizer::T2DecayModelParameterizer() +mitk::ExponentialDecayModelParameterizer::ExponentialDecayModelParameterizer() { }; -mitk::T2DecayModelParameterizer::~T2DecayModelParameterizer() +mitk::ExponentialDecayModelParameterizer::~ExponentialDecayModelParameterizer() { }; diff --git a/Modules/ModelFit/src/Models/mitkExponentialSaturationModel.cpp b/Modules/ModelFit/src/Models/mitkExponentialSaturationModel.cpp index 51bcecc086..eb6608c68a 100644 --- a/Modules/ModelFit/src/Models/mitkExponentialSaturationModel.cpp +++ b/Modules/ModelFit/src/Models/mitkExponentialSaturationModel.cpp @@ -1,112 +1,179 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkExponentialSaturationModel.h" #include "mitkNumericConstants.h" +const std::string mitk::ExponentialSaturationModel::NAME_PARAMETER_BAT = "onset"; +const std::string mitk::ExponentialSaturationModel::NAME_PARAMETER_y_bl = "baseline"; +const std::string mitk::ExponentialSaturationModel::NAME_PARAMETER_y_fin = "y_final"; +const std::string mitk::ExponentialSaturationModel::NAME_PARAMETER_k = "rate"; + +const unsigned int mitk::ExponentialSaturationModel::NUMBER_OF_PARAMETERS = 4; + +const std::string mitk::ExponentialSaturationModel::UNIT_PARAMETER_BAT = "[unit of x]"; +const std::string mitk::ExponentialSaturationModel::UNIT_PARAMETER_y_bl = "[unit of y]"; +const std::string mitk::ExponentialSaturationModel::UNIT_PARAMETER_y_fin = "[unit of y]"; +const std::string mitk::ExponentialSaturationModel::UNIT_PARAMETER_k = "1/[unit of x]"; + +const unsigned int mitk::ExponentialSaturationModel::POSITION_PARAMETER_BAT = 0; +const unsigned int mitk::ExponentialSaturationModel::POSITION_PARAMETER_y_bl = 1; +const unsigned int mitk::ExponentialSaturationModel::POSITION_PARAMETER_y_fin = 2; +const unsigned int mitk::ExponentialSaturationModel::POSITION_PARAMETER_k = 3; + +const unsigned int mitk::ExponentialSaturationModel::NUMBER_OF_STATIC_PARAMETERS = 0; + +const std::string mitk::ExponentialSaturationModel::MODEL_DISPLAY_NAME = "Exponential Saturation Model"; + +const std::string mitk::ExponentialSaturationModel::MODEL_TYPE = "Generic"; + +const std::string mitk::ExponentialSaturationModel::FUNCTION_STRING = "if xSetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; diff --git a/Modules/ModelFit/src/Models/mitkLinearModel.cpp b/Modules/ModelFit/src/Models/mitkLinearModel.cpp index 25e6ed786a..beaaf10d40 100644 --- a/Modules/ModelFit/src/Models/mitkLinearModel.cpp +++ b/Modules/ModelFit/src/Models/mitkLinearModel.cpp @@ -1,125 +1,209 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkLinearModel.h" +const std::string mitk::LinearModel::NAME_PARAMETER_b = "slope"; +const std::string mitk::LinearModel::NAME_PARAMETER_y0 = "y-intercept"; + +const unsigned int mitk::LinearModel::NUMBER_OF_PARAMETERS = 2; + +const std::string mitk::LinearModel::UNIT_PARAMETER_b = "[unit of y]/[unit of x]"; +const std::string mitk::LinearModel::UNIT_PARAMETER_y0 = "[unit of y]"; + +const unsigned int mitk::LinearModel::POSITION_PARAMETER_b = 0; +const unsigned int mitk::LinearModel::POSITION_PARAMETER_y0 = 1; + +const std::string mitk::LinearModel::NAME_DERIVED_PARAMETER_x_intercept = "x-intercept"; + +const unsigned int mitk::LinearModel::NUMBER_OF_DERIVED_PARAMETERS = 1; + +const std::string mitk::LinearModel::UNIT_DERIVED_PARAMETER_x_intercept = "[unit of x]"; + +const unsigned int mitk::LinearModel::NUMBER_OF_STATIC_PARAMETERS = 0; + +const std::string mitk::LinearModel::MODEL_DISPLAY_NAME = "Linear Model"; + +const std::string mitk::LinearModel::MODEL_TYPE = "Generic"; + +const std::string mitk::LinearModel::FUNCTION_STRING = "y(x) = y-intercept + slope*x"; + +const std::string mitk::LinearModel::X_NAME = "x"; + +const std::string mitk::LinearModel::X_AXIS_NAME = "X"; + +const std::string mitk::LinearModel::X_AXIS_UNIT = "unit of x"; + +const std::string mitk::LinearModel::Y_AXIS_NAME = "Y"; + +const std::string mitk::LinearModel::Y_AXIS_UNIT = "unit of y"; + + std::string mitk::LinearModel::GetModelDisplayName() const { - return "Linear Model"; + return MODEL_DISPLAY_NAME; }; std::string mitk::LinearModel::GetModelType() const { - return "Generic"; + return MODEL_TYPE; }; mitk::LinearModel::FunctionStringType mitk::LinearModel::GetFunctionString() const { - return "slope*x+offset"; + return FUNCTION_STRING; }; std::string mitk::LinearModel::GetXName() const { - return "x"; + return X_NAME; +}; + +std::string mitk::LinearModel::GetXAxisName() const +{ + return X_AXIS_NAME; +}; + +std::string mitk::LinearModel::GetXAxisUnit() const +{ + return X_AXIS_UNIT; +} + +std::string mitk::LinearModel::GetYAxisName() const +{ + return Y_AXIS_NAME; }; +std::string mitk::LinearModel::GetYAxisUnit() const +{ + return Y_AXIS_UNIT; +} + mitk::LinearModel::ParameterNamesType mitk::LinearModel::GetParameterNames() const { ParameterNamesType result; - result.push_back("slope"); - result.push_back("offset"); + result.push_back(NAME_PARAMETER_b); + result.push_back(NAME_PARAMETER_y0); return result; }; +mitk::LinearModel::ParamterUnitMapType mitk::LinearModel::GetParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_PARAMETER_b, UNIT_PARAMETER_b)); + result.insert(std::make_pair(NAME_PARAMETER_y0, UNIT_PARAMETER_y0)); + + return result; +} + mitk::LinearModel::ParametersSizeType mitk::LinearModel::GetNumberOfParameters() const { - return 2; + return NUMBER_OF_PARAMETERS; }; mitk::LinearModel::ParameterNamesType mitk::LinearModel::GetDerivedParameterNames() const { ParameterNamesType result; - result.push_back("x-intercept"); + result.push_back(NAME_DERIVED_PARAMETER_x_intercept); return result; }; mitk::LinearModel::ParametersSizeType mitk::LinearModel::GetNumberOfDerivedParameters() const { - return 1; + return NUMBER_OF_DERIVED_PARAMETERS; +}; + +mitk::LinearModel::ParamterUnitMapType mitk::LinearModel::GetDerivedParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_x_intercept, UNIT_DERIVED_PARAMETER_x_intercept)); + + return result; }; mitk::LinearModel::ModelResultType mitk::LinearModel::ComputeModelfunction(const ParametersType& parameters) const { + //Model Parameters + double b = parameters[POSITION_PARAMETER_b]; + double y0 = parameters[POSITION_PARAMETER_y0]; + ModelResultType signal(m_TimeGrid.GetSize()); TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); ModelResultType::iterator signalPos = signal.begin(); for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd; ++gridPos, ++signalPos) { - *signalPos = parameters[0] * (*gridPos) + parameters[1]; + *signalPos = b * (*gridPos) + y0; } return signal; }; mitk::LinearModel::ParameterNamesType mitk::LinearModel::GetStaticParameterNames() const { ParameterNamesType result; return result; } mitk::LinearModel::ParametersSizeType mitk::LinearModel::GetNumberOfStaticParameters() const { - return 0; + return NUMBER_OF_STATIC_PARAMETERS; } void mitk::LinearModel::SetStaticParameter(const ParameterNameType& /*name*/, const StaticParameterValuesType& /*values*/) { //do nothing }; mitk::LinearModel::StaticParameterValuesType mitk::LinearModel::GetStaticParameterValue( const ParameterNameType& /*name*/) const { StaticParameterValuesType result; //do nothing return result; }; mitk::ModelBase::DerivedParameterMapType mitk::LinearModel::ComputeDerivedParameters( const mitk::ModelBase::ParametersType& parameters) const { DerivedParameterMapType result; - double intercept = -1 * parameters[1] / parameters[0]; - result.insert(std::make_pair("x-intercept", intercept)); + + //Model Parameters + double b = parameters[POSITION_PARAMETER_b]; + double y0 = parameters[POSITION_PARAMETER_y0]; + + double intercept = -1 * y0 / b; + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_x_intercept, intercept)); return result; }; itk::LightObject::Pointer mitk::LinearModel::InternalClone() const { LinearModel::Pointer newClone = LinearModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; diff --git a/Modules/ModelFit/src/Models/mitkT2DecayModel.cpp b/Modules/ModelFit/src/Models/mitkT2DecayModel.cpp deleted file mode 100644 index 900a5a1bc7..0000000000 --- a/Modules/ModelFit/src/Models/mitkT2DecayModel.cpp +++ /dev/null @@ -1,123 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkT2DecayModel.h" -#include "mitkNumericConstants.h" - -std::string mitk::T2DecayModel::GetModelDisplayName() const -{ - return "T2 Decay Model"; -}; - -std::string mitk::T2DecayModel::GetModelType() const -{ - return "MRSignal"; -}; - -mitk::T2DecayModel::FunctionStringType mitk::T2DecayModel::GetFunctionString() const -{ - return "M0 * exp(-t/T2)"; -}; - -std::string mitk::T2DecayModel::GetXName() const -{ - return "t"; -}; - -mitk::T2DecayModel::ParameterNamesType -mitk::T2DecayModel::GetParameterNames() const -{ - ParameterNamesType result; - result.push_back("M0"); - result.push_back("T2"); - return result; -}; - -mitk::T2DecayModel::ParametersSizeType -mitk::T2DecayModel::GetNumberOfParameters() const -{ - return 2; -}; - -mitk::T2DecayModel::ModelResultType -mitk::T2DecayModel::ComputeModelfunction(const ParametersType& parameters) const -{ - ModelResultType signal(m_TimeGrid.GetSize()); - - ModelResultType::iterator signalPos = signal.begin(); - - for (const auto& gridPos : m_TimeGrid) - { - *signalPos = parameters[0] * exp(-1.0 * gridPos/ parameters[1]); - ++signalPos; - } - - return signal; -}; - -mitk::T2DecayModel::ParameterNamesType mitk::T2DecayModel::GetStaticParameterNames() const -{ - ParameterNamesType result; - - return result; -} - -mitk::T2DecayModel::ParametersSizeType mitk::T2DecayModel::GetNumberOfStaticParameters() const -{ - return 0; -} - -void mitk::T2DecayModel::SetStaticParameter(const ParameterNameType& /*name*/, - const StaticParameterValuesType& /*values*/) -{ - //do nothing -}; - -mitk::T2DecayModel::StaticParameterValuesType mitk::T2DecayModel::GetStaticParameterValue( - const ParameterNameType& /*name*/) const -{ - StaticParameterValuesType result; - - //do nothing - - return result; -}; - -mitk::T2DecayModel::DerivedParametersSizeType mitk::T2DecayModel::GetNumberOfDerivedParameters() const -{ - return 1; -} - -mitk::T2DecayModel::DerivedParameterNamesType mitk::T2DecayModel::GetDerivedParameterNames() const -{ - ParameterNamesType result; - result.push_back("R2"); - return result; -}; - -mitk::ModelBase::DerivedParameterMapType mitk::T2DecayModel::ComputeDerivedParameters( - const mitk::ModelBase::ParametersType ¶meters) const -{ - DerivedParameterMapType result; - double inverse = 1.0 / (parameters[1] + mitk::eps); - result.insert(std::make_pair("R2", inverse)); - return result; -}; - -itk::LightObject::Pointer mitk::T2DecayModel::InternalClone() const -{ - T2DecayModel::Pointer newClone = T2DecayModel::New(); - - newClone->SetTimeGrid(this->m_TimeGrid); - - return newClone.GetPointer(); -}; diff --git a/Modules/ModelFit/src/Models/mitkThreeStepLinearModel.cpp b/Modules/ModelFit/src/Models/mitkThreeStepLinearModel.cpp new file mode 100644 index 0000000000..6ec5cd98dc --- /dev/null +++ b/Modules/ModelFit/src/Models/mitkThreeStepLinearModel.cpp @@ -0,0 +1,321 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkThreeStepLinearModel.h" +#include + +const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_y_bl = "baseline"; +const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_x0 = "x_changepoint1"; +const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_x1 = "x_changepoint2"; +const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_b0 = "slope1"; +const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_b1 = "slope2"; + +const unsigned int mitk::ThreeStepLinearModel::NUMBER_OF_PARAMETERS = 5; + +const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_y_bl = "[unit of y]"; +const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_x0 = "[unit of x]"; +const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_x1 = "[unit of x]"; +const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_b0 = "[unit of y]/[unit of x]"; +const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_b1 = "[unit of y]/[unit of x]"; + +const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_y_bl = 0; +const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_x0 = 1; +const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_x1 = 2; +const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_b0 = 3; +const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_b1 = 4; + +const std::string mitk::ThreeStepLinearModel::NAME_DERIVED_PARAMETER_auc = "auc"; +const std::string mitk::ThreeStepLinearModel::NAME_DERIVED_PARAMETER_x_fin = "x_final"; +const std::string mitk::ThreeStepLinearModel::NAME_DERIVED_PARAMETER_y_fin = "y_final"; +const std::string mitk::ThreeStepLinearModel::NAME_DERIVED_PARAMETER_y_max = "y_max"; +const std::string mitk::ThreeStepLinearModel::NAME_DERIVED_PARAMETER_y1 = "y-intercept1"; +const std::string mitk::ThreeStepLinearModel::NAME_DERIVED_PARAMETER_y2 = "y-intercept2"; + +const unsigned int mitk::ThreeStepLinearModel::NUMBER_OF_DERIVED_PARAMETERS = 6; + +const std::string mitk::ThreeStepLinearModel::UNIT_DERIVED_PARAMETER_auc = "[unit of x]*[unit of y]"; +const std::string mitk::ThreeStepLinearModel::UNIT_DERIVED_PARAMETER_x_fin = "[unit of x]"; +const std::string mitk::ThreeStepLinearModel::UNIT_DERIVED_PARAMETER_y_fin = "[unit of y]"; +const std::string mitk::ThreeStepLinearModel::UNIT_DERIVED_PARAMETER_y_max = "[unit of y]"; +const std::string mitk::ThreeStepLinearModel::UNIT_DERIVED_PARAMETER_y1 = "[unit of y]"; +const std::string mitk::ThreeStepLinearModel::UNIT_DERIVED_PARAMETER_y2 = "[unit of y]"; + +const unsigned int mitk::ThreeStepLinearModel::NUMBER_OF_STATIC_PARAMETERS = 0; + +const std::string mitk::ThreeStepLinearModel::MODEL_DISPLAY_NAME = "Three Step Linear Model"; + +const std::string mitk::ThreeStepLinearModel::MODEL_TYPE = "Generic"; + +const std::string mitk::ThreeStepLinearModel::FUNCTION_STRING = "if x < x_changepoint1: y(x) = baseline, else if x_changepoint1 <= x <= x_changepoint2: y(x) = y-intercept1 + slope1*x, else if x>x_changepoint2: y(x) = y-intercept2 + slope2*x"; + +const std::string mitk::ThreeStepLinearModel::X_NAME = "x"; + +const std::string mitk::ThreeStepLinearModel::X_AXIS_NAME = "X"; + +const std::string mitk::ThreeStepLinearModel::X_AXIS_UNIT = "unit of x"; + +const std::string mitk::ThreeStepLinearModel::Y_AXIS_NAME = "Y"; + +const std::string mitk::ThreeStepLinearModel::Y_AXIS_UNIT = "unit of y"; + + +std::string mitk::ThreeStepLinearModel::GetModelDisplayName() const +{ + return MODEL_DISPLAY_NAME; +}; + +std::string mitk::ThreeStepLinearModel::GetModelType() const +{ + return MODEL_TYPE; +}; + +mitk::ThreeStepLinearModel::FunctionStringType mitk::ThreeStepLinearModel::GetFunctionString() const +{ + return FUNCTION_STRING; +}; + +std::string mitk::ThreeStepLinearModel::GetXName() const +{ + return X_NAME; +}; + +std::string mitk::ThreeStepLinearModel::GetXAxisName() const +{ + return X_AXIS_NAME; +}; + +std::string mitk::ThreeStepLinearModel::GetXAxisUnit() const +{ + return X_AXIS_UNIT; +} + +std::string mitk::ThreeStepLinearModel::GetYAxisName() const +{ + return Y_AXIS_NAME; +}; + +std::string mitk::ThreeStepLinearModel::GetYAxisUnit() const +{ + return Y_AXIS_UNIT; +} + +mitk::ThreeStepLinearModel::ParameterNamesType +mitk::ThreeStepLinearModel::GetParameterNames() const +{ + ParameterNamesType result; + result.push_back(NAME_PARAMETER_y_bl); + result.push_back(NAME_PARAMETER_x0); + result.push_back(NAME_PARAMETER_x1); + result.push_back(NAME_PARAMETER_b0); + result.push_back(NAME_PARAMETER_b1); + return result; +}; + +mitk::ThreeStepLinearModel::ParamterUnitMapType mitk::ThreeStepLinearModel::GetParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_PARAMETER_y_bl, UNIT_PARAMETER_y_bl)); + result.insert(std::make_pair(NAME_PARAMETER_x0, UNIT_PARAMETER_x0)); + result.insert(std::make_pair(NAME_PARAMETER_x1, UNIT_PARAMETER_x1)); + result.insert(std::make_pair(NAME_PARAMETER_b0, UNIT_PARAMETER_b0)); + result.insert(std::make_pair(NAME_PARAMETER_b1, UNIT_PARAMETER_b1)); + + return result; +} + +mitk::ThreeStepLinearModel::ParametersSizeType +mitk::ThreeStepLinearModel::GetNumberOfParameters() const +{ + return NUMBER_OF_PARAMETERS; +}; + +mitk::ThreeStepLinearModel::ParameterNamesType +mitk::ThreeStepLinearModel::GetDerivedParameterNames() const +{ + ParameterNamesType result; + result.push_back(NAME_DERIVED_PARAMETER_auc); + result.push_back(NAME_DERIVED_PARAMETER_x_fin); + result.push_back(NAME_DERIVED_PARAMETER_y_fin); + result.push_back(NAME_DERIVED_PARAMETER_y_max); + result.push_back(NAME_DERIVED_PARAMETER_y1); + result.push_back(NAME_DERIVED_PARAMETER_y2); + return result; +}; + +mitk::ThreeStepLinearModel::ParametersSizeType +mitk::ThreeStepLinearModel::GetNumberOfDerivedParameters() const +{ + return NUMBER_OF_DERIVED_PARAMETERS; +}; + +mitk::ThreeStepLinearModel::ParamterUnitMapType mitk::ThreeStepLinearModel::GetDerivedParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_auc, UNIT_DERIVED_PARAMETER_auc)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_x_fin, UNIT_DERIVED_PARAMETER_x_fin)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_fin, UNIT_DERIVED_PARAMETER_y_fin)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_max, UNIT_DERIVED_PARAMETER_y_max)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y1, UNIT_DERIVED_PARAMETER_y1)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y2, UNIT_DERIVED_PARAMETER_y2)); + + return result; +}; + + +double mitk::ThreeStepLinearModel::ComputeSignalFromParameters(double x, double y_bl, double x0, double x1, double b0, double b1, double y1, double y2) +{ + double signal = 0.0; + + if (x < x0) + { + signal = y_bl; + } + else if (x >= x0 && x <= x1) + { + signal = b0 * x + y1; + } + else + { + signal = b1 * x + y2; + } + + + return signal; +}; + + +mitk::ThreeStepLinearModel::ModelResultType +mitk::ThreeStepLinearModel::ComputeModelfunction(const ParametersType& parameters) const +{ + //Model Parameters + const double y_bl = (double) parameters[POSITION_PARAMETER_y_bl]; + const double x0 = (double) parameters[POSITION_PARAMETER_x0] ; + const double x1 = (double) parameters[POSITION_PARAMETER_x1] ; + const double b0 = (double) parameters[POSITION_PARAMETER_b0] ; + const double b1 = (double) parameters[POSITION_PARAMETER_b1] ; + + double y1 = y_bl - b0 * x0; + double y2 = (b0 * x1 + y1) - (b1 * x1); + + ModelResultType signal(m_TimeGrid.GetSize()); + + TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); + + ModelResultType::iterator signalPos = signal.begin(); + + for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd; ++gridPos, ++signalPos) + { + *signalPos = ComputeSignalFromParameters(*gridPos, y_bl, x0, x1, b0, b1, y1, y2); + } + + return signal; +}; + +mitk::ThreeStepLinearModel::ParameterNamesType mitk::ThreeStepLinearModel::GetStaticParameterNames() const +{ + ParameterNamesType result; + + return result; +} + +mitk::ThreeStepLinearModel::ParametersSizeType mitk::ThreeStepLinearModel::GetNumberOfStaticParameters() const +{ + return 0; +} + +void mitk::ThreeStepLinearModel::SetStaticParameter(const ParameterNameType&, + const StaticParameterValuesType&) +{ + //do nothing +}; + +mitk::ThreeStepLinearModel::StaticParameterValuesType mitk::ThreeStepLinearModel::GetStaticParameterValue( + const ParameterNameType&) const +{ + StaticParameterValuesType result; + + //do nothing + + return result; +}; + +mitk::ModelBase::DerivedParameterMapType mitk::ThreeStepLinearModel::ComputeDerivedParameters( + const mitk::ModelBase::ParametersType& parameters) const +{ + const double y_bl = (double) parameters[POSITION_PARAMETER_y_bl]; + const double x0 = (double) parameters[POSITION_PARAMETER_x0] ; + const double x1 = (double) parameters[POSITION_PARAMETER_x1] ; + const double b0 = (double) parameters[POSITION_PARAMETER_b0] ; + const double b1 = (double) parameters[POSITION_PARAMETER_b1] ; + + const double y1 = y_bl - b0 * x0; + const double y2 = (b0 * x1 + y1) - (b1 * x1); + + unsigned int timeSteps = m_TimeGrid.GetSize(); + + const double x_fin = (m_TimeGrid.empty() == false) ? (m_TimeGrid.GetElement(timeSteps - 1)) : ( mitkThrow() << "An exception occured because time grid is empty, method can't continue."); + + const double y_fin = b1 * x_fin + y2; + + double y_max = y_fin; + if ((b0 >= 0) && (b1 >= 0)) + y_max = y_fin; + else if ((b0 < 0) && (b1 < 0)) + y_max = y_bl; + else if ((b0 > 0) && (b1 < 0)) + y_max = (b0 * x1 + y1); + else + { + if (abs(b0 * (x1 - x0)) >= abs(b1 * (x_fin - x1))) + y_max = y_bl; + else y_max = y_fin; + } + + double auc = 0.0; + TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); + + for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd - 1; ++gridPos) + { + double currentGridPos = *gridPos; + double nextGridPos = *(++gridPos); + double deltaX = nextGridPos - currentGridPos; + double deltaY = ComputeSignalFromParameters(nextGridPos, y_bl, x0, x1, b0, b1, y1, y2) - ComputeSignalFromParameters(currentGridPos, y_bl, x0, x1, b0, b1, y1, y2); + double Yi = ComputeSignalFromParameters(currentGridPos, y_bl, x0, x1, b0, b1, y1, y2 ); + double intI = 0.5 * deltaX * deltaY + Yi * deltaX; + auc += std::abs(intI); + --gridPos; + } + + + DerivedParameterMapType result; + + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_auc, auc)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_x_fin, x_fin)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_fin, y_fin)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_max, y_max)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y1, y1)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y2, y2)); + + + return result; +}; + +itk::LightObject::Pointer mitk::ThreeStepLinearModel::InternalClone() const +{ + ThreeStepLinearModel::Pointer newClone = ThreeStepLinearModel::New(); + + newClone->SetTimeGrid(this->m_TimeGrid); + + return newClone.GetPointer(); +}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModelFactory.cpp b/Modules/ModelFit/src/Models/mitkThreeStepLinearModelFactory.cpp similarity index 100% rename from Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModelFactory.cpp rename to Modules/ModelFit/src/Models/mitkThreeStepLinearModelFactory.cpp diff --git a/Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModelParameterizer.cpp b/Modules/ModelFit/src/Models/mitkThreeStepLinearModelParameterizer.cpp similarity index 92% rename from Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModelParameterizer.cpp rename to Modules/ModelFit/src/Models/mitkThreeStepLinearModelParameterizer.cpp index 6eb6bcf471..3c4dfda211 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModelParameterizer.cpp +++ b/Modules/ModelFit/src/Models/mitkThreeStepLinearModelParameterizer.cpp @@ -1,29 +1,29 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkThreeStepLinearModelParameterizer.h" mitk::ThreeStepLinearModelParameterizer::ParametersType mitk::ThreeStepLinearModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(5); - initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_s0] = 0.0; - initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_t1] = 50.0; - initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_t2] = 100.0; - initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_a1] = 1.0; - initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_a2] = -1.0; + initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_y_bl] = 0.0; + initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_x0] = 50.0; + initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_x1] = 100.0; + initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_b0] = 1.0; + initialParameters[mitk:: ThreeStepLinearModel::POSITION_PARAMETER_b1] = -1.0; return initialParameters; }; diff --git a/Modules/ModelFit/src/Models/mitkTwoStepLinearModel.cpp b/Modules/ModelFit/src/Models/mitkTwoStepLinearModel.cpp new file mode 100644 index 0000000000..ab17e6770f --- /dev/null +++ b/Modules/ModelFit/src/Models/mitkTwoStepLinearModel.cpp @@ -0,0 +1,285 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkTwoStepLinearModel.h" +#include + + +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_y0 = "y-intercept"; +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_x0 = "x_changepoint"; +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_b0 = "slope1"; +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_b1 = "slope2"; + +const unsigned int mitk::TwoStepLinearModel::NUMBER_OF_PARAMETERS = 4; + +const std::string mitk::TwoStepLinearModel::UNIT_PARAMETER_y0 = "[unit of y]"; +const std::string mitk::TwoStepLinearModel::UNIT_PARAMETER_x0 = "[unit of x]"; +const std::string mitk::TwoStepLinearModel::UNIT_PARAMETER_b0 = "[unit of y]/[unit of x]"; +const std::string mitk::TwoStepLinearModel::UNIT_PARAMETER_b1 = "[unit of y]/[unit of x]"; + +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_y0 = 0; +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_x0 = 1; +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_b0 = 2; +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_b1 = 3; + +const std::string mitk::TwoStepLinearModel::NAME_DERIVED_PARAMETER_auc = "auc"; +const std::string mitk::TwoStepLinearModel::NAME_DERIVED_PARAMETER_y_fin = "y_final"; +const std::string mitk::TwoStepLinearModel::NAME_DERIVED_PARAMETER_y_max = "y_max"; +const std::string mitk::TwoStepLinearModel::NAME_DERIVED_PARAMETER_y1 = "y-intercept1"; + +const unsigned int mitk::TwoStepLinearModel::NUMBER_OF_DERIVED_PARAMETERS = 4; + +const std::string mitk::TwoStepLinearModel::UNIT_DERIVED_PARAMETER_auc = "[unit of x]*[unit of y]"; +const std::string mitk::TwoStepLinearModel::UNIT_DERIVED_PARAMETER_y_fin = "[unit of y]"; +const std::string mitk::TwoStepLinearModel::UNIT_DERIVED_PARAMETER_y_max = "[unit of y]"; +const std::string mitk::TwoStepLinearModel::UNIT_DERIVED_PARAMETER_y1 = "[unit of y]"; + +const unsigned int mitk::TwoStepLinearModel::NUMBER_OF_STATIC_PARAMETERS = 0; + +const std::string mitk::TwoStepLinearModel::MODEL_DISPLAY_NAME = "Two Step Linear Model"; + +const std::string mitk::TwoStepLinearModel::MODEL_TYPE = "Generic"; + +const std::string mitk::TwoStepLinearModel::FUNCTION_STRING = "if x < x_changepoint: y(x) = y-intercept + slope1*x, else: y(x) = y-intercept1 + slope2*x"; + +const std::string mitk::TwoStepLinearModel::X_NAME = "x"; + +const std::string mitk::TwoStepLinearModel::X_AXIS_NAME = "X"; + +const std::string mitk::TwoStepLinearModel::X_AXIS_UNIT = "unit of x"; + +const std::string mitk::TwoStepLinearModel::Y_AXIS_NAME = "Y"; + +const std::string mitk::TwoStepLinearModel::Y_AXIS_UNIT = "unit of y"; + + +std::string mitk::TwoStepLinearModel::GetModelDisplayName() const +{ + return MODEL_DISPLAY_NAME; +}; + +std::string mitk::TwoStepLinearModel::GetModelType() const +{ + return MODEL_TYPE; +}; + +mitk::TwoStepLinearModel::FunctionStringType mitk::TwoStepLinearModel::GetFunctionString() const +{ + return FUNCTION_STRING; +}; + +std::string mitk::TwoStepLinearModel::GetXName() const +{ + return X_NAME; +}; + +std::string mitk::TwoStepLinearModel::GetXAxisName() const +{ + return X_AXIS_NAME; +}; + +std::string mitk::TwoStepLinearModel::GetXAxisUnit() const +{ + return X_AXIS_UNIT; +} + +std::string mitk::TwoStepLinearModel::GetYAxisName() const +{ + return Y_AXIS_NAME; +}; + +std::string mitk::TwoStepLinearModel::GetYAxisUnit() const +{ + return Y_AXIS_UNIT; +} + +mitk::TwoStepLinearModel::ParameterNamesType +mitk::TwoStepLinearModel::GetParameterNames() const +{ + ParameterNamesType result; + result.push_back(NAME_PARAMETER_y0); + result.push_back(NAME_PARAMETER_x0); + result.push_back(NAME_PARAMETER_b0); + result.push_back(NAME_PARAMETER_b1); + return result; +}; + +mitk::TwoStepLinearModel::ParamterUnitMapType mitk::TwoStepLinearModel::GetParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_PARAMETER_y0, UNIT_PARAMETER_y0)); + result.insert(std::make_pair(NAME_PARAMETER_x0, UNIT_PARAMETER_x0)); + result.insert(std::make_pair(NAME_PARAMETER_b0, UNIT_PARAMETER_b0)); + result.insert(std::make_pair(NAME_PARAMETER_b1, UNIT_PARAMETER_b1)); + + return result; +} + +mitk::TwoStepLinearModel::ParametersSizeType +mitk::TwoStepLinearModel::GetNumberOfParameters() const +{ + return NUMBER_OF_PARAMETERS; +}; + +mitk::TwoStepLinearModel::ParameterNamesType +mitk::TwoStepLinearModel::GetDerivedParameterNames() const +{ + ParameterNamesType result; + result.push_back(NAME_DERIVED_PARAMETER_auc); + result.push_back(NAME_DERIVED_PARAMETER_y_fin); + result.push_back(NAME_DERIVED_PARAMETER_y_max); + result.push_back(NAME_DERIVED_PARAMETER_y1); + return result; +}; + +mitk::TwoStepLinearModel::ParametersSizeType +mitk::TwoStepLinearModel::GetNumberOfDerivedParameters() const +{ + return NUMBER_OF_DERIVED_PARAMETERS; +}; + +mitk::TwoStepLinearModel::ParamterUnitMapType mitk::TwoStepLinearModel::GetDerivedParameterUnits() const +{ + ParamterUnitMapType result; + + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_auc, UNIT_DERIVED_PARAMETER_auc)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_fin, UNIT_DERIVED_PARAMETER_y_fin)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_max, UNIT_DERIVED_PARAMETER_y_max)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y1, UNIT_DERIVED_PARAMETER_y1)); + + return result; +}; + +double mitk::TwoStepLinearModel::ComputeSignalFromParameters(double x, double x0, double b0, double b1, double y0, double y1) +{ + return (x < x0) ? (b0 * x + y0) : (b1 * x + y1); +}; + + + + +mitk::TwoStepLinearModel::ModelResultType +mitk::TwoStepLinearModel::ComputeModelfunction(const ParametersType& parameters) const +{ + + //Model Parameters + const auto y0 = parameters[POSITION_PARAMETER_y0]; + const auto x0 = parameters[POSITION_PARAMETER_x0] ; + const auto b0 = parameters[POSITION_PARAMETER_b0] ; + const auto b1 = parameters[POSITION_PARAMETER_b1] ; + + double y1 = (b0 - b1) * x0 + y0; + + ModelResultType signal(m_TimeGrid.GetSize()); + + TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); + + ModelResultType::iterator signalPos = signal.begin(); + + for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd; ++gridPos, ++signalPos) + { + *signalPos = ComputeSignalFromParameters(*gridPos, x0, b0, b1, y0, y1); + } + + return signal; +}; + +mitk::TwoStepLinearModel::ParameterNamesType mitk::TwoStepLinearModel::GetStaticParameterNames() const +{ + ParameterNamesType result; + + return result; +} + +mitk::TwoStepLinearModel::ParametersSizeType mitk::TwoStepLinearModel::GetNumberOfStaticParameters() const +{ + return 0; +} + +void mitk::TwoStepLinearModel::SetStaticParameter(const ParameterNameType& /*name*/, + const StaticParameterValuesType& /*values*/) +{ + //do nothing +}; + +mitk::TwoStepLinearModel::StaticParameterValuesType mitk::TwoStepLinearModel::GetStaticParameterValue( + const ParameterNameType& /*name*/) const +{ + StaticParameterValuesType result; + + //do nothing + + return result; +}; + +mitk::ModelBase::DerivedParameterMapType mitk::TwoStepLinearModel::ComputeDerivedParameters( + const mitk::ModelBase::ParametersType& parameters) const +{ + const auto y0 = parameters[POSITION_PARAMETER_y0]; + const auto x0 = parameters[POSITION_PARAMETER_x0] ; + const auto b0 = parameters[POSITION_PARAMETER_b0] ; + const auto b1 = parameters[POSITION_PARAMETER_b1] ; + const auto y1 = (b0 - b1) * x0 + y0; + + unsigned int timeSteps = m_TimeGrid.GetSize(); + + const double taq = (m_TimeGrid.empty() == false) ? (m_TimeGrid.GetElement(timeSteps - 1)) : (mitkThrow() << "An exception occured because time grid is empty, method can't continue."); + + const double y_fin = b1 * taq + y1; + + double y_max = y_fin; + if ((b0 >= 0) && (b1 >= 0)) + y_max = y_fin; + else if ((b0 < 0) && (b1 < 0)) + y_max = y0; + else if ((b0 > 0) && (b1 < 0)) + y_max = (b0 * x0 + y0); + else + { + if (abs(b0 * x0) >= abs(b1 * (taq - x0))) + y_max = y0; + else y_max = y_fin; + } + + double auc = 0.0; + TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); + for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd -1; ++gridPos) + { + double currentGridPos = *gridPos; + double nextGridPos = *(++gridPos); + double deltaX = nextGridPos - currentGridPos; + double deltaY = ComputeSignalFromParameters(nextGridPos, x0, b0, b1, y0, y1) - ComputeSignalFromParameters(currentGridPos, x0, b0, b1, y0, y1); + double Yi = ComputeSignalFromParameters(currentGridPos, x0, b0, b1, y0, y1); + double intI = 0.5 * deltaX * deltaY + Yi * deltaX; + auc += std::abs(intI); + --gridPos; + } + + DerivedParameterMapType result; + + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_auc, auc)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_fin, y_fin)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y_max, y_max)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_y1, y1)); + + return result; +}; + +itk::LightObject::Pointer mitk::TwoStepLinearModel::InternalClone() const +{ + TwoStepLinearModel::Pointer newClone = TwoStepLinearModel::New(); + + newClone->SetTimeGrid(this->m_TimeGrid); + + return newClone.GetPointer(); +}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelFactory.cpp b/Modules/ModelFit/src/Models/mitkTwoStepLinearModelFactory.cpp similarity index 100% rename from Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelFactory.cpp rename to Modules/ModelFit/src/Models/mitkTwoStepLinearModelFactory.cpp diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelParameterizer.cpp b/Modules/ModelFit/src/Models/mitkTwoStepLinearModelParameterizer.cpp similarity index 94% rename from Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelParameterizer.cpp rename to Modules/ModelFit/src/Models/mitkTwoStepLinearModelParameterizer.cpp index 29f6b5287c..b41341ed65 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelParameterizer.cpp +++ b/Modules/ModelFit/src/Models/mitkTwoStepLinearModelParameterizer.cpp @@ -1,28 +1,28 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoStepLinearModelParameterizer.h" mitk::TwoStepLinearModelParameterizer::ParametersType mitk::TwoStepLinearModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(4); - initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_y1] = 0.0; - initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_t] = 50; - initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_a1] = 1.0; - initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_a2] = -1.0; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_y0] = 0.0; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_x0] = 50; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_b0] = 1.0; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_b1] = -1.0; return initialParameters; }; diff --git a/Modules/ModelFit/test/files.cmake b/Modules/ModelFit/test/files.cmake index e0b2725304..c201b63062 100644 --- a/Modules/ModelFit/test/files.cmake +++ b/Modules/ModelFit/test/files.cmake @@ -1,19 +1,22 @@ SET(MODULE_TESTS itkMultiOutputNaryFunctorImageFilterTest.cpp itkMaskedStatisticsImageFilterTest.cpp itkMaskedNaryStatisticsImageFilterTest.cpp mitkLevenbergMarquardtModelFitFunctorTest.cpp mitkPixelBasedParameterFitImageGeneratorTest.cpp mitkROIBasedParameterFitImageGeneratorTest.cpp mitkMaskedDynamicImageStatisticsGeneratorTest.cpp mitkModelFitInfoTest.cpp mitkModelFitStaticParameterMapTest.cpp mitkSimpleBarrierConstraintCheckerTest.cpp mitkMVConstrainedCostFunctionDecoratorTest.cpp mitkConcreteModelFactoryBaseTest.cpp mitkFormulaParserTest.cpp mitkModelFitResultRelationRuleTest.cpp - mitkT2DecayModelTest.cpp + mitkExponentialDecayModelTest.cpp mitkLinearModelTest.cpp mitkExpDecayOffsetModelTest.cpp + mitkTwoStepLinearModelTest.cpp + mitkThreeStepLinearModelTest.cpp + mitkExponentialSaturationModelTest.cpp ) diff --git a/Modules/ModelFit/test/mitkT2DecayModelTest.cpp b/Modules/ModelFit/test/mitkExponentialDecayModelTest.cpp similarity index 72% copy from Modules/ModelFit/test/mitkT2DecayModelTest.cpp copy to Modules/ModelFit/test/mitkExponentialDecayModelTest.cpp index b66b4f5398..4a2cfc9150 100644 --- a/Modules/ModelFit/test/mitkT2DecayModelTest.cpp +++ b/Modules/ModelFit/test/mitkExponentialDecayModelTest.cpp @@ -1,66 +1,66 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Testing #include "mitkModelTestFixture.h" //MITK includes -#include "mitkT2DecayModel.h" +#include "mitkExponentialDecayModel.h" - class mitkT2DecayModelTestSuite : public mitk::mitkModelTestFixture + class mitkExponentialDecayModelTestSuite : public mitk::mitkModelTestFixture { - CPPUNIT_TEST_SUITE(mitkT2DecayModelTestSuite); + CPPUNIT_TEST_SUITE(mitkExponentialDecayModelTestSuite); MITK_TEST(GetModelInfoTest); MITK_TEST(ComputeModelfunctionTest); MITK_TEST(ComputeDerivedParametersTest); CPPUNIT_TEST_SUITE_END(); private: json m_profile_json_obj; json m_modelValues_json_obj; mitk::ModelBase::Pointer m_testmodel; public: void setUp() override { // Parse JSON files - m_profile_json_obj = ParseJSONFile("ModelFit/mitkT2DecayModelTest_profile.json"); - m_modelValues_json_obj = ParseJSONFile("ModelFit/mitkT2DecayModelTest_modelValues.json"); + m_profile_json_obj = ParseJSONFile("ModelFit/mitkExponentialDecayModelTest_profile.json"); + m_modelValues_json_obj = ParseJSONFile("ModelFit/mitkExponentialDecayModelTest_modelValues.json"); // Generate test model - m_testmodel = mitk::T2DecayModel::New(); + m_testmodel = mitk::ExponentialDecayModel::New(); } void tearDown() override { } void GetModelInfoTest() { // comparison of reference and testmodel profile CompareModelAndReferenceProfile(m_testmodel, m_profile_json_obj); } void ComputeModelfunctionTest() { CompareModelAndReferenceSignal(m_testmodel, m_modelValues_json_obj, m_profile_json_obj); } void ComputeDerivedParametersTest() { CompareModelAndReferenceDerivedParameters(m_testmodel, m_modelValues_json_obj); } }; -MITK_TEST_SUITE_REGISTRATION(mitkT2DecayModel) +MITK_TEST_SUITE_REGISTRATION(mitkExponentialDecayModel) diff --git a/Modules/ModelFit/test/mitkT2DecayModelTest.cpp b/Modules/ModelFit/test/mitkExponentialSaturationModelTest.cpp similarity index 71% rename from Modules/ModelFit/test/mitkT2DecayModelTest.cpp rename to Modules/ModelFit/test/mitkExponentialSaturationModelTest.cpp index b66b4f5398..88e36f007a 100644 --- a/Modules/ModelFit/test/mitkT2DecayModelTest.cpp +++ b/Modules/ModelFit/test/mitkExponentialSaturationModelTest.cpp @@ -1,66 +1,66 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Testing #include "mitkModelTestFixture.h" //MITK includes -#include "mitkT2DecayModel.h" +#include "mitkExponentialSaturationModel.h" - class mitkT2DecayModelTestSuite : public mitk::mitkModelTestFixture + class mitkExponentialSaturationModelTestSuite : public mitk::mitkModelTestFixture { - CPPUNIT_TEST_SUITE(mitkT2DecayModelTestSuite); + CPPUNIT_TEST_SUITE(mitkExponentialSaturationModelTestSuite); MITK_TEST(GetModelInfoTest); MITK_TEST(ComputeModelfunctionTest); MITK_TEST(ComputeDerivedParametersTest); CPPUNIT_TEST_SUITE_END(); private: json m_profile_json_obj; json m_modelValues_json_obj; mitk::ModelBase::Pointer m_testmodel; public: void setUp() override { // Parse JSON files - m_profile_json_obj = ParseJSONFile("ModelFit/mitkT2DecayModelTest_profile.json"); - m_modelValues_json_obj = ParseJSONFile("ModelFit/mitkT2DecayModelTest_modelValues.json"); + m_profile_json_obj = ParseJSONFile("ModelFit/mitkExponentialSaturationModelTest_profile.json"); + m_modelValues_json_obj = ParseJSONFile("ModelFit/mitkExponentialSaturationModelTest_modelValues.json"); // Generate test model - m_testmodel = mitk::T2DecayModel::New(); + m_testmodel = mitk::ExponentialSaturationModel::New(); } void tearDown() override { } void GetModelInfoTest() { // comparison of reference and testmodel profile CompareModelAndReferenceProfile(m_testmodel, m_profile_json_obj); } void ComputeModelfunctionTest() { CompareModelAndReferenceSignal(m_testmodel, m_modelValues_json_obj, m_profile_json_obj); } void ComputeDerivedParametersTest() { CompareModelAndReferenceDerivedParameters(m_testmodel, m_modelValues_json_obj); } }; -MITK_TEST_SUITE_REGISTRATION(mitkT2DecayModel) +MITK_TEST_SUITE_REGISTRATION(mitkExponentialSaturationModel) diff --git a/Modules/ModelFit/test/mitkPixelBasedParameterFitImageGeneratorTest.cpp b/Modules/ModelFit/test/mitkPixelBasedParameterFitImageGeneratorTest.cpp index 021df68dee..2fa166c061 100644 --- a/Modules/ModelFit/test/mitkPixelBasedParameterFitImageGeneratorTest.cpp +++ b/Modules/ModelFit/test/mitkPixelBasedParameterFitImageGeneratorTest.cpp @@ -1,155 +1,155 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include "itkImageRegionIterator.h" #include "mitkTestingMacros.h" #include "mitkImage.h" #include "mitkImagePixelReadAccessor.h" #include "mitkPixelBasedParameterFitImageGenerator.h" #include "mitkLinearModelParameterizer.h" #include "mitkLevenbergMarquardtModelFitFunctor.h" #include "mitkTestDynamicImageGenerator.h" int mitkPixelBasedParameterFitImageGeneratorTest(int /*argc*/, char*[] /*argv[]*/) { // always start with this! MITK_TEST_BEGIN("mitkPixelBasedParameterFitImageGenerator") //Prepare test artifacts and helper itk::Index<3> testIndex1; testIndex1[0] = 0; testIndex1[1] = 0; testIndex1[2] = 0; itk::Index<3> testIndex2; testIndex2[0] = 2; testIndex2[1] = 0; testIndex2[2] = 1; itk::Index<3> testIndex3; testIndex3[0] = 1; testIndex3[1] = 1; testIndex3[2] = 2; itk::Index<3> testIndex4; testIndex4[0] = 2; testIndex4[1] = 2; testIndex4[2] = 0; itk::Index<3> testIndex5; testIndex5[0] = 1; testIndex5[1] = 1; testIndex5[2] = 1; itk::Index<3> testIndex6; testIndex6[0] = 2; testIndex6[1] = 1; testIndex6[2] = 1; mitk::Image::Pointer dynamicImage = mitk::GenerateDynamicTestImageMITK(); mitk::LinearModel::Pointer model = mitk::LinearModel::New(); mitk::LevenbergMarquardtModelFitFunctor::Pointer testFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); //Test default usage of filter mitk::PixelBasedParameterFitImageGenerator::Pointer generator = mitk::PixelBasedParameterFitImageGenerator::New(); mitk::LinearModelParameterizer::Pointer parameterizer = mitk::LinearModelParameterizer::New(); generator->SetDynamicImage(dynamicImage); generator->SetModelParameterizer(parameterizer); generator->SetFitFunctor(testFunctor); generator->Generate(); mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType resultImages = generator->GetParameterImages(); mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType derivedResultImages = generator->GetDerivedParameterImages(); CPPUNIT_ASSERT_MESSAGE("Check number of parameter images", 2 == resultImages.size()); MITK_TEST_CONDITION(resultImages.find("slope") != resultImages.end(),"Check if \"slope\" parameter image exists."); - MITK_TEST_CONDITION(resultImages.find("offset") != resultImages.end(),"Check if \"offset\" parameter image exists."); + MITK_TEST_CONDITION(resultImages.find("y-intercept") != resultImages.end(),"Check if \"y-intercept\" parameter image exists."); CPPUNIT_ASSERT_MESSAGE("Check number of derived parameter images", 1 == derivedResultImages.size()); MITK_TEST_CONDITION(derivedResultImages.find("x-intercept") != derivedResultImages.end(),"Check if \"x-intercept\" derived parameter image exists."); mitk::ImagePixelReadAccessor slopeAccessor(resultImages["slope"]); - mitk::ImagePixelReadAccessor offsetAccessor(resultImages["offset"]); + mitk::ImagePixelReadAccessor yinterceptAccessor(resultImages["y-intercept"]); double testValue = slopeAccessor.GetPixelByIndex(testIndex1); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #1"); testValue = slopeAccessor.GetPixelByIndex(testIndex2); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(2000,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #2"); testValue = slopeAccessor.GetPixelByIndex(testIndex3); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(4000,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #3"); testValue = slopeAccessor.GetPixelByIndex(testIndex4); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(8000,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #4"); - testValue = offsetAccessor.GetPixelByIndex(testIndex1); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #1"); - testValue = offsetAccessor.GetPixelByIndex(testIndex2); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(10,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #2"); - testValue = offsetAccessor.GetPixelByIndex(testIndex3); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(20,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #3"); - testValue = offsetAccessor.GetPixelByIndex(testIndex4); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #4"); + testValue = yinterceptAccessor.GetPixelByIndex(testIndex1); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #1"); + testValue = yinterceptAccessor.GetPixelByIndex(testIndex2); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(10,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #2"); + testValue = yinterceptAccessor.GetPixelByIndex(testIndex3); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(20,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #3"); + testValue = yinterceptAccessor.GetPixelByIndex(testIndex4); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #4"); //Test with mask set mitk::Image::Pointer maskImage = mitk::GenerateTestMaskMITK(); generator->SetMask(maskImage); generator->Generate(); resultImages = generator->GetParameterImages(); derivedResultImages = generator->GetDerivedParameterImages(); CPPUNIT_ASSERT_MESSAGE("Check number of parameter images", 2 == resultImages.size()); MITK_TEST_CONDITION(resultImages.find("slope") != resultImages.end(),"Check if \"slope\" parameter image exists."); - MITK_TEST_CONDITION(resultImages.find("offset") != resultImages.end(),"Check if \"offset\" parameter image exists."); + MITK_TEST_CONDITION(resultImages.find("y-intercept") != resultImages.end(),"Check if \"y-intercept\" parameter image exists."); CPPUNIT_ASSERT_MESSAGE("Check number of derived parameter images", 1 == derivedResultImages.size()); MITK_TEST_CONDITION(derivedResultImages.find("x-intercept") != derivedResultImages.end(),"Check if \"x-intercept\" derived parameter image exists."); mitk::ImagePixelReadAccessor slopeAccessor2(resultImages["slope"]); - mitk::ImagePixelReadAccessor offsetAccessor2(resultImages["offset"]); + mitk::ImagePixelReadAccessor yinterceptAccessor2(resultImages["y-intercept"]); testValue = slopeAccessor2.GetPixelByIndex(testIndex1); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #1"); testValue = slopeAccessor2.GetPixelByIndex(testIndex2); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(2000,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #2"); testValue = slopeAccessor2.GetPixelByIndex(testIndex3); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #3"); testValue = slopeAccessor2.GetPixelByIndex(testIndex4); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(8000,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #4"); testValue = slopeAccessor2.GetPixelByIndex(testIndex5); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(4000,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #5"); testValue = slopeAccessor2.GetPixelByIndex(testIndex6); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #6"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex1); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #1"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex2); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(10,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #2"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex3); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #3"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex4); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #4"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex5); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(10,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #5"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex6); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #6"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex1); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #1"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex2); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(10,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #2"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex3); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #3"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex4); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #4"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex5); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(10,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #5"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex6); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #6"); MITK_TEST_END() } diff --git a/Modules/ModelFit/test/mitkROIBasedParameterFitImageGeneratorTest.cpp b/Modules/ModelFit/test/mitkROIBasedParameterFitImageGeneratorTest.cpp index 8a7c122a57..43f24ca5dd 100644 --- a/Modules/ModelFit/test/mitkROIBasedParameterFitImageGeneratorTest.cpp +++ b/Modules/ModelFit/test/mitkROIBasedParameterFitImageGeneratorTest.cpp @@ -1,138 +1,138 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include "itkImageRegionIterator.h" #include "mitkTestingMacros.h" #include "mitkImage.h" #include "mitkImagePixelReadAccessor.h" #include "mitkROIBasedParameterFitImageGenerator.h" #include "mitkLinearModelParameterizer.h" #include "mitkLevenbergMarquardtModelFitFunctor.h" #include "mitkTestDynamicImageGenerator.h" int mitkROIBasedParameterFitImageGeneratorTest(int /*argc*/, char*[] /*argv[]*/) { // always start with this! MITK_TEST_BEGIN("mitkROIBasedParameterFitImageGenerator") //Prepare test artifacts and helper itk::Index<3> testIndex1; testIndex1[0] = 0; testIndex1[1] = 0; testIndex1[2] = 0; itk::Index<3> testIndex2; testIndex2[0] = 2; testIndex2[1] = 0; testIndex2[2] = 1; itk::Index<3> testIndex3; testIndex3[0] = 1; testIndex3[1] = 1; testIndex3[2] = 2; itk::Index<3> testIndex4; testIndex4[0] = 2; testIndex4[1] = 2; testIndex4[2] = 0; itk::Index<3> testIndex5; testIndex5[0] = 1; testIndex5[1] = 1; testIndex5[2] = 1; itk::Index<3> testIndex6; testIndex6[0] = 2; testIndex6[1] = 1; testIndex6[2] = 1; mitk::Image::Pointer maskImage = mitk::GenerateTestMaskMITK(); mitk::ROIBasedParameterFitImageGenerator::TimeGridType timeGrid; timeGrid.SetSize(5); timeGrid[0] = 0; timeGrid[1] = 1; timeGrid[2] = 2; timeGrid[3] = 3; timeGrid[4] = 4; mitk::ROIBasedParameterFitImageGenerator::SignalType signal; signal.SetSize(5); signal[0] = 3; signal[1] = 5; signal[2] = 7; signal[3] = 9; signal[4] = 11; mitk::LinearModel::Pointer model = mitk::LinearModel::New(); mitk::LevenbergMarquardtModelFitFunctor::Pointer testFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); //Test default usage of filter mitk::ROIBasedParameterFitImageGenerator::Pointer generator = mitk::ROIBasedParameterFitImageGenerator::New(); mitk::LinearModelParameterizer::Pointer parameterizer = mitk::LinearModelParameterizer::New(); generator->SetModelParameterizer(parameterizer); generator->SetFitFunctor(testFunctor); generator->SetMask(maskImage); generator->SetSignal(signal); generator->SetTimeGrid(timeGrid); generator->Generate(); mitk::ROIBasedParameterFitImageGenerator::ParameterImageMapType resultImages = generator->GetParameterImages(); mitk::ROIBasedParameterFitImageGenerator::ParameterImageMapType derivedResultImages = generator->GetDerivedParameterImages(); CPPUNIT_ASSERT_MESSAGE("Check number of parameter images", 2 == resultImages.size()); MITK_TEST_CONDITION(resultImages.find("slope") != resultImages.end(),"Check if \"slope\" parameter image exists."); - MITK_TEST_CONDITION(resultImages.find("offset") != resultImages.end(),"Check if \"offset\" parameter image exists."); + MITK_TEST_CONDITION(resultImages.find("y-intercept") != resultImages.end(),"Check if \"y-intercept\" parameter image exists."); CPPUNIT_ASSERT_MESSAGE("Check number of derived parameter images", 1 == derivedResultImages.size()); MITK_TEST_CONDITION(derivedResultImages.find("x-intercept") != derivedResultImages.end(),"Check if \"x-intercept\" derived parameter image exists."); mitk::ImagePixelReadAccessor slopeAccessor2(resultImages["slope"]); - mitk::ImagePixelReadAccessor offsetAccessor2(resultImages["offset"]); + mitk::ImagePixelReadAccessor yinterceptAccessor2(resultImages["y-intercept"]); double testValue = slopeAccessor2.GetPixelByIndex(testIndex1); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(2,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #1"); testValue = slopeAccessor2.GetPixelByIndex(testIndex2); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(2,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #2"); testValue = slopeAccessor2.GetPixelByIndex(testIndex3); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #3"); testValue = slopeAccessor2.GetPixelByIndex(testIndex4); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(2,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #4"); testValue = slopeAccessor2.GetPixelByIndex(testIndex5); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(2,testValue, 1e-4, true)==true, "Check param #1 (slope) at index #5"); testValue = slopeAccessor2.GetPixelByIndex(testIndex6); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #1 (slope) at index #6"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex1); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #1"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex2); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #2"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex3); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #3"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex4); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #4"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex5); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #5"); - testValue = offsetAccessor2.GetPixelByIndex(testIndex6); - MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (offset) at index #6"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex1); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #1"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex2); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #2"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex3); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #3"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex4); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #4"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex5); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(3,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #5"); + testValue = yinterceptAccessor2.GetPixelByIndex(testIndex6); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(0,testValue, 1e-5, true)==true, "Check param #2 (y-intercept) at index #6"); MITK_TEST_END() } diff --git a/Modules/Pharmacokinetics/test/mitkThreeStepLinearModelTest.cpp b/Modules/ModelFit/test/mitkThreeStepLinearModelTest.cpp similarity index 87% rename from Modules/Pharmacokinetics/test/mitkThreeStepLinearModelTest.cpp rename to Modules/ModelFit/test/mitkThreeStepLinearModelTest.cpp index 074f783c6b..ac5116f7fe 100644 --- a/Modules/Pharmacokinetics/test/mitkThreeStepLinearModelTest.cpp +++ b/Modules/ModelFit/test/mitkThreeStepLinearModelTest.cpp @@ -1,66 +1,66 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //Testing #include "mitkModelTestFixture.h" //MITK includes #include "mitkThreeStepLinearModel.h" class mitkThreeStepLinearModelTestSuite : public mitk::mitkModelTestFixture { CPPUNIT_TEST_SUITE(mitkThreeStepLinearModelTestSuite); MITK_TEST(GetModelInfoTest); MITK_TEST(ComputeModelfunctionTest); MITK_TEST(ComputeDerivedParametersTest); CPPUNIT_TEST_SUITE_END(); private: mitk::ThreeStepLinearModel::Pointer m_testmodel; json m_profile_json_obj; json m_modelValues_json_obj; public: void setUp() override { // Parse JSON files - m_profile_json_obj = ParseJSONFile("Pharmacokinetics/mitkThreeStepLinearModelTest_profile.json"); - m_modelValues_json_obj = ParseJSONFile("Pharmacokinetics/mitkThreeStepLinearModelTest_modelValues.json"); + m_profile_json_obj = ParseJSONFile("ModelFit/mitkThreeStepLinearModelTest_profile.json"); + m_modelValues_json_obj = ParseJSONFile("ModelFit/mitkThreeStepLinearModelTest_modelValues.json"); // Generate test model m_testmodel = mitk::ThreeStepLinearModel::New(); } void tearDown() override { } void GetModelInfoTest() { // comparison of reference and testmodel profile CompareModelAndReferenceProfile(m_testmodel, m_profile_json_obj); } void ComputeModelfunctionTest() { CompareModelAndReferenceSignal(m_testmodel, m_modelValues_json_obj, m_profile_json_obj); } void ComputeDerivedParametersTest() { CompareModelAndReferenceDerivedParameters(m_testmodel, m_modelValues_json_obj); } }; MITK_TEST_SUITE_REGISTRATION(mitkThreeStepLinearModel) diff --git a/Modules/Pharmacokinetics/test/mitkTwoStepLinearModelTest.cpp b/Modules/ModelFit/test/mitkTwoStepLinearModelTest.cpp similarity index 88% rename from Modules/Pharmacokinetics/test/mitkTwoStepLinearModelTest.cpp rename to Modules/ModelFit/test/mitkTwoStepLinearModelTest.cpp index de8b2e160f..5fcb2448a8 100644 --- a/Modules/Pharmacokinetics/test/mitkTwoStepLinearModelTest.cpp +++ b/Modules/ModelFit/test/mitkTwoStepLinearModelTest.cpp @@ -1,66 +1,66 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //Testing #include "mitkModelTestFixture.h" //MITK includes #include "mitkTwoStepLinearModel.h" class mitkTwoStepLinearModelTestSuite : public mitk::mitkModelTestFixture { CPPUNIT_TEST_SUITE(mitkTwoStepLinearModelTestSuite); MITK_TEST(GetModelInfoTest); MITK_TEST(ComputeModelfunctionTest); MITK_TEST(ComputeDerivedParametersTest); CPPUNIT_TEST_SUITE_END(); private: mitk::TwoStepLinearModel::Pointer m_testmodel; json m_profile_json_obj; json m_modelValues_json_obj; public: void setUp() override { // Parse JSON files - m_profile_json_obj = ParseJSONFile("Pharmacokinetics/mitkTwoStepLinearModelTest_profile.json"); - m_modelValues_json_obj = ParseJSONFile("Pharmacokinetics/mitkTwoStepLinearModelTest_modelValues.json"); + m_profile_json_obj = ParseJSONFile("ModelFit/mitkTwoStepLinearModelTest_profile.json"); + m_modelValues_json_obj = ParseJSONFile("ModelFit/mitkTwoStepLinearModelTest_modelValues.json"); // Generate test model m_testmodel = mitk::TwoStepLinearModel::New(); } void tearDown() override { } void GetModelInfoTest() { // comparison of reference and testmodel profile CompareModelAndReferenceProfile(m_testmodel, m_profile_json_obj); } void ComputeModelfunctionTest() { CompareModelAndReferenceSignal(m_testmodel, m_modelValues_json_obj, m_profile_json_obj); } void ComputeDerivedParametersTest() { CompareModelAndReferenceDerivedParameters(m_testmodel, m_modelValues_json_obj); } }; MITK_TEST_SUITE_REGISTRATION(mitkTwoStepLinearModel) diff --git a/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp b/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp index d67c683c15..f406aa87b1 100644 --- a/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp +++ b/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp @@ -1,82 +1,73 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include //MR perfusion models #include "mitkDescriptivePharmacokineticBrixModelFactory.h" #include "mitkExtendedToftsModelFactory.h" #include "mitkStandardToftsModelFactory.h" #include "mitkTwoCompartmentExchangeModelFactory.h" -#include "mitkNumericTwoCompartmentExchangeModelFactory.h" //PET perfusion models #include "mitkOneTissueCompartmentModelFactory.h" #include "mitkExtendedOneTissueCompartmentModelFactory.h" #include "mitkTwoTissueCompartmentModelFactory.h" #include "mitkTwoTissueCompartmentFDGModelFactory.h" -#include "mitkNumericTwoTissueCompartmentModelFactory.h" -//general models -#include "mitkTwoStepLinearModelFactory.h" -#include "mitkThreeStepLinearModelFactory.h" namespace mitk { /* * This is the module activator for the IO aspects of the "pharmacokinetics" module. */ class PharmacokineticModelsActivator : public us::ModuleActivator { public: template void RegisterProvider(us::ModuleContext* context) { auto provider = new TProvider(); provider->RegisterService(context); m_RegisteredProviders.push_back(std::unique_ptr(provider)); } void Load(us::ModuleContext* context) override { m_RegisteredProviders.clear(); RegisterProvider >(context); - RegisterProvider >(context); - RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); - RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); - RegisterProvider >(context); } void Unload(us::ModuleContext* ) override { } private: std::vector > m_RegisteredProviders; }; } US_EXPORT_MODULE_ACTIVATOR(mitk::PharmacokineticModelsActivator) diff --git a/Modules/Pharmacokinetics/files.cmake b/Modules/Pharmacokinetics/files.cmake index 03780a2490..48ead4c7e1 100644 --- a/Modules/Pharmacokinetics/files.cmake +++ b/Modules/Pharmacokinetics/files.cmake @@ -1,67 +1,55 @@ file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") set(CPP_FILES Common/mitkAterialInputFunctionGenerator.cpp Common/mitkAIFParametrizerHelper.cpp Common/mitkConcentrationCurveGenerator.cpp Common/mitkDescriptionParameterImageGeneratorBase.cpp Common/mitkPixelBasedDescriptionParameterImageGenerator.cpp DescriptionParameters/mitkCurveDescriptionParameterBase.cpp DescriptionParameters/mitkAreaUnderTheCurveDescriptionParameter.cpp DescriptionParameters/mitkAreaUnderFirstMomentDescriptionParameter.cpp DescriptionParameters/mitkMeanResidenceTimeDescriptionParameter.cpp DescriptionParameters/mitkTimeToPeakCurveDescriptionParameter.cpp DescriptionParameters/mitkMaximumCurveDescriptionParameter.cpp Functors/mitkCurveParameterFunctor.cpp Models/mitkAIFBasedModelBase.cpp Models/mitkDescriptivePharmacokineticBrixModel.cpp Models/mitkDescriptivePharmacokineticBrixModelFactory.cpp Models/mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.cpp Models/mitkDescriptivePharmacokineticBrixModelParameterizer.cpp - Models/mitkThreeStepLinearModel.cpp - Models/mitkThreeStepLinearModelFactory.cpp - Models/mitkThreeStepLinearModelParameterizer.cpp Models/mitkTwoCompartmentExchangeModel.cpp Models/mitkTwoCompartmentExchangeModelFactory.cpp Models/mitkTwoCompartmentExchangeModelParameterizer.cpp - Models/mitkNumericTwoCompartmentExchangeModel.cpp - Models/mitkNumericTwoCompartmentExchangeModelFactory.cpp - Models/mitkNumericTwoCompartmentExchangeModelParameterizer.cpp Models/mitkExtendedToftsModel.cpp Models/mitkExtendedToftsModelFactory.cpp Models/mitkExtendedToftsModelParameterizer.cpp Models/mitkStandardToftsModel.cpp Models/mitkStandardToftsModelFactory.cpp Models/mitkStandardToftsModelParameterizer.cpp Models/mitkOneTissueCompartmentModel.cpp Models/mitkOneTissueCompartmentModelFactory.cpp Models/mitkOneTissueCompartmentModelParameterizer.cpp Models/mitkExtendedOneTissueCompartmentModel.cpp Models/mitkExtendedOneTissueCompartmentModelFactory.cpp Models/mitkExtendedOneTissueCompartmentModelParameterizer.cpp - Models/mitkTwoStepLinearModel.cpp - Models/mitkTwoStepLinearModelFactory.cpp - Models/mitkTwoStepLinearModelParameterizer.cpp Models/mitkTwoTissueCompartmentModel.cpp Models/mitkTwoTissueCompartmentModelFactory.cpp Models/mitkTwoTissueCompartmentModelParameterizer.cpp Models/mitkTwoTissueCompartmentFDGModel.cpp Models/mitkTwoTissueCompartmentFDGModelFactory.cpp Models/mitkTwoTissueCompartmentFDGModelParameterizer.cpp - Models/mitkNumericTwoTissueCompartmentModel.cpp - Models/mitkNumericTwoTissueCompartmentModelFactory.cpp - Models/mitkNumericTwoTissueCompartmentModelParameterizer.cpp SimulationFramework/mitkImageGenerationHelper.cpp ) set(HXX_FILES mitkDICOMSegmentationConstants.h ) set(MOC_H_FILES ) diff --git a/Modules/Pharmacokinetics/include/mitkAIFBasedModelBase.h b/Modules/Pharmacokinetics/include/mitkAIFBasedModelBase.h index 057a7817c6..0a9a18b411 100644 --- a/Modules/Pharmacokinetics/include/mitkAIFBasedModelBase.h +++ b/Modules/Pharmacokinetics/include/mitkAIFBasedModelBase.h @@ -1,114 +1,124 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkAIFBasedModelBase_h #define mitkAIFBasedModelBase_h #include "MitkPharmacokineticsExports.h" #include "mitkModelBase.h" #include "itkArray2D.h" namespace mitk { /** \class AIFBasedModelBase * \brief Base Class for all physiological perfusion models using an Aterial Input Function * All AIF based models come with an array of AIF values and the corresponding TimeGrid ( AIF(t)) * This class provides functions for setting the AIF Values and optionally a specific AIF TimeGrid. * It also provides a method for interpolation of the AIF source array to a specified Timegrid that differs from * AIFTimeGrid. The AIF must be set with an itk::Array. If no AIFTimeGrid is specified with the Setter, it is assumed * that the AIFTimeGrid is the same as the ModelTimegrid (e.g. AIF is derived from data set to be fitted). In this * case, AIFvalues must have the same length as ModelTimeGrid, otherwise an exception is generated*/ class MITKPHARMACOKINETICS_EXPORT AIFBasedModelBase : public mitk::ModelBase { public: typedef AIFBasedModelBase Self; typedef ModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Run-time type information (and related methods). */ itkTypeMacro(PhysiologciModelBase, AIFBasedModelBase); static const std::string NAME_STATIC_PARAMETER_AIF; static const std::string NAME_STATIC_PARAMETER_AIFTimeGrid; static const std::string UNIT_STATIC_PARAMETER_AIF; static const std::string UNIT_STATIC_PARAMETER_AIFTimeGrid; + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; + /** Typedef for Aterial InputFunction AIF(t)*/ typedef itk::Array AterialInputFunctionType; itkGetConstReferenceMacro(AterialInputFunctionValues, AterialInputFunctionType); itkGetConstReferenceMacro(AterialInputFunctionTimeGrid, TimeGridType); itkSetMacro(AterialInputFunctionValues, AterialInputFunctionType); itkSetMacro(AterialInputFunctionTimeGrid, TimeGridType); std::string GetXAxisName() const override; std::string GetXAxisUnit() const override; std::string GetYAxisName() const override; std::string GetYAxisUnit() const override; /** Returns the TimeGrid used for the AIF. Either the externally set AIF time grid * or the time grid of the model if nothing is set.*/ const TimeGridType& GetCurrentAterialInputFunctionTimeGrid() const; /** Returns the Aterial Input function matching currentTimeGrid * The original values are interpolated to the passed TimeGrid * if currentTimeGrid.Size() = 0 , the Original AIF will be returned*/ const AterialInputFunctionType GetAterialInputFunction(TimeGridType currentTimeGrid) const; ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; ParamterUnitMapType GetStaticParameterUnits() const override; protected: AIFBasedModelBase(); ~AIFBasedModelBase() override; /** Reimplementation that checks if AIF and timegrid settings are valid. * @param [out] error Set internally to indicate the error reason if method returns false. Is used by GetSignal() for the * exception comment. * @return Returns true if the model is valid and can compute a signal. Otherwise it returns false.*/ bool ValidateModel(std::string& error) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; TimeGridType m_AterialInputFunctionTimeGrid; AterialInputFunctionType m_AterialInputFunctionValues; private: //No copy constructor allowed AIFBasedModelBase(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkDescriptivePharmacokineticBrixModel.h b/Modules/Pharmacokinetics/include/mitkDescriptivePharmacokineticBrixModel.h index 818cc01427..44c4f3fd8e 100644 --- a/Modules/Pharmacokinetics/include/mitkDescriptivePharmacokineticBrixModel.h +++ b/Modules/Pharmacokinetics/include/mitkDescriptivePharmacokineticBrixModel.h @@ -1,131 +1,143 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkDescriptivePharmacokineticBrixModel_h #define mitkDescriptivePharmacokineticBrixModel_h #include #include "mitkModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { class MITKPHARMACOKINETICS_EXPORT DescriptivePharmacokineticBrixModel : public ModelBase { public: typedef DescriptivePharmacokineticBrixModel Self; typedef ModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(DescriptivePharmacokineticBrixModel, ModelBase); static const std::string MODEL_DISPLAY_NAME; static const std::string NAME_PARAMETER_A; static const std::string NAME_PARAMETER_kep; static const std::string NAME_PARAMETER_kel; - static const std::string NAME_PARAMETER_tlag; - static const std::string NAME_STATIC_PARAMETER_Tau; - static const std::string NAME_STATIC_PARAMETER_S0; + static const std::string NAME_PARAMETER_BAT; + + static const std::string NAME_STATIC_PARAMETER_tau; + static const std::string NAME_STATIC_PARAMETER_s0; static const std::string UNIT_PARAMETER_A; static const std::string UNIT_PARAMETER_kep; static const std::string UNIT_PARAMETER_kel; - static const std::string UNIT_PARAMETER_tlag; - static const std::string UNIT_STATIC_PARAMETER_Tau; - static const std::string UNIT_STATIC_PARAMETER_S0; + static const std::string UNIT_PARAMETER_BAT; + + static const std::string UNIT_STATIC_PARAMETER_tau; + static const std::string UNIT_STATIC_PARAMETER_s0; static const unsigned int POSITION_PARAMETER_A; static const unsigned int POSITION_PARAMETER_kep; static const unsigned int POSITION_PARAMETER_kel; - - //tlag in minutes - static const unsigned int POSITION_PARAMETER_tlag; + static const unsigned int POSITION_PARAMETER_BAT; static const unsigned int NUMBER_OF_PARAMETERS; + static const unsigned int NUMBER_OF_STATIC_PARAMETERS; + + static const std::string MODEL_TYPE; + + static const std::string X_AXIS_NAME; + + static const std::string X_AXIS_UNIT; + + static const std::string Y_AXIS_NAME; + + static const std::string Y_AXIS_UNIT; + itkSetMacro(Tau, double); itkGetConstReferenceMacro(Tau, double); itkSetMacro(S0, double); itkGetConstReferenceMacro(S0, double); std::string GetModelDisplayName() const override; std::string GetModelType() const override; std::string GetXAxisName() const override; std::string GetXAxisUnit() const override; std::string GetYAxisName() const override; std::string GetYAxisUnit() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; ParameterNamesType GetStaticParameterNames() const override; ParametersSizeType GetNumberOfStaticParameters() const override; ParamterUnitMapType GetStaticParameterUnits() const override; protected: DescriptivePharmacokineticBrixModel(); ~DescriptivePharmacokineticBrixModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: /**injection time Tau in minutes [min]*/ double m_Tau; /**Value of the first time step, thus base value to scale the signal. * Default is 1.*/ double m_S0; //No copy constructor allowed DescriptivePharmacokineticBrixModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkExtendedOneTissueCompartmentModel.h b/Modules/Pharmacokinetics/include/mitkExtendedOneTissueCompartmentModel.h index 05c5b21d2c..00420e355f 100644 --- a/Modules/Pharmacokinetics/include/mitkExtendedOneTissueCompartmentModel.h +++ b/Modules/Pharmacokinetics/include/mitkExtendedOneTissueCompartmentModel.h @@ -1,96 +1,94 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkExtendedOneTissueCompartmentModel_h #define mitkExtendedOneTissueCompartmentModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { - /** @class OneTissueCompartmentModel - * @brief Implementation of the Model function of the Tofts pharmacokinetic model, using an Aterial Input Function - * The Model calculates the Concentration-Time-Curve as a convolution of the plasma curve Cp (the AIF) and a tissue specific - * residue function (in this case an exponential: R(t) = ktrans * exp(-ktrans/ve * (t)) ). - * C(t) = vp * Cp(t) + conv(Cp(t),R(t)) - * The parameters ktrans, ve and ve are subject to the fitting routine*/ + class MITKPHARMACOKINETICS_EXPORT ExtendedOneTissueCompartmentModel : public AIFBasedModelBase { public: typedef ExtendedOneTissueCompartmentModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(ExtendedOneTissueCompartmentModel, ModelBase); static const std::string MODEL_DISPLAY_NAME; - static const std::string NAME_PARAMETER_k1; + static const std::string NAME_PARAMETER_K1; static const std::string NAME_PARAMETER_k2; - static const std::string NAME_PARAMETER_VB; + static const std::string NAME_PARAMETER_vb; - static const std::string UNIT_PARAMETER_k1; + static const std::string UNIT_PARAMETER_K1; static const std::string UNIT_PARAMETER_k2; - static const std::string UNIT_PARAMETER_VB; + static const std::string UNIT_PARAMETER_vb; - static const unsigned int POSITION_PARAMETER_k1; + static const unsigned int POSITION_PARAMETER_K1; static const unsigned int POSITION_PARAMETER_k2; - static const unsigned int POSITION_PARAMETER_VB; + static const unsigned int POSITION_PARAMETER_vb; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string MODEL_TYPE; + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; + ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; protected: ExtendedOneTissueCompartmentModel(); ~ExtendedOneTissueCompartmentModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed ExtendedOneTissueCompartmentModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkExtendedToftsModel.h b/Modules/Pharmacokinetics/include/mitkExtendedToftsModel.h index 64f03b7aff..9a85e67f69 100644 --- a/Modules/Pharmacokinetics/include/mitkExtendedToftsModel.h +++ b/Modules/Pharmacokinetics/include/mitkExtendedToftsModel.h @@ -1,106 +1,115 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkExtendedToftsModel_h #define mitkExtendedToftsModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { /** @class ExtendedToftsModel * @brief Implementation of the Model function of the Tofts pharmacokinetic model, using an Aterial Input Function * The Model calculates the Concentration-Time-Curve as a convolution of the plasma curve Cp (the AIF) and a tissue specific * residue function (in this case an exponential: R(t) = ktrans * exp(-ktrans/ve * (t)) ). * C(t) = vp * Cp(t) + conv(Cp(t),R(t)) * The parameters ktrans, ve and ve are subject to the fitting routine*/ class MITKPHARMACOKINETICS_EXPORT ExtendedToftsModel : public AIFBasedModelBase { public: typedef ExtendedToftsModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(ExtendedToftsModel, ModelBase); - static const std::string MODEL_DISPLAY_NAME; - static const std::string NAME_PARAMETER_Ktrans; static const std::string NAME_PARAMETER_ve; static const std::string NAME_PARAMETER_vp; static const std::string UNIT_PARAMETER_Ktrans; static const std::string UNIT_PARAMETER_ve; static const std::string UNIT_PARAMETER_vp; static const unsigned int POSITION_PARAMETER_Ktrans; static const unsigned int POSITION_PARAMETER_ve; static const unsigned int POSITION_PARAMETER_vp; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string NAME_DERIVED_PARAMETER_kep; + + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; + + static const std::string UNIT_DERIVED_PARAMETER_kep; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; ParameterNamesType GetDerivedParameterNames() const override; ParametersSizeType GetNumberOfDerivedParameters() const override; ParamterUnitMapType GetDerivedParameterUnits() const override; protected: ExtendedToftsModel(); ~ExtendedToftsModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed ExtendedToftsModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModel.h b/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModel.h deleted file mode 100644 index b8bcc20432..0000000000 --- a/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModel.h +++ /dev/null @@ -1,128 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkNumericTwoCompartmentExchangeModel_h -#define mitkNumericTwoCompartmentExchangeModel_h - -#include "mitkAIFBasedModelBase.h" -#include "MitkPharmacokineticsExports.h" - - -namespace mitk -{ - /** @class NumericTwoCompartmentExchangeModel - * @brief Implementation of the numeric model function of the 2 Compartment Exchange model, using an Aterial Input Function - * The Model calculates the measured Concentration-Time-Curve from the mass balance equations of the 2-tissue compartent Model - * - * vp * dCp(t)/dt = F * (CA(t) - Cp(t)) - PS * (Cp(t) - Ci(t)) - * ve * dCi(t)/dt = PS * (Cp(t) - Ci(t)) - * - * with concentration curve Cp(t) of the Blood Plasma p and Ce(t) of the Extracellular Extravascular Space(EES)(interstitial volume). CA(t) is the aterial concentration, i.e. the AIF - * Cp(t) and Ce(t) are found numerical via Runge-Kutta methode, implemented in Boosts numeric library ODEINT. Here we use a runge_kutta_cash_karp54 stepper with - * adaptive step size and error controll. - * From the resulting curves Cp(t) and Ce(t) the measured concentration Ctotal(t) is found vial - * - * Ctotal(t) = vp * Cp(t) + ve * Ce(t) - * - * where vp=Vp/VT and ve=Ve/VT are the portion of Plasma/EES volume Vp/Ve of the total volume VT respectively. - * The parameters PS, F, vp and ve are subject to the fitting routine*/ - - class MITKPHARMACOKINETICS_EXPORT NumericTwoCompartmentExchangeModel : public AIFBasedModelBase - { - - public: - typedef NumericTwoCompartmentExchangeModel Self; - typedef AIFBasedModelBase Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - - /** Method for creation through the object factory. */ - itkFactorylessNewMacro(Self); - itkCloneMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(NumericTwoCompartmentExchangeModel, ModelBase); - - typedef std::vector state_type; - - - static const std::string MODEL_DISPLAY_NAME; - - static const std::string NAME_PARAMETER_F; - static const std::string NAME_PARAMETER_PS; - static const std::string NAME_PARAMETER_ve; - static const std::string NAME_PARAMETER_vp; - static const std::string NAME_STATIC_PARAMETER_ODEINTStepSize; - - static const std::string UNIT_PARAMETER_F; - static const std::string UNIT_PARAMETER_PS; - static const std::string UNIT_PARAMETER_ve; - static const std::string UNIT_PARAMETER_vp; - - static const unsigned int POSITION_PARAMETER_F; - static const unsigned int POSITION_PARAMETER_PS; - static const unsigned int POSITION_PARAMETER_ve; - static const unsigned int POSITION_PARAMETER_vp; - - static const unsigned int NUMBER_OF_PARAMETERS; - - std::string GetModelDisplayName() const override; - - std::string GetModelType() const override; - - itkGetConstReferenceMacro(ODEINTStepSize, double); - itkSetMacro(ODEINTStepSize, double); - - - ParameterNamesType GetParameterNames() const override; - ParametersSizeType GetNumberOfParameters() const override; - - ParamterUnitMapType GetParameterUnits() const override; - - ParameterNamesType GetStaticParameterNames() const override; - ParametersSizeType GetNumberOfStaticParameters() const override; - - - protected: - NumericTwoCompartmentExchangeModel(); - ~NumericTwoCompartmentExchangeModel() override; - - /** - * Actual implementation of the clone method. This method should be reimplemeted - * in subclasses to clone the extra required parameters. - */ - itk::LightObject::Pointer InternalClone() const override; - - ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; - - void SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) override; - StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const override; - - void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; - - private: - - - - //No copy constructor allowed - NumericTwoCompartmentExchangeModel(const Self& source); - void operator=(const Self&); //purposely not implemented - - double m_ODEINTStepSize; - - - - }; -} - -#endif diff --git a/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModelFactory.h b/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModelFactory.h deleted file mode 100644 index f94e55ef59..0000000000 --- a/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModelFactory.h +++ /dev/null @@ -1,46 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ -#ifndef mitkNumericTwoCompartmentExchangeModelFactory_h -#define mitkNumericTwoCompartmentExchangeModelFactory_h - -#include "mitkTwoCompartmentExchangeModelFactoryBase.h" -#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" - -namespace mitk -{ - - class MITKPHARMACOKINETICS_EXPORT NumericTwoCompartmentExchangeModelFactory : public - mitk::TwoCompartmentExchangeModelFactoryBase - { - public: - mitkClassMacro(NumericTwoCompartmentExchangeModelFactory, - TwoCompartmentExchangeModelFactoryBase); - itkFactorylessNewMacro(Self); - - protected: - - ModelParameterizerBase::Pointer DoCreateParameterizer(const modelFit::ModelFitInfo* fit) const override; - - NumericTwoCompartmentExchangeModelFactory(); - - ~NumericTwoCompartmentExchangeModelFactory() override; - - private: - - //No copy constructor allowed - NumericTwoCompartmentExchangeModelFactory(const Self& source); - void operator=(const Self&); //purposely not implemented - - }; - -} -#endif diff --git a/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModelParameterizer.h b/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModelParameterizer.h deleted file mode 100644 index 076952c6c3..0000000000 --- a/Modules/Pharmacokinetics/include/mitkNumericTwoCompartmentExchangeModelParameterizer.h +++ /dev/null @@ -1,77 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkNumericTwoCompartmentExchangeModelParameterizer_h -#define mitkNumericTwoCompartmentExchangeModelParameterizer_h - -#include "mitkAIFBasedModelParameterizerBase.h" -#include "mitkNumericTwoCompartmentExchangeModel.h" - -#include "MitkPharmacokineticsExports.h" - -namespace mitk -{ - - class MITKPHARMACOKINETICS_EXPORT NumericTwoCompartmentExchangeModelParameterizer : public - mitk::AIFBasedModelParameterizerBase - { - public: - typedef NumericTwoCompartmentExchangeModelParameterizer Self; - typedef mitk::AIFBasedModelParameterizerBase Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - itkTypeMacro(NumericTwoCompartmentExchangeModelParameterizer, - mitk::AIFBasedModelParameterizerBase); - itkFactorylessNewMacro(Self); - - typedef Superclass::ModelBaseType ModelBaseType; - typedef Superclass::ModelBasePointer ModelBasePointer; - - typedef Superclass::ModelType ModelType; - typedef ModelType::Pointer ModelPointer; - - typedef Superclass::StaticParameterValueType StaticParameterValueType; - typedef Superclass::StaticParameterValuesType StaticParameterValuesType; - typedef Superclass::StaticParameterMapType StaticParameterMapType; - - typedef Superclass::IndexType IndexType; - - itkSetMacro(ODEINTStepSize, double); - itkGetConstReferenceMacro(ODEINTStepSize, double); - - /** Returns the global static parameters for the model. - * @remark this default implementation assumes only AIF and its timegrid as static parameters. - * Reimplement in derived classes to change this behavior.*/ - StaticParameterMapType GetGlobalStaticParameters() const override; - - - /** This function returns the default parameterization (e.g. initial parametrization for fitting) - defined by the model developer for for the given model.*/ - ParametersType GetDefaultInitialParameterization() const override; - - protected: - - double m_ODEINTStepSize; - - NumericTwoCompartmentExchangeModelParameterizer(); - - ~NumericTwoCompartmentExchangeModelParameterizer() override; - - private: - - //No copy constructor allowed - NumericTwoCompartmentExchangeModelParameterizer(const Self& source); - void operator=(const Self&); //purposely not implemented - }; -} -#endif diff --git a/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModel.h b/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModel.h deleted file mode 100644 index 0364852861..0000000000 --- a/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModel.h +++ /dev/null @@ -1,97 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkNumericTwoTissueCompartmentModel_h -#define mitkNumericTwoTissueCompartmentModel_h - -#include "mitkAIFBasedModelBase.h" -#include "MitkPharmacokineticsExports.h" - - -namespace mitk -{ - class MITKPHARMACOKINETICS_EXPORT NumericTwoTissueCompartmentModel : public AIFBasedModelBase - { - - public: - typedef NumericTwoTissueCompartmentModel Self; - typedef AIFBasedModelBase Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - /** Method for creation through the object factory. */ - itkFactorylessNewMacro(Self); - itkCloneMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(NumericTwoTissueCompartmentModel, ModelBase); - - typedef std::vector state_type; - - - /** Model Specifications */ - static const std::string MODEL_DISPLAY_NAME; - - static const std::string NAME_PARAMETER_K1; - static const std::string NAME_PARAMETER_k2; - static const std::string NAME_PARAMETER_k3; - static const std::string NAME_PARAMETER_k4; - static const std::string NAME_PARAMETER_VB; - - static const std::string UNIT_PARAMETER_K1; - static const std::string UNIT_PARAMETER_k2; - static const std::string UNIT_PARAMETER_k3; - static const std::string UNIT_PARAMETER_k4; - static const std::string UNIT_PARAMETER_VB; - - static const unsigned int POSITION_PARAMETER_K1; - static const unsigned int POSITION_PARAMETER_k2; - static const unsigned int POSITION_PARAMETER_k3; - static const unsigned int POSITION_PARAMETER_k4; - static const unsigned int POSITION_PARAMETER_VB; - - static const unsigned int NUMBER_OF_PARAMETERS; - - std::string GetModelDisplayName() const override; - - std::string GetModelType() const override; - - ParameterNamesType GetParameterNames() const override; - ParametersSizeType GetNumberOfParameters() const override; - - ParamterUnitMapType GetParameterUnits() const override; - - protected: - NumericTwoTissueCompartmentModel(); - ~NumericTwoTissueCompartmentModel() override; - - /** - * Actual implementation of the clone method. This method should be reimplemeted - * in subclasses to clone the extra required parameters. - */ - itk::LightObject::Pointer InternalClone() const override; - - ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; - - void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; - - private: - - - //No copy constructor allowed - NumericTwoTissueCompartmentModel(const Self& source); - void operator=(const Self&); //purposely not implemented - - }; -} - -#endif diff --git a/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModelFactory.h b/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModelFactory.h deleted file mode 100644 index 6157d8b36a..0000000000 --- a/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModelFactory.h +++ /dev/null @@ -1,48 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkNumericTwoTissueCompartmentModelFactory_h -#define mitkNumericTwoTissueCompartmentModelFactory_h - -#include "mitkTwoTissueCompartmentModelFactoryBase.h" -#include "mitkNumericTwoTissueCompartmentModelParameterizer.h" - -namespace mitk -{ - - - class MITKPHARMACOKINETICS_EXPORT NumericTwoTissueCompartmentModelFactory : public - mitk::TwoTissueCompartmentModelFactoryBase - { - public: - mitkClassMacro(NumericTwoTissueCompartmentModelFactory, - TwoTissueCompartmentModelFactoryBase); - itkFactorylessNewMacro(Self); - - protected: - - NumericTwoTissueCompartmentModelFactory(); - - ~NumericTwoTissueCompartmentModelFactory() override; - - private: - - //No copy constructor allowed - NumericTwoTissueCompartmentModelFactory(const Self& source); - void operator=(const Self&); //purposely not implemented - - }; - -} - - -#endif diff --git a/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModelParameterizer.h b/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModelParameterizer.h deleted file mode 100644 index 07f71e2720..0000000000 --- a/Modules/Pharmacokinetics/include/mitkNumericTwoTissueCompartmentModelParameterizer.h +++ /dev/null @@ -1,65 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkNumericTwoTissueCompartmentModelParameterizer_h -#define mitkNumericTwoTissueCompartmentModelParameterizer_h - -#include "mitkAIFBasedModelParameterizerBase.h" -#include "mitkNumericTwoTissueCompartmentModel.h" - -#include "MitkPharmacokineticsExports.h" - -namespace mitk -{ - - class MITKPHARMACOKINETICS_EXPORT NumericTwoTissueCompartmentModelParameterizer : public - mitk::AIFBasedModelParameterizerBase - { - public: - typedef NumericTwoTissueCompartmentModelParameterizer Self; - typedef mitk::AIFBasedModelParameterizerBase Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - itkTypeMacro(NumericTwoTissueCompartmentModelParameterizer, - mitk::AIFBasedModelParameterizerBase); - itkFactorylessNewMacro(Self); - - typedef Superclass::ModelBaseType ModelBaseType; - typedef Superclass::ModelBasePointer ModelBasePointer; - - typedef Superclass::ModelType ModelType; - typedef ModelType::Pointer ModelPointer; - - typedef Superclass::StaticParameterValueType StaticParameterValueType; - typedef Superclass::StaticParameterValuesType StaticParameterValuesType; - typedef Superclass::StaticParameterMapType StaticParameterMapType; - - typedef Superclass::IndexType IndexType; - - /** This function returns the default parameterization (e.g. initial parametrization for fitting) - defined by the model developer for for the given model.*/ - ParametersType GetDefaultInitialParameterization() const override; - - protected: - NumericTwoTissueCompartmentModelParameterizer(); - - ~NumericTwoTissueCompartmentModelParameterizer() override; - - private: - - //No copy constructor allowed - NumericTwoTissueCompartmentModelParameterizer(const Self& source); - void operator=(const Self&); //purposely not implemented - }; -} -#endif diff --git a/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h b/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h index 6da9c3a278..1211729ddb 100644 --- a/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h +++ b/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h @@ -1,94 +1,88 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkOneTissueCompartmentModel_h #define mitkOneTissueCompartmentModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { - /** @class OneTissueCompartmentModel - * @brief Implementation of the Model function of the Tofts pharmacokinetic model, using an Aterial Input Function - * The Model calculates the Concentration-Time-Curve as a convolution of the plasma curve Cp (the AIF) and a tissue specific - * residue function (in this case an exponential: R(t) = ktrans * exp(-ktrans/ve * (t)) ). - * C(t) = vp * Cp(t) + conv(Cp(t),R(t)) - * The parameters ktrans, ve and ve are subject to the fitting routine*/ - class MITKPHARMACOKINETICS_EXPORT OneTissueCompartmentModel : public AIFBasedModelBase { public: typedef OneTissueCompartmentModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(OneTissueCompartmentModel, ModelBase); - static const std::string MODEL_DISPLAY_NAME; - - static const std::string NAME_PARAMETER_k1; + static const std::string NAME_PARAMETER_K1; static const std::string NAME_PARAMETER_k2; - static const std::string UNIT_PARAMETER_k1; + static const std::string UNIT_PARAMETER_K1; static const std::string UNIT_PARAMETER_k2; - static const unsigned int POSITION_PARAMETER_k1; + static const unsigned int POSITION_PARAMETER_K1; static const unsigned int POSITION_PARAMETER_k2; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; - protected: OneTissueCompartmentModel(); ~OneTissueCompartmentModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed OneTissueCompartmentModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkStandardToftsModel.h b/Modules/Pharmacokinetics/include/mitkStandardToftsModel.h index 209bc84646..bea02f08d2 100644 --- a/Modules/Pharmacokinetics/include/mitkStandardToftsModel.h +++ b/Modules/Pharmacokinetics/include/mitkStandardToftsModel.h @@ -1,106 +1,113 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkStandardToftsModel_h #define mitkStandardToftsModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { /** @class StandardToftsModel * @brief Implementation of the Model function of the Tofts pharmacokinetic model, using an Aterial Input Function * The Model calculates the Concentration-Time-Curve as a convolution of the plasma curve Cp (the AIF) and a tissue specific * residue function (in this case an exponential: R(t) = ktrans * exp(-ktrans/ve * (t)) ). * C(t) = vp * Cp(t) + conv(Cp(t),R(t)) * The parameters ktrans, ve and ve are subject to the fitting routine*/ class MITKPHARMACOKINETICS_EXPORT StandardToftsModel : public AIFBasedModelBase { public: typedef StandardToftsModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(StandardToftsModel, ModelBase); - static const std::string MODEL_DISPLAY_NAME; - static const std::string NAME_PARAMETER_Ktrans; static const std::string NAME_PARAMETER_ve; - static const std::string NAME_PARAMETER_vp; static const std::string UNIT_PARAMETER_Ktrans; static const std::string UNIT_PARAMETER_ve; - static const std::string UNIT_PARAMETER_vp; static const unsigned int POSITION_PARAMETER_Ktrans; static const unsigned int POSITION_PARAMETER_ve; - static const unsigned int POSITION_PARAMETER_vp; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string NAME_DERIVED_PARAMETER_kep; + + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; + + static const std::string UNIT_DERIVED_PARAMETER_kep; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + + + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; ParameterNamesType GetDerivedParameterNames() const override; ParametersSizeType GetNumberOfDerivedParameters() const override; ParamterUnitMapType GetDerivedParameterUnits() const override; protected: StandardToftsModel(); ~StandardToftsModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed StandardToftsModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModel.h b/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModel.h index d01d5b51c4..bb4071d24d 100644 --- a/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModel.h +++ b/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModel.h @@ -1,113 +1,116 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkTwoCompartmentExchangeModel_h #define mitkTwoCompartmentExchangeModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { /** @class TwoCompartmentExchangeModel * @brief Implementation of the analystical model function of the Physiological Pharmacokinetic Brix model, using an Aterial Input Function * The Model calculates the Concentration-Time-Curve as a convolution of the Aterial Input funciton CA(t) and a tissue specific * residue function R(t). The Residue funktion consists of two parts: The Residue funktion Qp(t) of the Blood Plasma p and the residue funktion Qi(t) of the * interstitial volume I. * Ctotal(t) = vp * Cp(t) + fi * Ci(t) = [vp * Qp(t) + fi * Qi(t)] conv CA(t) * = Qtotal(t) conv CA(t) * where vp=Vp/VT and fi=Vi/VT are the portion of Plasma/interstitial volume Vp/VI of the total volume VT respectively. * The Residuefunctions are described by * Qp(t) = F/Vp * PS/Vp * 1/(l2 - l1) *[ µ2 exp(l1*t) - µ1 exp(l2*t)]* sig(t) * Qi(t) = F/Vp * PS/Vi * 1/(l1 - l2) *[ exp(l1*t) - exp(l2*t)]* sig(t) * = F/Vp * PS/Vp * vp/fi * 1/(l1 - l2) *[ exp(l1*t) - exp(l2*t)]* sig(t) * with * l1/2 = -1/2 (PS/Vp * vp/fi + PS/Vp + F/Vp) +/- sqrt((PS/Vp * vp/fi + PS/Vp + F/Vp)² - 4* F/Vp * PS/Vp * vp/fi) * µ1/2 = F/Vp * Vp/PS + 1 + Vp/PS* l1/2 * * The parameters PS/Vp, F/Vp, vp and fi are subject to the fitting routine*/ class MITKPHARMACOKINETICS_EXPORT TwoCompartmentExchangeModel : public AIFBasedModelBase { public: typedef TwoCompartmentExchangeModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(TwoCompartmentExchangeModel, ModelBase); /** Model Specifications */ - static const std::string MODEL_DISPLAY_NAME; static const std::string NAME_PARAMETER_F; static const std::string NAME_PARAMETER_PS; static const std::string NAME_PARAMETER_ve; static const std::string NAME_PARAMETER_vp; static const unsigned int POSITION_PARAMETER_F; static const unsigned int POSITION_PARAMETER_PS; static const unsigned int POSITION_PARAMETER_ve; static const unsigned int POSITION_PARAMETER_vp; static const std::string UNIT_PARAMETER_F; static const std::string UNIT_PARAMETER_PS; static const std::string UNIT_PARAMETER_ve; static const std::string UNIT_PARAMETER_vp; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; protected: TwoCompartmentExchangeModel(); ~TwoCompartmentExchangeModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed TwoCompartmentExchangeModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModelDifferentialEquations.h b/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModelDifferentialEquations.h deleted file mode 100644 index f9e4b461fa..0000000000 --- a/Modules/Pharmacokinetics/include/mitkTwoCompartmentExchangeModelDifferentialEquations.h +++ /dev/null @@ -1,114 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkTwoCompartmentExchangeModelDifferentialEquations_h -#define mitkTwoCompartmentExchangeModelDifferentialEquations_h - -#include "mitkNumericTwoCompartmentExchangeModel.h" - -namespace mitk{ -/** @class TwoCompartmentExchangeModelDifferentialEquations - * @brief Helper Class for NumericTwoCompartmentExchangeModel: Defines the differential equations (Mass Balance Equations) in the 2 Compartment Exchange model. - * The 2 Compartment Exchange model is defined via the mass balance equations - * vp * dCp(t)/dt = F * (CA(t) - Cp(t)) - PS * (Cp(t) - Ce(t)) - * ve * dCe(t)/dt = PS * (Cp(t) - Ce(t)) - * Boost ODEINT performs a stepwise numeric integration (e.g. via Runge-Kutta method) of the initial value problem - * x' = dx/dt = f(x,t) - * It needs an operator () (a functor) that calculates dx/dt = dxdt for a given x and t. - * Parameters are F, PS, ve and vp and the time dependent Ca(t) =AIF, that is interpolated to the current step t -*/ - -class TwoCompartmentExchangeModelDifferentialEquations -{ -public: - - typedef std::vector< double > AIFType; - - /** @brief Functor for differential equation of Physiological Pharmacokinetic Brix Model - * Takes current state x = x(t) and time t and calculates the corresponding dxdt = dx/dt - */ - void operator() (const mitk::NumericTwoCompartmentExchangeModel::state_type &x, mitk::NumericTwoCompartmentExchangeModel::state_type &dxdt, const double t) - { - double Ca_t = InterpolateAIFToCurrentTimeStep(t); - -// dxdt[0] = -(this->FVP + this->PSVP)*x[0] - this->PSVP*x[1]+this->FVP*Ca_t; - dxdt[0] = (1/this->vp) * ( this->F*(Ca_t - x[0]) - this->PS*(x[0] - x[1]) ); - dxdt[1] = (1/this->ve) * this->PS * (x[0] - x[1]); - - } - - TwoCompartmentExchangeModelDifferentialEquations() : F(0), PS(0), ve(0), vp(0), m_AIF(0), m_AIFTimeGrid(0) - { - } - - /** @brief Initialize class with parameters F/Vp, PS/Vp, fi and fp that are free fit parameters*/ - void initialize(double Fp, double ps, double fi, double fp) - { - this->F = Fp; - this->PS = ps; - this->ve = fi; - this->vp = fp; - } - - - void setAIF(AIFType &aif) - { - this->m_AIF = aif; - } - - - void setAIFTimeGrid(AIFType &grid) - { - this->m_AIFTimeGrid = grid; - } - -private: - - double F; - double PS; - double ve; - double vp; - - AIFType m_AIF; - AIFType m_AIFTimeGrid; - - - /** @brief Internal routine to interpolate the AIF to the current time point t used for integration - * The numerical integration of ODEINT is performed on an adaptive timegrid (adaptive step size dt) different from the time grid of the AIF and model function. - * Thus, the AIF value Ca(t) has to be interpolated from the set AIF - */ - double InterpolateAIFToCurrentTimeStep(double t) - { - double lastValue = m_AIF[0]; - double lastTime = std::numeric_limits::min(); - - AIFType::const_iterator posITime = m_AIFTimeGrid.begin(); - AIFType::const_iterator posValue = m_AIF.begin(); - - while(t > *posITime) - { - lastValue = *posValue; - lastTime = *posITime; - ++posValue; - ++posITime; - } - double weightLast = 1 - (t - lastTime)/(*posITime - lastTime); - double weightNext = 1- (*posITime - t)/(*posITime - lastTime); - double result = weightLast * lastValue + weightNext * (*posValue); - - return result; - } - -}; -} - -#endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModel.h b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModel.h deleted file mode 100644 index 92b03e5903..0000000000 --- a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModel.h +++ /dev/null @@ -1,106 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkTwoStepLinearModel_h -#define mitkTwoStepLinearModel_h - -#include "mitkModelBase.h" - -#include "MitkPharmacokineticsExports.h" - -namespace mitk -{ - - class MITKPHARMACOKINETICS_EXPORT TwoStepLinearModel : public mitk::ModelBase - { - - public: - typedef TwoStepLinearModel Self; - typedef mitk::ModelBase Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef Superclass::ParameterNameType ParameterNameType; - typedef Superclass::ParametersSizeType ParametersSizeType; - - /** Method for creation through the object factory. */ - itkFactorylessNewMacro(Self); - itkCloneMacro(Self); - - /** Run-time type information (and related methods). */ - itkTypeMacro(TwoStepLinearModel, ModelBase) - - static const std::string MODELL_NAME; - static const std::string NAME_PARAMETER_y1; - static const std::string NAME_PARAMETER_t; - static const std::string NAME_PARAMETER_a1; - static const std::string NAME_PARAMETER_a2; - - static const unsigned int POSITION_PARAMETER_y1; - static const unsigned int POSITION_PARAMETER_t; - static const unsigned int POSITION_PARAMETER_a1; - static const unsigned int POSITION_PARAMETER_a2; - - static const unsigned int NUMBER_OF_PARAMETERS; - - virtual std::string GetModelDisplayName() const override; - - virtual std::string GetModelType() const override; - - virtual FunctionStringType GetFunctionString() const override; - - virtual std::string GetXName() const override; - - virtual ParameterNamesType GetParameterNames() const override; - - virtual ParametersSizeType GetNumberOfParameters() const override; - - virtual ParameterNamesType GetStaticParameterNames() const override; - - virtual ParametersSizeType GetNumberOfStaticParameters() const override; - - virtual ParameterNamesType GetDerivedParameterNames() const override; - - virtual ParametersSizeType GetNumberOfDerivedParameters() const override; - - - protected: - TwoStepLinearModel() {}; - virtual ~TwoStepLinearModel(){}; - - - /** - * Actual implementation of the clone method. This method should be reimplemeted - * in subclasses to clone the extra required parameters. - */ - virtual itk::LightObject::Pointer InternalClone() const; - - virtual ModelResultType ComputeModelfunction(const ParametersType& parameters) const; - virtual DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& - parameters) const; - - virtual void SetStaticParameter(const ParameterNameType& name, - const StaticParameterValuesType& values); - virtual StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const; - - static double ComputeSignalFromParameters(double x, double t, double a1, double a2, double b1, double b2); - - private: - - //No copy constructor allowed - TwoStepLinearModel(const Self& source); - void operator=(const Self&); //purposely not implemented - }; -} - - -#endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentFDGModel.h b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentFDGModel.h index d6e2240302..981d44cd0e 100644 --- a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentFDGModel.h +++ b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentFDGModel.h @@ -1,92 +1,94 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkTwoTissueCompartmentFDGModel_h #define mitkTwoTissueCompartmentFDGModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { class MITKPHARMACOKINETICS_EXPORT TwoTissueCompartmentFDGModel : public AIFBasedModelBase { public: typedef TwoTissueCompartmentFDGModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(TwoTissueCompartmentFDGModel, ModelBase); /** Model Specifications */ static const std::string MODEL_DISPLAY_NAME; static const std::string NAME_PARAMETER_K1; static const std::string NAME_PARAMETER_k2; static const std::string NAME_PARAMETER_k3; - static const std::string NAME_PARAMETER_VB; + static const std::string NAME_PARAMETER_vb; static const std::string UNIT_PARAMETER_K1; static const std::string UNIT_PARAMETER_k2; static const std::string UNIT_PARAMETER_k3; - static const std::string UNIT_PARAMETER_VB; + static const std::string UNIT_PARAMETER_vb; static const unsigned int POSITION_PARAMETER_K1; static const unsigned int POSITION_PARAMETER_k2; static const unsigned int POSITION_PARAMETER_k3; - static const unsigned int POSITION_PARAMETER_VB; + static const unsigned int POSITION_PARAMETER_vb; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string MODEL_TYPE; + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; protected: TwoTissueCompartmentFDGModel(); ~TwoTissueCompartmentFDGModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed TwoTissueCompartmentFDGModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModel.h b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModel.h index a20c922009..5f1ebe6506 100644 --- a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModel.h +++ b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModel.h @@ -1,94 +1,97 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkTwoTissueCompartmentModel_h #define mitkTwoTissueCompartmentModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { class MITKPHARMACOKINETICS_EXPORT TwoTissueCompartmentModel : public AIFBasedModelBase { public: typedef TwoTissueCompartmentModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(TwoTissueCompartmentModel, ModelBase); /** Model Specifications */ - static const std::string MODEL_DISPLAY_NAME; static const std::string NAME_PARAMETER_K1; static const std::string NAME_PARAMETER_k2; static const std::string NAME_PARAMETER_k3; static const std::string NAME_PARAMETER_k4; - static const std::string NAME_PARAMETER_VB; + static const std::string NAME_PARAMETER_vb; static const std::string UNIT_PARAMETER_K1; static const std::string UNIT_PARAMETER_k2; static const std::string UNIT_PARAMETER_k3; static const std::string UNIT_PARAMETER_k4; - static const std::string UNIT_PARAMETER_VB; + static const std::string UNIT_PARAMETER_vb; static const unsigned int POSITION_PARAMETER_K1; static const unsigned int POSITION_PARAMETER_k2; static const unsigned int POSITION_PARAMETER_k3; static const unsigned int POSITION_PARAMETER_k4; - static const unsigned int POSITION_PARAMETER_VB; + static const unsigned int POSITION_PARAMETER_vb; static const unsigned int NUMBER_OF_PARAMETERS; + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; protected: TwoTissueCompartmentModel(); ~TwoTissueCompartmentModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed TwoTissueCompartmentModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelDifferentialEquations.h b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelDifferentialEquations.h deleted file mode 100644 index b892bef899..0000000000 --- a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelDifferentialEquations.h +++ /dev/null @@ -1,114 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#ifndef mitkTwoTissueCompartmentModelDifferentialEquations_h -#define mitkTwoTissueCompartmentModelDifferentialEquations_h -#include "mitkNumericTwoTissueCompartmentModel.h" - -namespace mitk{ -/** @class TwoTissueCompartmentModelDifferentialEquations - * @brief Helper Class for NumericTwoTissueCompartment Model: Defines the differential equations (Mass Balance Equations) in the - * 2-tissue-compartment model for dynamic PET data modeling. - * The 2-Tissue Compartment model is defined via the mass balance equations - * dC1(t)/dt = K1*Ca(t) - (k2 + k3)*C1(t) + k4*C2(t) - * dC2(t)/dt = k3*C1(t) - k4*C2(t) - * CT(t) = C_a(t)*VB + (1-VB)*(C1(t)+C2(t) - * where Ca(t) is the plasma concentration(aterial input function) - * Boost ODEINT performs a stepwise numeric integration (e.g. via Runge-Kutta method) of the initial value problem - * x' = dx/dt = f(x,t) - * It needs an operator () (a functor) that calculates dx/dt = dxdt for a given x and t. - * Parameters are K1,k2,k3,k4, VB and the time dependent Ca(t) =AIF, that is interpolated to the current step t -*/ - -class TwoTissueCompartmentModelDifferentialEquations -{ -public: - - typedef std::vector< double > AIFType; - - /** @brief Functor for differential equation of Two Tissue Compartment Model - * Takes current state x = x(t) and time t and calculates the corresponding dxdt = dx/dt - */ - void operator() (const mitk::NumericTwoTissueCompartmentModel::state_type &x, mitk::NumericTwoTissueCompartmentModel::state_type &dxdt, const double t) - { - double Ca_t = InterpolateAIFToCurrentTimeStep(t); - - dxdt[0] = this->K1*Ca_t-(this->k2+this->k3)*x[0] + this->k4*x[1]; - dxdt[1] = this->k3*x[0] - this->k4*x[1]; - } - - TwoTissueCompartmentModelDifferentialEquations() : K1(0), k2(0), k3(0), k4(0), m_AIF(0), m_AIFTimeGrid(0) - { - } - - /** @brief Initialize class with parameters K1, k2, k3 and k4 that are free fit parameters*/ - void initialize(double k_1, double k_2, double k_3, double k_4) - { - this->K1 = k_1; - this->k2 = k_2; - this->k3 = k_3; - this->k4 = k_4; - } - - - void setAIF(AIFType &aif) - { - this->m_AIF = aif; - } - - - void setAIFTimeGrid(AIFType &grid) - { - this->m_AIFTimeGrid = grid; - } - -private: - - double K1; - double k2; - double k3; - double k4; - - AIFType m_AIF; - AIFType m_AIFTimeGrid; - - - /** @brief Internal routine to interpolate the AIF to the current time point t used for integration - * The numerical integration of ODEINT is performed on an adaptive timegrid (adaptive step size dt) different from the time grid of the AIF and model function. - * Thus, the AIF value Ca(t) has to be interpolated from the set AIF - */ - double InterpolateAIFToCurrentTimeStep(double t) - { - double lastValue = m_AIF[0]; - double lastTime = std::numeric_limits::min(); - - AIFType::const_iterator posITime = m_AIFTimeGrid.begin(); - AIFType::const_iterator posValue = m_AIF.begin(); - - while(t > *posITime) - { - lastValue = *posValue; - lastTime = *posITime; - ++posValue; - ++posITime; - } - double weightLast = 1 - (t - lastTime)/(*posITime - lastTime); - double weightNext = 1- (*posITime - t)/(*posITime - lastTime); - double result = weightLast * lastValue + weightNext * (*posValue); - - return result; - } - -}; -} - -#endif diff --git a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelFactoryBase.h b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelFactoryBase.h index 2430ab8a15..ad8047cf3b 100644 --- a/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelFactoryBase.h +++ b/Modules/Pharmacokinetics/include/mitkTwoTissueCompartmentModelFactoryBase.h @@ -1,81 +1,81 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkTwoTissueCompartmentModelFactoryBase_h #define mitkTwoTissueCompartmentModelFactoryBase_h #include "mitkConcreteAIFBasedModelFactory.h" #include "mitkAIFBasedModelParameterizerBase.h" #include "mitkSimpleBarrierConstraintChecker.h" namespace mitk { template class TwoTissueCompartmentModelFactoryBase : public mitk::ConcreteAIFBasedModelFactory< TModelParameterizer > { public: mitkClassMacro(TwoTissueCompartmentModelFactoryBase, ConcreteAIFBasedModelFactory< TModelParameterizer >); itkFactorylessNewMacro(Self); typedef typename Superclass::ModelType ModelType; typedef typename Superclass::ModelParameterizerType ModelParameterizerType; typedef typename Superclass::ParametersType ParametersType; ConstraintCheckerBase::Pointer CreateDefaultConstraints() const override { SimpleBarrierConstraintChecker::Pointer constraints = SimpleBarrierConstraintChecker::New(); /**@todo Mit Charlie klaren ob es eine sinnvolle default Einstellung gibt.*/ constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_K1, 0, 0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k2, 0, 0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k3, 0, 0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k4, 0, 0); - constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_VB, 0, 0); - constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_VB, 1, 0); + constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_vb, 0, 0); + constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_vb, 1, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_K1, 1.0, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k2, 1.0, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k3, 1.0, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k4, 1.0, 0); return constraints.GetPointer(); }; ParametersType GetDefaultInitialParameterization() const override { typename ModelParameterizerType::Pointer modelParameterizer = ModelParameterizerType::New(); return modelParameterizer->GetDefaultInitialParameterization(); }; protected: TwoTissueCompartmentModelFactoryBase() { }; ~TwoTissueCompartmentModelFactoryBase() override { }; private: //No copy constructor allowed TwoTissueCompartmentModelFactoryBase(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/src/Common/mitkPixelBasedDescriptionParameterImageGenerator.cpp b/Modules/Pharmacokinetics/src/Common/mitkPixelBasedDescriptionParameterImageGenerator.cpp index 287ca01c4a..301fd846cb 100644 --- a/Modules/Pharmacokinetics/src/Common/mitkPixelBasedDescriptionParameterImageGenerator.cpp +++ b/Modules/Pharmacokinetics/src/Common/mitkPixelBasedDescriptionParameterImageGenerator.cpp @@ -1,191 +1,191 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "itkCommand.h" #include "itkMultiOutputNaryFunctorImageFilter.h" #include "mitkPixelBasedDescriptionParameterImageGenerator.h" #include "mitkImageTimeSelector.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkSimpleFunctorPolicy.h" #include "mitkModelBase.h" void mitk::PixelBasedDescriptionParameterImageGenerator:: onFitProgressEvent(::itk::Object* caller, const ::itk::EventObject& /*eventObject*/) { - this->InvokeEvent(::itk::ProgressEvent()); itk::ProcessObject* process = dynamic_cast(caller); if (process) { this->m_Progress = process->GetProgress(); } + this->InvokeEvent(::itk::ProgressEvent()); }; template void mitk::PixelBasedDescriptionParameterImageGenerator::DoPrepareMask(itk::Image* image) { m_InternalMask = dynamic_cast(image); if (m_InternalMask.IsNull()) { MITK_INFO << "Parameter Fit Generator. Need to cast mask for parameter fit."; typedef itk::Image InputImageType; typedef itk::CastImageFilter< InputImageType, InternalMaskType > CastFilterType; typename CastFilterType::Pointer spImageCaster = CastFilterType::New(); spImageCaster->SetInput(image); m_InternalMask = spImageCaster->GetOutput(); spImageCaster->Update(); } } template mitk::PixelBasedDescriptionParameterImageGenerator::ParameterImageMapType StoreResultImages(const mitk::CurveParameterFunctor::ParameterNamesType ¶mNames, itk::ImageSource* source) { if (source->GetNumberOfOutputs() != paramNames.size()) { mitkThrow() << "Error while generating fitted parameter images. Number of sources does not match expected parameter number. Output size: " << source->GetNumberOfOutputs() << "; number of param names: " << paramNames.size(); } mitk::PixelBasedDescriptionParameterImageGenerator::ParameterImageMapType result; for (mitk::CurveParameterFunctor::ParameterNamesType::size_type j = 0; j < paramNames.size(); ++j) { mitk::Image::Pointer paramImage = mitk::Image::New(); typename TImage::ConstPointer outputImg = source->GetOutput(j); mitk::CastToMitkImage(outputImg, paramImage); result.insert(std::make_pair(paramNames[j],paramImage)); } return result; } template void mitk::PixelBasedDescriptionParameterImageGenerator::DoParameterCalculation(itk::Image* /*image*/) { typedef itk::Image InputFrameImageType; typedef itk::Image ParameterImageType; typedef itk::MultiOutputNaryFunctorImageFilter DescriptorFilterType; typename DescriptorFilterType::Pointer descFilter = DescriptorFilterType::New(); typename ::itk::MemberCommand::Pointer spProgressCommand = ::itk::MemberCommand::New(); spProgressCommand->SetCallbackFunction(this, &Self::onFitProgressEvent); descFilter->AddObserver(::itk::ProgressEvent(), spProgressCommand); //add the time frames to the descriptor filter std::vector frameCache; for (unsigned int i = 0; i < this->m_DynamicImage->GetTimeSteps(); ++i) { typename InputFrameImageType::Pointer frameImage; mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(this->m_DynamicImage); imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); Image::Pointer frameMITKImage = imageTimeSelector->GetOutput(); frameCache.push_back(frameMITKImage); mitk::CastToItkImage(frameMITKImage, frameImage); descFilter->SetInput(i,frameImage); } SimpleFunctorPolicy functor; functor.SetFunctor(this->m_Functor); descFilter->SetFunctor(functor); if (this->m_InternalMask.IsNotNull()) { descFilter->SetMask(this->m_InternalMask); } //generate the fits descFilter->Update(); //convert the outputs into mitk images and fill the parameter image map CurveParameterFunctor::ParameterNamesType paramNames = this->m_Functor->GetDescriptionParameterNames(); if (descFilter->GetNumberOfOutputs() != (paramNames.size())) { mitkThrow() << "Error while generating fitted parameter images. Fit filter output size does not match expected parameter number. Output size: "<< descFilter->GetNumberOfOutputs(); } this->m_TempResultMap = StoreResultImages(paramNames,descFilter); } bool mitk::PixelBasedDescriptionParameterImageGenerator::HasOutdatedResult() const { bool result = Superclass::HasOutdatedResult(); if (m_DynamicImage.IsNotNull()) { if (m_DynamicImage->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_Mask.IsNotNull()) { if (m_Mask->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } return result; }; void mitk::PixelBasedDescriptionParameterImageGenerator::CheckValidInputs() const { Superclass::CheckValidInputs(); if (m_DynamicImage.IsNull()) { mitkThrow() << "Cannot generate fitted parameter images. Input dynamic image is not set."; } }; void mitk::PixelBasedDescriptionParameterImageGenerator::DoParameterCalculationAndGetResults(ParameterImageMapType& parameterImages) { this->m_Progress = 0; if(this->m_Mask.IsNotNull()) { AccessFixedDimensionByItk(m_Mask, mitk::PixelBasedDescriptionParameterImageGenerator::DoPrepareMask, 3); } else { this->m_InternalMask = nullptr; } AccessFixedDimensionByItk(m_DynamicImage, mitk::PixelBasedDescriptionParameterImageGenerator::DoParameterCalculation, 4); parameterImages = this->m_TempResultMap; }; double mitk::PixelBasedDescriptionParameterImageGenerator::GetProgress() const { return m_Progress; }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkAIFBasedModelBase.cpp b/Modules/Pharmacokinetics/src/Models/mitkAIFBasedModelBase.cpp index b746b38fec..78fe64e9b3 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkAIFBasedModelBase.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkAIFBasedModelBase.cpp @@ -1,183 +1,192 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkAIFBasedModelBase.h" #include "mitkTimeGridHelper.h" #include "mitkAIFParametrizerHelper.h" #include "itkArray2D.h" +const unsigned int mitk::AIFBasedModelBase::NUMBER_OF_STATIC_PARAMETERS = 2; -const std::string mitk::AIFBasedModelBase::NAME_STATIC_PARAMETER_AIF = "Aterial Input Function"; +const std::string mitk::AIFBasedModelBase::NAME_STATIC_PARAMETER_AIF = "Arterial Input Function"; const std::string mitk::AIFBasedModelBase::NAME_STATIC_PARAMETER_AIFTimeGrid = - "Aterial Input Function Timegrid"; + "Arterial Input Function Timegrid"; //Assumed AIF is always extracted from concentration image -const std::string mitk::AIFBasedModelBase::UNIT_STATIC_PARAMETER_AIF = "C"; +const std::string mitk::AIFBasedModelBase::UNIT_STATIC_PARAMETER_AIF = "mM"; const std::string mitk::AIFBasedModelBase::UNIT_STATIC_PARAMETER_AIFTimeGrid = "s"; +const std::string mitk::AIFBasedModelBase::X_AXIS_NAME = "Time"; + +const std::string mitk::AIFBasedModelBase::X_AXIS_UNIT = "s"; + +const std::string mitk::AIFBasedModelBase::Y_AXIS_NAME = "Concentration"; + +const std::string mitk::AIFBasedModelBase::Y_AXIS_UNIT = "mM"; + std::string mitk::AIFBasedModelBase::GetXAxisName() const { - return "Time"; + return X_AXIS_NAME; }; std::string mitk::AIFBasedModelBase::GetXAxisUnit() const { - return "s"; + return X_AXIS_UNIT; } std::string mitk::AIFBasedModelBase::GetYAxisName() const { - return ""; + return Y_AXIS_NAME; }; std::string mitk::AIFBasedModelBase::GetYAxisUnit() const { - return ""; + return Y_AXIS_UNIT; } mitk::AIFBasedModelBase::AIFBasedModelBase() { } mitk::AIFBasedModelBase::~AIFBasedModelBase() { } const mitk::AIFBasedModelBase::TimeGridType& mitk::AIFBasedModelBase::GetCurrentAterialInputFunctionTimeGrid() const { if (!m_AterialInputFunctionTimeGrid.empty()) { return m_AterialInputFunctionTimeGrid; } else { return m_TimeGrid; } }; const mitk::AIFBasedModelBase::AterialInputFunctionType mitk::AIFBasedModelBase::GetAterialInputFunction(TimeGridType CurrentTimeGrid) const { if (CurrentTimeGrid.GetSize() == 0) { return this->m_AterialInputFunctionValues; } else { return mitk::InterpolateSignalToNewTimeGrid(m_AterialInputFunctionValues, GetCurrentAterialInputFunctionTimeGrid(), CurrentTimeGrid); } } mitk::AIFBasedModelBase::ParameterNamesType mitk::AIFBasedModelBase::GetStaticParameterNames() const { ParameterNamesType result; result.push_back(NAME_STATIC_PARAMETER_AIF); result.push_back(NAME_STATIC_PARAMETER_AIFTimeGrid); return result; } mitk::AIFBasedModelBase::ParametersSizeType mitk::AIFBasedModelBase::GetNumberOfStaticParameters() const { - return 2; + return NUMBER_OF_STATIC_PARAMETERS; } mitk::AIFBasedModelBase::ParamterUnitMapType mitk::AIFBasedModelBase::GetStaticParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_STATIC_PARAMETER_AIF, UNIT_STATIC_PARAMETER_AIF)); result.insert(std::make_pair(NAME_STATIC_PARAMETER_AIFTimeGrid, UNIT_STATIC_PARAMETER_AIFTimeGrid)); return result; }; void mitk::AIFBasedModelBase::SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) { if (name == NAME_STATIC_PARAMETER_AIF) { AterialInputFunctionType aif = mitk::convertParameterToArray(values); SetAterialInputFunctionValues(aif); } if (name == NAME_STATIC_PARAMETER_AIFTimeGrid) { TimeGridType timegrid = mitk::convertParameterToArray(values); SetAterialInputFunctionTimeGrid(timegrid); } }; mitk::AIFBasedModelBase::StaticParameterValuesType mitk::AIFBasedModelBase::GetStaticParameterValue( const ParameterNameType& name) const { StaticParameterValuesType result; if (name == NAME_STATIC_PARAMETER_AIF) { result = mitk::convertArrayToParameter(this->m_AterialInputFunctionValues); } if (name == NAME_STATIC_PARAMETER_AIFTimeGrid) { result = mitk::convertArrayToParameter(this->m_AterialInputFunctionTimeGrid); } return result; }; bool mitk::AIFBasedModelBase::ValidateModel(std::string& error) const { bool result = Superclass::ValidateModel(error); if (result) { if (m_AterialInputFunctionTimeGrid.empty()) { if (this->m_TimeGrid.GetSize() != m_AterialInputFunctionValues.GetSize()) { result = false; error = "Number of elements of Model Time Grid does not match number of elements in Aterial Input Function! Set valid aif or aif time grid."; } } else { if (m_AterialInputFunctionTimeGrid.GetSize() != m_AterialInputFunctionValues.GetSize()) { result = false; error = "Number of elements of Aterial Input Function Time Grid does not match number of elements of Aterial Input Function Values! Set valid curve"; } } } return result; }; void mitk::AIFBasedModelBase::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); - os << indent << "Aterial Input Function: " << m_AterialInputFunctionValues; - os << indent << "Aterial Input Function Time Grid: " << m_AterialInputFunctionTimeGrid; + os << indent << "Arterial Input Function: " << m_AterialInputFunctionValues; + os << indent << "Arterial Input Function Time Grid: " << m_AterialInputFunctionTimeGrid; }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModel.cpp index 438f0353c3..81aef2e2ba 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModel.cpp @@ -1,263 +1,271 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkDescriptivePharmacokineticBrixModel.h" const std::string mitk::DescriptivePharmacokineticBrixModel::MODEL_DISPLAY_NAME = "Descriptive Pharmacokinetic Brix Model"; +const std::string mitk::DescriptivePharmacokineticBrixModel::MODEL_TYPE = +"Perfusion.MR"; + const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_A = "A"; -const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_kep = "kep"; -const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_kel = "kel"; -//tlag in minutes -const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_tlag = "tlag"; +const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_kep = "k_{e->p}"; +const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_kel = "k_{el}"; +const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_PARAMETER_BAT = "BAT"; const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_PARAMETER_A = "a.u."; const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_PARAMETER_kep = "1/min"; const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_PARAMETER_kel = "1/min"; -//tlag in minutes -const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_PARAMETER_tlag = "min"; +const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_PARAMETER_BAT = "min"; -const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_Tau = "Tau"; -const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_S0 = "S0"; +const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_tau = "Injection_time"; +const std::string mitk::DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_s0 = "Pre_contrast_signal"; -const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_STATIC_PARAMETER_Tau = "min"; -const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_STATIC_PARAMETER_S0 = "I"; +const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_STATIC_PARAMETER_tau = "min"; +const std::string mitk::DescriptivePharmacokineticBrixModel::UNIT_STATIC_PARAMETER_s0 = "a.u."; const unsigned int mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_A = 0; const unsigned int mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_kep = 1; const unsigned int mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_kel = 2; -const unsigned int mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_tlag = 3; +const unsigned int mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_BAT = 3; const unsigned int mitk::DescriptivePharmacokineticBrixModel::NUMBER_OF_PARAMETERS = 4; +const unsigned int mitk::DescriptivePharmacokineticBrixModel::NUMBER_OF_STATIC_PARAMETERS = 2; + +const std::string mitk::DescriptivePharmacokineticBrixModel::X_AXIS_NAME = "Time"; +const std::string mitk::DescriptivePharmacokineticBrixModel::X_AXIS_UNIT = "s"; +const std::string mitk::DescriptivePharmacokineticBrixModel::Y_AXIS_NAME = "Signal"; +const std::string mitk::DescriptivePharmacokineticBrixModel::Y_AXIS_UNIT = "a.u."; + std::string mitk::DescriptivePharmacokineticBrixModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::DescriptivePharmacokineticBrixModel::GetModelType() const { - return "Perfusion.MR"; + return MODEL_TYPE; }; std::string mitk::DescriptivePharmacokineticBrixModel::GetXAxisName() const { - return "Time"; + return X_AXIS_NAME; }; std::string mitk::DescriptivePharmacokineticBrixModel::GetXAxisUnit() const { - return "s"; + return X_AXIS_UNIT; } std::string mitk::DescriptivePharmacokineticBrixModel::GetYAxisName() const { - return ""; + return Y_AXIS_NAME; }; std::string mitk::DescriptivePharmacokineticBrixModel::GetYAxisUnit() const { - return ""; + return Y_AXIS_UNIT; } mitk::DescriptivePharmacokineticBrixModel::DescriptivePharmacokineticBrixModel(): m_Tau(0), m_S0(1) { } mitk::DescriptivePharmacokineticBrixModel::~DescriptivePharmacokineticBrixModel() { } mitk::DescriptivePharmacokineticBrixModel::ParameterNamesType mitk::DescriptivePharmacokineticBrixModel::GetParameterNames() const { ParameterNamesType result; result.push_back(NAME_PARAMETER_A); result.push_back(NAME_PARAMETER_kep); result.push_back(NAME_PARAMETER_kel); - result.push_back(NAME_PARAMETER_tlag); + result.push_back(NAME_PARAMETER_BAT); return result; } mitk::DescriptivePharmacokineticBrixModel::ParametersSizeType mitk::DescriptivePharmacokineticBrixModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::DescriptivePharmacokineticBrixModel::ParamterUnitMapType mitk::DescriptivePharmacokineticBrixModel::GetParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_PARAMETER_A, UNIT_PARAMETER_A)); result.insert(std::make_pair(NAME_PARAMETER_kep, UNIT_PARAMETER_kep)); result.insert(std::make_pair(NAME_PARAMETER_kel, UNIT_PARAMETER_kel)); - result.insert(std::make_pair(NAME_PARAMETER_tlag, UNIT_PARAMETER_tlag)); + result.insert(std::make_pair(NAME_PARAMETER_BAT, UNIT_PARAMETER_BAT)); return result; }; mitk::DescriptivePharmacokineticBrixModel::ParameterNamesType mitk::DescriptivePharmacokineticBrixModel::GetStaticParameterNames() const { ParameterNamesType result; - result.push_back(NAME_STATIC_PARAMETER_Tau); - result.push_back(NAME_STATIC_PARAMETER_S0); + result.push_back(NAME_STATIC_PARAMETER_tau); + result.push_back(NAME_STATIC_PARAMETER_s0); return result; } mitk::DescriptivePharmacokineticBrixModel::ParamterUnitMapType mitk::DescriptivePharmacokineticBrixModel::GetStaticParameterUnits() const { ParamterUnitMapType result; - result.insert(std::make_pair(NAME_STATIC_PARAMETER_Tau, UNIT_STATIC_PARAMETER_Tau)); - result.insert(std::make_pair(NAME_STATIC_PARAMETER_S0, UNIT_STATIC_PARAMETER_S0)); + result.insert(std::make_pair(NAME_STATIC_PARAMETER_tau, UNIT_STATIC_PARAMETER_tau)); + result.insert(std::make_pair(NAME_STATIC_PARAMETER_s0, UNIT_STATIC_PARAMETER_s0)); return result; }; mitk::DescriptivePharmacokineticBrixModel::ParametersSizeType mitk::DescriptivePharmacokineticBrixModel::GetNumberOfStaticParameters() const { - return 2; + return NUMBER_OF_STATIC_PARAMETERS; } mitk::DescriptivePharmacokineticBrixModel::ModelResultType mitk::DescriptivePharmacokineticBrixModel::ComputeModelfunction(const ParametersType& parameters) const { if (m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } if (m_Tau == 0) { itkExceptionMacro("Injection time is 0! Cannot Calculate Signal"); } ModelResultType signal(m_TimeGrid.GetSize()); double tx = 0; double amplitude = parameters[POSITION_PARAMETER_A]; double kel = parameters[POSITION_PARAMETER_kel]; double kep = parameters[POSITION_PARAMETER_kep]; - double tlag = parameters[POSITION_PARAMETER_tlag]; + double bat = parameters[POSITION_PARAMETER_BAT]; if (kep == kel) { itkExceptionMacro("(kep-kel) is 0! Cannot Calculate Signal"); } TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); ModelResultType::iterator signalPos = signal.begin(); for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd; ++gridPos, ++signalPos) { double t = (*gridPos) / 60.0; //convert from [sec] to [min] - if (t <= tlag) + if (t <= bat) { tx = 0; } - else if ((t > tlag) && (t < (m_Tau + tlag))) + else if ((t > bat) && (t < (m_Tau + bat))) { - tx = t - tlag; + tx = t - bat; } - else if (t >= (m_Tau + tlag)) + else if (t >= (m_Tau + bat)) { tx = m_Tau; } double kDiff = kep - kel; - double tDiff = t - tlag; + double tDiff = t - bat; double expkel = (kep * exp(-kel * tDiff)); double expkeltx = exp(kel * tx); double expkep = exp(-kep * tDiff); double expkeptx = exp(kep * tx); double value = 1 + (amplitude / m_Tau) * (((expkel / (kel * kDiff)) * (expkeltx - 1)) - (( expkep / kDiff) * (expkeptx - 1))); *signalPos = value * m_S0; } return signal; } void mitk::DescriptivePharmacokineticBrixModel::SetStaticParameter(const ParameterNameType& name, const StaticParameterValuesType& values) { - if (name == NAME_STATIC_PARAMETER_Tau) + if (name == NAME_STATIC_PARAMETER_tau) { SetTau(values[0]); } - if (name == NAME_STATIC_PARAMETER_S0) + if (name == NAME_STATIC_PARAMETER_s0) { SetS0(values[0]); } }; mitk::DescriptivePharmacokineticBrixModel::StaticParameterValuesType mitk::DescriptivePharmacokineticBrixModel::GetStaticParameterValue(const ParameterNameType& name) const { StaticParameterValuesType result; - if (name == NAME_STATIC_PARAMETER_Tau) + if (name == NAME_STATIC_PARAMETER_tau) { result.push_back(GetTau()); } - if (name == NAME_STATIC_PARAMETER_S0) + if (name == NAME_STATIC_PARAMETER_s0) { result.push_back(GetS0()); } return result; }; itk::LightObject::Pointer mitk::DescriptivePharmacokineticBrixModel::InternalClone() const { DescriptivePharmacokineticBrixModel::Pointer newClone = DescriptivePharmacokineticBrixModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); newClone->SetTau(this->m_Tau); newClone->SetS0(this->m_S0); return newClone.GetPointer(); }; void mitk::DescriptivePharmacokineticBrixModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); os << indent << "Tau (injection time): " << m_Tau; - os << indent << "S0 (base value): " << m_S0; + os << indent << "S0 (baseline value): " << m_S0; }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelFactory.cpp index 906a9bc909..14be13fc5b 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelFactory.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelFactory.cpp @@ -1,90 +1,90 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include "mitkDescriptivePharmacokineticBrixModelFactory.h" #include "mitkDescriptivePharmacokineticBrixModelParameterizer.h" #include "mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.h" mitk::DescriptivePharmacokineticBrixModelFactory::DescriptivePharmacokineticBrixModelFactory() { }; mitk::DescriptivePharmacokineticBrixModelFactory::~DescriptivePharmacokineticBrixModelFactory() { }; mitk::ModelParameterizerBase::ParametersType mitk::DescriptivePharmacokineticBrixModelFactory::GetDefaultInitialParameterization() const { return DescriptivePharmacokineticBrixModelParameterizer::New()->GetDefaultInitialParameterization(); }; mitk::ModelParameterizerBase::Pointer mitk::DescriptivePharmacokineticBrixModelFactory::DoCreateParameterizer( const mitk::modelFit::ModelFitInfo* fit) const { mitk::ModelParameterizerBase::Pointer result; if (fit->fitType == ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED()) { DescriptivePharmacokineticBrixModelParameterizer::Pointer modelParameterizer = DescriptivePharmacokineticBrixModelParameterizer::New(); modelFit::StaticParameterMap::ValueType tau = fit->staticParamMap.Get( - DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_Tau); + DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_tau); modelParameterizer->SetTau(tau[0]); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(fit->inputImage); imageTimeSelector->SetTimeNr(0); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::DescriptivePharmacokineticBrixModelParameterizer::BaseImageType::Pointer baseImage; mitk::CastToItkImage(imageTimeSelector->GetOutput(), baseImage); modelParameterizer->SetBaseImage(baseImage); result = modelParameterizer.GetPointer(); } else if (fit->fitType == ModelFitConstants::FIT_TYPE_VALUE_ROIBASED()) { DescriptivePharmacokineticBrixModelValueBasedParameterizer::Pointer modelParameterizer = DescriptivePharmacokineticBrixModelValueBasedParameterizer::New(); modelFit::StaticParameterMap::ValueType tau = fit->staticParamMap.Get( - DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_Tau); + DescriptivePharmacokineticBrixModel::NAME_STATIC_PARAMETER_tau); modelParameterizer->SetTau(tau[0]); if (!fit->inputData.ValueExists("ROI")) { mitkThrow() << "Cannot generate parameterizer for fit of type ROIbased. Input data with the lable \"ROI\" is missing in fit."; } ScalarListLookupTable::ValueType signal = fit->inputData.GetTableValue("ROI"); if (signal.empty()) { mitkThrow() << "Cannot generate parameterizer for fit of type ROIbased. Input data with the lable \"ROI\" is invalid: No values available."; } modelParameterizer->SetBaseValue(signal[0]); result = modelParameterizer.GetPointer(); } return result; }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelParameterizer.cpp index 9ca922d049..0b75907320 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelParameterizer.cpp @@ -1,62 +1,62 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include "mitkDescriptivePharmacokineticBrixModel.h" #include "mitkDescriptivePharmacokineticBrixModelParameterizer.h" mitk::DescriptivePharmacokineticBrixModelParameterizer::StaticParameterMapType mitk::DescriptivePharmacokineticBrixModelParameterizer::GetGlobalStaticParameters() const { StaticParameterMapType result; StaticParameterValuesType values; values.push_back(m_Tau); - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_Tau, values)); + result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_tau, values)); return result; }; mitk::DescriptivePharmacokineticBrixModelParameterizer::StaticParameterMapType mitk::DescriptivePharmacokineticBrixModelParameterizer::GetLocalStaticParameters( const IndexType& currentPosition) const { StaticParameterMapType result; double s0 = m_BaseImage->GetPixel(currentPosition); StaticParameterValuesType values; values.push_back(s0); - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_S0, values)); + result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_s0, values)); return result; }; mitk::DescriptivePharmacokineticBrixModelParameterizer::ParametersType mitk::DescriptivePharmacokineticBrixModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(4); initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_A] = 1.0; initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_kep] = 4.0; initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_kel] = 0.2; - initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_tlag] = 1.0; + initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_BAT] = 1.0; return initialParameters; } mitk::DescriptivePharmacokineticBrixModelParameterizer::DescriptivePharmacokineticBrixModelParameterizer() { }; mitk::DescriptivePharmacokineticBrixModelParameterizer::~DescriptivePharmacokineticBrixModelParameterizer() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.cpp index da6f2a4acd..767c1f42a0 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.cpp @@ -1,61 +1,61 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include "mitkDescriptivePharmacokineticBrixModel.h" #include "mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.h" mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::StaticParameterMapType mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::GetGlobalStaticParameters() const { StaticParameterMapType result; StaticParameterValuesType values; values.push_back(m_Tau); - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_Tau, values)); + result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_tau, values)); return result; }; mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::StaticParameterMapType mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::GetLocalStaticParameters( const IndexType&) const { StaticParameterMapType result; StaticParameterValuesType values; values.push_back(m_BaseValue); - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_S0, values)); + result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_s0, values)); return result; }; mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::ParametersType mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(4); initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_A] = 1.0; initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_kep] = 4.0; initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_kel] = 0.2; - initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_tlag] = 1.0; + initialParameters[mitk::DescriptivePharmacokineticBrixModel::POSITION_PARAMETER_BAT] = 1.0; return initialParameters; } mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::DescriptivePharmacokineticBrixModelValueBasedParameterizer() { }; mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::~DescriptivePharmacokineticBrixModelValueBasedParameterizer() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModel.cpp index 7cfa46a0c3..355683f1cb 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModel.cpp @@ -1,144 +1,146 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkExtendedOneTissueCompartmentModel.h" #include "mitkConvolutionHelper.h" #include #include const std::string mitk::ExtendedOneTissueCompartmentModel::MODEL_DISPLAY_NAME = "Extended One Tissue Compartment Model (with blood volume)"; -const std::string mitk::ExtendedOneTissueCompartmentModel::NAME_PARAMETER_k1 = "K1"; -const std::string mitk::ExtendedOneTissueCompartmentModel::NAME_PARAMETER_k2 = "k2"; -const std::string mitk::ExtendedOneTissueCompartmentModel::NAME_PARAMETER_VB = "VB"; +const std::string mitk::ExtendedOneTissueCompartmentModel::NAME_PARAMETER_K1 = "K_1"; +const std::string mitk::ExtendedOneTissueCompartmentModel::NAME_PARAMETER_k2 = "k_2"; +const std::string mitk::ExtendedOneTissueCompartmentModel::NAME_PARAMETER_vb = "v_b"; -const std::string mitk::ExtendedOneTissueCompartmentModel::UNIT_PARAMETER_k1 = "1/min"; +const std::string mitk::ExtendedOneTissueCompartmentModel::UNIT_PARAMETER_K1 = "1/min"; const std::string mitk::ExtendedOneTissueCompartmentModel::UNIT_PARAMETER_k2 = "1/min"; -const std::string mitk::ExtendedOneTissueCompartmentModel::UNIT_PARAMETER_VB = "ml/ml"; +const std::string mitk::ExtendedOneTissueCompartmentModel::UNIT_PARAMETER_vb = "ml/ml"; -const unsigned int mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_k1 = 0; +const unsigned int mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_K1 = 0; const unsigned int mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_k2 = 1; -const unsigned int mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_VB = 2; +const unsigned int mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_vb = 2; const unsigned int mitk::ExtendedOneTissueCompartmentModel::NUMBER_OF_PARAMETERS = 3; +const std::string mitk::ExtendedOneTissueCompartmentModel::MODEL_TYPE = "Dynamic.PET"; + std::string mitk::ExtendedOneTissueCompartmentModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::ExtendedOneTissueCompartmentModel::GetModelType() const { - return "Dynamic.PET"; + return MODEL_TYPE; }; mitk::ExtendedOneTissueCompartmentModel::ExtendedOneTissueCompartmentModel() { } mitk::ExtendedOneTissueCompartmentModel::~ExtendedOneTissueCompartmentModel() { } mitk::ExtendedOneTissueCompartmentModel::ParameterNamesType mitk::ExtendedOneTissueCompartmentModel::GetParameterNames() const { ParameterNamesType result; - result.push_back(NAME_PARAMETER_k1); + result.push_back(NAME_PARAMETER_K1); result.push_back(NAME_PARAMETER_k2); - result.push_back(NAME_PARAMETER_VB); + result.push_back(NAME_PARAMETER_vb); return result; } mitk::ExtendedOneTissueCompartmentModel::ParametersSizeType mitk::ExtendedOneTissueCompartmentModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::ExtendedOneTissueCompartmentModel::ParamterUnitMapType mitk::ExtendedOneTissueCompartmentModel::GetParameterUnits() const { ParamterUnitMapType result; - result.insert(std::make_pair(NAME_PARAMETER_k1, UNIT_PARAMETER_k1)); + result.insert(std::make_pair(NAME_PARAMETER_K1, UNIT_PARAMETER_K1)); result.insert(std::make_pair(NAME_PARAMETER_k2, UNIT_PARAMETER_k2)); - result.insert(std::make_pair(NAME_PARAMETER_VB, UNIT_PARAMETER_VB)); + result.insert(std::make_pair(NAME_PARAMETER_vb, UNIT_PARAMETER_vb)); return result; }; mitk::ExtendedOneTissueCompartmentModel::ModelResultType mitk::ExtendedOneTissueCompartmentModel::ComputeModelfunction( const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters - double K1 = (double) parameters[POSITION_PARAMETER_k1] / 60.0; + double K1 = (double) parameters[POSITION_PARAMETER_K1] / 60.0; double k2 = (double) parameters[POSITION_PARAMETER_k2] / 60.0; - double VB = parameters[POSITION_PARAMETER_VB]; + double vb = parameters[POSITION_PARAMETER_vb]; mitk::ModelBase::ModelResultType convolution = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, k2); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); AterialInputFunctionType::const_iterator aifPos = aterialInputFunction.begin(); for (mitk::ModelBase::ModelResultType::const_iterator res = convolution.begin(); res != convolution.end(); ++res, ++signalPos, ++aifPos) { - *signalPos = VB * (*aifPos) + (1 - VB) * K1 * (*res); + *signalPos = vb * (*aifPos) + (1 - vb) * K1 * (*res); } return signal; } itk::LightObject::Pointer mitk::ExtendedOneTissueCompartmentModel::InternalClone() const { ExtendedOneTissueCompartmentModel::Pointer newClone = ExtendedOneTissueCompartmentModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; void mitk::ExtendedOneTissueCompartmentModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelFactory.cpp index d3ec6b0bdb..1fa785b5b1 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelFactory.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelFactory.cpp @@ -1,53 +1,53 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkExtendedOneTissueCompartmentModelFactory.h" #include #include #include mitk::ConstraintCheckerBase::Pointer mitk::ExtendedOneTissueCompartmentModelFactory::CreateDefaultConstraints() const { SimpleBarrierConstraintChecker::Pointer constraints = SimpleBarrierConstraintChecker::New(); - constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k1, 0.0); + constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_K1, 0.0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k2, 0.0); - constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_VB, 0.0); + constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_vb, 0.0); - constraints->SetUpperBarrier (ModelType::POSITION_PARAMETER_k1, 1.0); + constraints->SetUpperBarrier (ModelType::POSITION_PARAMETER_K1, 1.0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k2, 1.0); - constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_VB, 1.0); + constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_vb, 1.0); SimpleBarrierConstraintChecker::ParameterIndexVectorType indices; - indices.push_back(ModelType::POSITION_PARAMETER_k1); + indices.push_back(ModelType::POSITION_PARAMETER_K1); indices.push_back(ModelType::POSITION_PARAMETER_k2); - indices.push_back(ModelType::POSITION_PARAMETER_VB); + indices.push_back(ModelType::POSITION_PARAMETER_vb); return constraints.GetPointer(); }; mitk::ModelParameterizerBase::ParametersType mitk::ExtendedOneTissueCompartmentModelFactory::GetDefaultInitialParameterization() const { return ExtendedOneTissueCompartmentModelParameterizer::New()->GetDefaultInitialParameterization(); }; mitk::ExtendedOneTissueCompartmentModelFactory::ExtendedOneTissueCompartmentModelFactory() { }; mitk::ExtendedOneTissueCompartmentModelFactory::~ExtendedOneTissueCompartmentModelFactory() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelParameterizer.cpp index 575ebf12d0..9a5cc1948f 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkExtendedOneTissueCompartmentModelParameterizer.cpp @@ -1,34 +1,34 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkExtendedOneTissueCompartmentModelParameterizer.h" mitk::ExtendedOneTissueCompartmentModelParameterizer::ParametersType mitk::ExtendedOneTissueCompartmentModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(3); - initialParameters[mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_k1] = 0.5; + initialParameters[mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_K1] = 0.5; initialParameters[mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_k2] = 0.5; - initialParameters[mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_VB] = 0.5; + initialParameters[mitk::ExtendedOneTissueCompartmentModel::POSITION_PARAMETER_vb] = 0.5; return initialParameters; }; mitk::ExtendedOneTissueCompartmentModelParameterizer::ExtendedOneTissueCompartmentModelParameterizer() { }; mitk::ExtendedOneTissueCompartmentModelParameterizer::~ExtendedOneTissueCompartmentModelParameterizer() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkExtendedToftsModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkExtendedToftsModel.cpp index dedc6d3917..d178fa721c 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkExtendedToftsModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkExtendedToftsModel.cpp @@ -1,182 +1,191 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkExtendedToftsModel.h" #include "mitkConvolutionHelper.h" #include #include const std::string mitk::ExtendedToftsModel::MODEL_DISPLAY_NAME = "Extended Tofts Model"; -const std::string mitk::ExtendedToftsModel::NAME_PARAMETER_Ktrans = "KTrans"; -const std::string mitk::ExtendedToftsModel::NAME_PARAMETER_ve = "ve"; -const std::string mitk::ExtendedToftsModel::NAME_PARAMETER_vp = "vp"; +const std::string mitk::ExtendedToftsModel::NAME_PARAMETER_Ktrans = "K^trans"; +const std::string mitk::ExtendedToftsModel::NAME_PARAMETER_ve = "v_e"; +const std::string mitk::ExtendedToftsModel::NAME_PARAMETER_vp = "v_p"; const std::string mitk::ExtendedToftsModel::UNIT_PARAMETER_Ktrans = "ml/min/100ml"; const std::string mitk::ExtendedToftsModel::UNIT_PARAMETER_ve = "ml/ml"; const std::string mitk::ExtendedToftsModel::UNIT_PARAMETER_vp = "ml/ml"; const unsigned int mitk::ExtendedToftsModel::POSITION_PARAMETER_Ktrans = 0; const unsigned int mitk::ExtendedToftsModel::POSITION_PARAMETER_ve = 1; const unsigned int mitk::ExtendedToftsModel::POSITION_PARAMETER_vp = 2; const unsigned int mitk::ExtendedToftsModel::NUMBER_OF_PARAMETERS = 3; +const std::string mitk::ExtendedToftsModel::NAME_DERIVED_PARAMETER_kep = "k_{e->p}"; + +const unsigned int mitk::ExtendedToftsModel::NUMBER_OF_DERIVED_PARAMETERS = 1; + +const std::string mitk::ExtendedToftsModel::UNIT_DERIVED_PARAMETER_kep = "1/min"; + +const std::string mitk::ExtendedToftsModel::MODEL_TYPE = "Perfusion.MR"; + + std::string mitk::ExtendedToftsModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::ExtendedToftsModel::GetModelType() const { - return "Perfusion.MR"; + return MODEL_TYPE; }; mitk::ExtendedToftsModel::ExtendedToftsModel() { } mitk::ExtendedToftsModel::~ExtendedToftsModel() { } mitk::ExtendedToftsModel::ParameterNamesType mitk::ExtendedToftsModel::GetParameterNames() const { ParameterNamesType result; result.push_back(NAME_PARAMETER_Ktrans); result.push_back(NAME_PARAMETER_ve); result.push_back(NAME_PARAMETER_vp); return result; } mitk::ExtendedToftsModel::ParametersSizeType mitk::ExtendedToftsModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::ExtendedToftsModel::ParamterUnitMapType mitk::ExtendedToftsModel::GetParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_PARAMETER_Ktrans, UNIT_PARAMETER_Ktrans)); result.insert(std::make_pair(NAME_PARAMETER_vp, UNIT_PARAMETER_vp)); result.insert(std::make_pair(NAME_PARAMETER_ve, UNIT_PARAMETER_ve)); return result; }; mitk::ExtendedToftsModel::ParameterNamesType mitk::ExtendedToftsModel::GetDerivedParameterNames() const { ParameterNamesType result; - result.push_back("kep"); + result.push_back(NAME_DERIVED_PARAMETER_kep); return result; }; mitk::ExtendedToftsModel::ParametersSizeType mitk::ExtendedToftsModel::GetNumberOfDerivedParameters() const { - return 1; + return NUMBER_OF_DERIVED_PARAMETERS; }; mitk::ExtendedToftsModel::ParamterUnitMapType mitk::ExtendedToftsModel::GetDerivedParameterUnits() const { ParamterUnitMapType result; - result.insert(std::make_pair("kep", "1/min")); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_kep, UNIT_DERIVED_PARAMETER_kep)); return result; }; mitk::ExtendedToftsModel::ModelResultType mitk::ExtendedToftsModel::ComputeModelfunction( const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters double ktrans = parameters[POSITION_PARAMETER_Ktrans] / 6000.0; double ve = parameters[POSITION_PARAMETER_ve]; double vp = parameters[POSITION_PARAMETER_vp]; if (ve == 0.0) { itkExceptionMacro("ve is 0! Cannot calculate signal"); } double lambda = ktrans / ve; mitk::ModelBase::ModelResultType convolution = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, lambda); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); mitk::ModelBase::ModelResultType::const_iterator res = convolution.begin(); for (AterialInputFunctionType::iterator Cp = aterialInputFunction.begin(); Cp != aterialInputFunction.end(); ++res, ++signalPos, ++Cp) { *signalPos = (*Cp) * vp + ktrans * (*res); } return signal; } mitk::ModelBase::DerivedParameterMapType mitk::ExtendedToftsModel::ComputeDerivedParameters( const mitk::ModelBase::ParametersType& parameters) const { DerivedParameterMapType result; double kep = parameters[POSITION_PARAMETER_Ktrans] / parameters[POSITION_PARAMETER_ve]; - result.insert(std::make_pair("kep", kep)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_kep, kep)); return result; }; itk::LightObject::Pointer mitk::ExtendedToftsModel::InternalClone() const { ExtendedToftsModel::Pointer newClone = ExtendedToftsModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; void mitk::ExtendedToftsModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModel.cpp deleted file mode 100644 index 2d95cd5e57..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModel.cpp +++ /dev/null @@ -1,286 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkNumericTwoCompartmentExchangeModel.h" -#include "mitkAIFParametrizerHelper.h" -#include "mitkTimeGridHelper.h" -#include "mitkTwoCompartmentExchangeModelDifferentialEquations.h" -#include -#include -#include - -const std::string mitk::NumericTwoCompartmentExchangeModel::MODEL_DISPLAY_NAME = - "Numeric Two Compartment Exchange Model"; - -const std::string mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_F = "F"; -const std::string mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_PS = "PS"; -const std::string mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_ve = "ve"; -const std::string mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_vp = "vp"; - -const std::string mitk::NumericTwoCompartmentExchangeModel::UNIT_PARAMETER_F = "ml/min/100ml"; -const std::string mitk::NumericTwoCompartmentExchangeModel::UNIT_PARAMETER_PS = "ml/min/100ml"; -const std::string mitk::NumericTwoCompartmentExchangeModel::UNIT_PARAMETER_ve = "ml/ml"; -const std::string mitk::NumericTwoCompartmentExchangeModel::UNIT_PARAMETER_vp = "ml/ml"; - -const unsigned int mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_F = 0; -const unsigned int mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_PS = 1; -const unsigned int mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_ve = 2; -const unsigned int mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_vp = 3; - -const unsigned int mitk::NumericTwoCompartmentExchangeModel::NUMBER_OF_PARAMETERS = 4; - -const std::string mitk::NumericTwoCompartmentExchangeModel::NAME_STATIC_PARAMETER_ODEINTStepSize = "ODEIntStepSize"; - - -std::string mitk::NumericTwoCompartmentExchangeModel::GetModelDisplayName() const -{ - return MODEL_DISPLAY_NAME; -}; - -std::string mitk::NumericTwoCompartmentExchangeModel::GetModelType() const -{ - return "Perfusion.MR"; -}; - - -mitk::NumericTwoCompartmentExchangeModel::NumericTwoCompartmentExchangeModel() -{ - -} - -mitk::NumericTwoCompartmentExchangeModel::~NumericTwoCompartmentExchangeModel() -{ - -} - -mitk::NumericTwoCompartmentExchangeModel::ParameterNamesType mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterNames() const -{ - ParameterNamesType result; - - result.push_back(NAME_STATIC_PARAMETER_AIF); - result.push_back(NAME_STATIC_PARAMETER_AIFTimeGrid); - result.push_back(NAME_STATIC_PARAMETER_ODEINTStepSize); - - return result; -} - -mitk::NumericTwoCompartmentExchangeModel::ParametersSizeType mitk::NumericTwoCompartmentExchangeModel::GetNumberOfStaticParameters() -const -{ - return 3; -} - - -void mitk::NumericTwoCompartmentExchangeModel::SetStaticParameter(const ParameterNameType& name, - const StaticParameterValuesType& values) -{ - if (name == NAME_STATIC_PARAMETER_AIF) - { - AterialInputFunctionType aif = mitk::convertParameterToArray(values); - - SetAterialInputFunctionValues(aif); - } - - if (name == NAME_STATIC_PARAMETER_AIFTimeGrid) - { - TimeGridType timegrid = mitk::convertParameterToArray(values); - - SetAterialInputFunctionTimeGrid(timegrid); - } - - if (name == NAME_STATIC_PARAMETER_ODEINTStepSize) - { - SetODEINTStepSize(values[0]); - } -}; - -mitk::NumericTwoCompartmentExchangeModel::StaticParameterValuesType mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterValue( - const ParameterNameType& name) const -{ - StaticParameterValuesType result; - - if (name == NAME_STATIC_PARAMETER_AIF) - { - result = mitk::convertArrayToParameter(this->m_AterialInputFunctionValues); - } - - if (name == NAME_STATIC_PARAMETER_AIFTimeGrid) - { - result = mitk::convertArrayToParameter(this->m_AterialInputFunctionTimeGrid); - } - if (name == NAME_STATIC_PARAMETER_ODEINTStepSize) - { - result.push_back(GetODEINTStepSize()); - } - - return result; -}; - - -mitk::NumericTwoCompartmentExchangeModel::ParameterNamesType -mitk::NumericTwoCompartmentExchangeModel::GetParameterNames() const -{ - ParameterNamesType result; - - result.push_back(NAME_PARAMETER_F); - result.push_back(NAME_PARAMETER_PS); - result.push_back(NAME_PARAMETER_ve); - result.push_back(NAME_PARAMETER_vp); - - return result; -} - -mitk::NumericTwoCompartmentExchangeModel::ParametersSizeType -mitk::NumericTwoCompartmentExchangeModel::GetNumberOfParameters() const -{ - return NUMBER_OF_PARAMETERS; -} - - -mitk::NumericTwoCompartmentExchangeModel::ParamterUnitMapType -mitk::NumericTwoCompartmentExchangeModel::GetParameterUnits() const -{ - ParamterUnitMapType result; - - result.insert(std::make_pair(NAME_PARAMETER_F, UNIT_PARAMETER_F)); - result.insert(std::make_pair(NAME_PARAMETER_PS, UNIT_PARAMETER_PS)); - result.insert(std::make_pair(NAME_PARAMETER_vp, UNIT_PARAMETER_vp)); - result.insert(std::make_pair(NAME_PARAMETER_ve, UNIT_PARAMETER_ve)); - - return result; -}; - -mitk::NumericTwoCompartmentExchangeModel::ModelResultType -mitk::NumericTwoCompartmentExchangeModel::ComputeModelfunction(const ParametersType& parameters) -const -{ - typedef itk::Array ConcentrationCurveType; - typedef std::vector ConcentrationVectorType; - - if (this->m_TimeGrid.GetSize() == 0) - { - itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); - } - - AterialInputFunctionType aterialInputFunction; - aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); - - unsigned int timeSteps = this->m_TimeGrid.GetSize(); - - /** @brief Boost::numeric::odeint works with type std::vector thus, aif and grid are converted to ModelParameters( of type std::vector) - */ - mitk::TwoCompartmentExchangeModelDifferentialEquations::AIFType aif = mitk::convertArrayToParameter( - aterialInputFunction); - mitk::TwoCompartmentExchangeModelDifferentialEquations::AIFType grid = - mitk::convertArrayToParameter(m_TimeGrid); - - mitk::TwoCompartmentExchangeModelDifferentialEquations::AIFType aifODE = aif; - aifODE.push_back(aif[timeSteps - 1]); - mitk::TwoCompartmentExchangeModelDifferentialEquations::AIFType gridODE = grid; - gridODE.push_back(grid[timeSteps - 1] + (grid[timeSteps - 1] - grid[timeSteps - 2])); - - - - //Model Parameters - double F = (double) parameters[POSITION_PARAMETER_F] / 6000.0; - double PS = (double) parameters[POSITION_PARAMETER_PS] / 6000.0; - double ve = (double) parameters[POSITION_PARAMETER_ve]; - double vp = (double) parameters[POSITION_PARAMETER_vp]; - - - /** @brief Initialize class TwoCompartmentExchangeModelDifferentialEquations defining the differential equations. AIF and Grid must be set so that at step t the aterial Concentration Ca(t) can be interpolated from AIF*/ - mitk::TwoCompartmentExchangeModelDifferentialEquations ode; - ode.initialize(F, PS, ve, vp); - ode.setAIF(aifODE); - ode.setAIFTimeGrid(gridODE); - - state_type x(2); - x[0] = 0.0; - x[1] = 0.0; - typedef boost::numeric::odeint::runge_kutta_cash_karp54 error_stepper_type; - //typedef boost::numeric::odeint::runge_kutta4< state_type > stepper_type; - - /** @brief Results of odeeint x[0] and x[1]*/ - ConcentrationVectorType Cp; - ConcentrationVectorType Ce; - ConcentrationVectorType odeTimeGrid; - - error_stepper_type stepper; - - - /** @brief Stepsize. Should be adapted by stepper (runge_kutta_cash_karp54) */ -// const double dt = 0.05; - const double dt = this->m_ODEINTStepSize; - - - /** @brief perform Step t -> t+dt to calculate approximate value x(t+dt)*/ - for (double t = 0.0; t < this->m_TimeGrid(this->m_TimeGrid.GetSize() - 1) - 2*dt; t += dt) - { - stepper.do_step(ode, x, t, dt); - Cp.push_back(x[0]); - Ce.push_back(x[1]); - odeTimeGrid.push_back(t); - } - - /** @brief transfom result of Differential equations back to itk::Array and interpolate to m_TimeGrid (they are calculated on a different grid defined by stepsize of odeint)*/ - ConcentrationCurveType plasmaConcentration = mitk::convertParameterToArray(Cp); - ConcentrationCurveType EESConcentration = mitk::convertParameterToArray(Ce); - ConcentrationCurveType rungeKuttaTimeGrid = mitk::convertParameterToArray(odeTimeGrid); - - mitk::ModelBase::ModelResultType C_Plasma = mitk::InterpolateSignalToNewTimeGrid(plasmaConcentration, rungeKuttaTimeGrid, m_TimeGrid); - mitk::ModelBase::ModelResultType C_EES = mitk::InterpolateSignalToNewTimeGrid(EESConcentration, rungeKuttaTimeGrid, m_TimeGrid); - - - //Signal that will be returned by ComputeModelFunction - mitk::ModelBase::ModelResultType signal(timeSteps); - signal.fill(0.0); - - mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); - mitk::ModelBase::ModelResultType::const_iterator CePos = C_EES.begin(); - - mitk::ModelBase::ModelResultType::const_iterator t = this->m_TimeGrid.begin(); - mitk::ModelBase::ModelResultType::const_iterator Cin = aterialInputFunction.begin(); - - - - for (mitk::ModelBase::ModelResultType::const_iterator CpPos = C_Plasma.begin(); - CpPos != C_Plasma.end(); ++CpPos, ++CePos, ++signalPos, ++t, ++Cin) - { - *signalPos = vp * (*CpPos) + ve * (*CePos); - - } - - return signal; - -} - - - - -itk::LightObject::Pointer mitk::NumericTwoCompartmentExchangeModel::InternalClone() const -{ - NumericTwoCompartmentExchangeModel::Pointer newClone = NumericTwoCompartmentExchangeModel::New(); - - newClone->SetTimeGrid(this->m_TimeGrid); - - return newClone.GetPointer(); -} - -void mitk::NumericTwoCompartmentExchangeModel::PrintSelf(std::ostream& os, - ::itk::Indent indent) const -{ - Superclass::PrintSelf(os, indent); - - -} - - diff --git a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModelFactory.cpp deleted file mode 100644 index ef04fa136a..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModelFactory.cpp +++ /dev/null @@ -1,54 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkNumericTwoCompartmentExchangeModelFactory.h" - - -#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" -#include "mitkAIFParametrizerHelper.h" - -mitk::NumericTwoCompartmentExchangeModelFactory::NumericTwoCompartmentExchangeModelFactory() -{ -}; - -mitk::NumericTwoCompartmentExchangeModelFactory::~NumericTwoCompartmentExchangeModelFactory() -{ -}; - -mitk::ModelParameterizerBase::Pointer -mitk::NumericTwoCompartmentExchangeModelFactory::DoCreateParameterizer( - const modelFit::ModelFitInfo* fit) -const -{ - mitk::ModelParameterizerBase::Pointer result; - - ModelParameterizerType::Pointer modelParameterizer = - ModelParameterizerType::New(); - - modelFit::StaticParameterMap::ValueType aif = fit->staticParamMap.Get( - ModelType::NAME_STATIC_PARAMETER_AIF); - - modelParameterizer->SetAIF(mitk::convertParameterToArray(aif)); - - modelFit::StaticParameterMap::ValueType aifGrid = fit->staticParamMap.Get( - ModelType::NAME_STATIC_PARAMETER_AIFTimeGrid); - modelParameterizer->SetAIFTimeGrid(mitk::convertParameterToArray(aifGrid)); - - modelFit::StaticParameterMap::ValueType odeStepSize = fit->staticParamMap.Get( - ModelType::NAME_STATIC_PARAMETER_ODEINTStepSize); - modelParameterizer->SetODEINTStepSize(odeStepSize[0]); - - - result = modelParameterizer.GetPointer(); - - return result; -}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModelParameterizer.cpp deleted file mode 100644 index 25910af578..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoCompartmentExchangeModelParameterizer.cpp +++ /dev/null @@ -1,49 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" - -mitk::NumericTwoCompartmentExchangeModelParameterizer::ParametersType -mitk::NumericTwoCompartmentExchangeModelParameterizer::GetDefaultInitialParameterization() const -{ - ParametersType initialParameters; - initialParameters.SetSize(4); - initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_PS] = 5.0; - initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_F] = 20.0; - initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_ve] = 0.1; - initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_vp] = 0.04; - - return initialParameters; -}; - -mitk::NumericTwoCompartmentExchangeModelParameterizer::NumericTwoCompartmentExchangeModelParameterizer() -{ -}; - -mitk::NumericTwoCompartmentExchangeModelParameterizer::~NumericTwoCompartmentExchangeModelParameterizer() -{ -}; - -mitk::NumericTwoCompartmentExchangeModelParameterizer::StaticParameterMapType mitk::NumericTwoCompartmentExchangeModelParameterizer::GetGlobalStaticParameters() const -{ - StaticParameterMapType result; - StaticParameterValuesType valuesAIF = mitk::convertArrayToParameter(this->m_AIF); - StaticParameterValuesType valuesAIFGrid = mitk::convertArrayToParameter(this->m_AIFTimeGrid); - StaticParameterValuesType values; - values.push_back(m_ODEINTStepSize); - - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_AIF, valuesAIF)); - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_AIFTimeGrid, valuesAIFGrid)); - result.insert(std::make_pair(ModelType::NAME_STATIC_PARAMETER_ODEINTStepSize, values)); - - return result; -}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModel.cpp deleted file mode 100644 index bb7226a2d9..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModel.cpp +++ /dev/null @@ -1,216 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkNumericTwoTissueCompartmentModel.h" -#include "mitkAIFParametrizerHelper.h" -#include "mitkTimeGridHelper.h" -#include "mitkTwoTissueCompartmentModelDifferentialEquations.h" -#include -#include -#include - -const std::string mitk::NumericTwoTissueCompartmentModel::MODEL_DISPLAY_NAME = - "Numeric Two Tissue Compartment Model"; - -const std::string mitk::NumericTwoTissueCompartmentModel::NAME_PARAMETER_K1 = "K1"; -const std::string mitk::NumericTwoTissueCompartmentModel::NAME_PARAMETER_k2 = "k2"; -const std::string mitk::NumericTwoTissueCompartmentModel::NAME_PARAMETER_k3 = "k3"; -const std::string mitk::NumericTwoTissueCompartmentModel::NAME_PARAMETER_k4 = "k4"; -const std::string mitk::NumericTwoTissueCompartmentModel::NAME_PARAMETER_VB = "V_B"; - -const std::string mitk::NumericTwoTissueCompartmentModel::UNIT_PARAMETER_K1 = "1/min"; -const std::string mitk::NumericTwoTissueCompartmentModel::UNIT_PARAMETER_k2 = "1/min"; -const std::string mitk::NumericTwoTissueCompartmentModel::UNIT_PARAMETER_k3 = "1/min"; -const std::string mitk::NumericTwoTissueCompartmentModel::UNIT_PARAMETER_k4 = "1/min"; -const std::string mitk::NumericTwoTissueCompartmentModel::UNIT_PARAMETER_VB = "ml/ml"; - -const unsigned int mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_K1 = 0; -const unsigned int mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k2 = 1; -const unsigned int mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k3 = 2; -const unsigned int mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k4 = 3; -const unsigned int mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_VB = 4; - -const unsigned int mitk::NumericTwoTissueCompartmentModel::NUMBER_OF_PARAMETERS = 5; - - -std::string mitk::NumericTwoTissueCompartmentModel::GetModelDisplayName() const -{ - return MODEL_DISPLAY_NAME; -}; - -std::string mitk::NumericTwoTissueCompartmentModel::GetModelType() const -{ - return "Dynamic.PET"; -}; - -mitk::NumericTwoTissueCompartmentModel::NumericTwoTissueCompartmentModel() -{ - -} - -mitk::NumericTwoTissueCompartmentModel::~NumericTwoTissueCompartmentModel() -{ - -} - -mitk::NumericTwoTissueCompartmentModel::ParameterNamesType -mitk::NumericTwoTissueCompartmentModel::GetParameterNames() const -{ - ParameterNamesType result; - - result.push_back(NAME_PARAMETER_K1); - result.push_back(NAME_PARAMETER_k2); - result.push_back(NAME_PARAMETER_k3); - result.push_back(NAME_PARAMETER_k4); - result.push_back(NAME_PARAMETER_VB); - - return result; -} - -mitk::NumericTwoTissueCompartmentModel::ParametersSizeType -mitk::NumericTwoTissueCompartmentModel::GetNumberOfParameters() const -{ - return NUMBER_OF_PARAMETERS; -} - -mitk::NumericTwoTissueCompartmentModel::ParamterUnitMapType -mitk::NumericTwoTissueCompartmentModel::GetParameterUnits() const -{ - ParamterUnitMapType result; - - result.insert(std::make_pair(NAME_PARAMETER_K1, UNIT_PARAMETER_K1)); - result.insert(std::make_pair(NAME_PARAMETER_k2, UNIT_PARAMETER_k2)); - result.insert(std::make_pair(NAME_PARAMETER_k3, UNIT_PARAMETER_k3)); - result.insert(std::make_pair(NAME_PARAMETER_k4, UNIT_PARAMETER_k4)); - result.insert(std::make_pair(NAME_PARAMETER_VB, UNIT_PARAMETER_VB)); - - return result; -}; - - -mitk::NumericTwoTissueCompartmentModel::ModelResultType -mitk::NumericTwoTissueCompartmentModel::ComputeModelfunction(const ParametersType& parameters) const -{ - typedef itk::Array ConcentrationCurveType; - typedef std::vector ConcentrationVectorType; - - if (this->m_TimeGrid.GetSize() == 0) - { - itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); - } - - AterialInputFunctionType aterialInputFunction; - aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); - - unsigned int timeSteps = this->m_TimeGrid.GetSize(); - - /** @brief Boost::numeric::odeint works with type std::vector thus, aif and grid are converted to ModelParameters( of type std::vector) - */ - mitk::TwoTissueCompartmentModelDifferentialEquations::AIFType aif = mitk::convertArrayToParameter( - aterialInputFunction); - mitk::TwoTissueCompartmentModelDifferentialEquations::AIFType grid = mitk::convertArrayToParameter( - m_TimeGrid); - - mitk::TwoTissueCompartmentModelDifferentialEquations::AIFType aifODE = aif; - aifODE.push_back(aif[timeSteps - 1]); - mitk::TwoTissueCompartmentModelDifferentialEquations::AIFType gridODE = grid; - gridODE.push_back(grid[timeSteps - 1] + (grid[timeSteps - 1] - grid[timeSteps - 2])); - - //Model Parameters - double K1 = (double)parameters[POSITION_PARAMETER_K1] / 60.0; - double k2 = (double)parameters[POSITION_PARAMETER_k2] / 60.0; - double k3 = (double)parameters[POSITION_PARAMETER_k3] / 60.0; - double k4 = (double)parameters[POSITION_PARAMETER_k4] / 60.0; - double VB = parameters[POSITION_PARAMETER_VB]; - - - /** @brief Initialize class TwpTissueCompartmentModelDifferentialEquations defining the differential equations. AIF and Grid must be set so that at step t the aterial Concentration Ca(t) can be interpolated from AIF*/ - mitk::TwoTissueCompartmentModelDifferentialEquations ode; - ode.initialize(K1, k2, k3, k4); - ode.setAIF(aifODE); - ode.setAIFTimeGrid(gridODE); - - state_type x(2); - x[0] = 0.0; - x[1] = 0.0; - typedef boost::numeric::odeint::runge_kutta_cash_karp54 error_stepper_type; - //typedef boost::numeric::odeint::runge_kutta4< state_type > stepper_type; - - /** @brief Results of odeeint x[0] and x[1]*/ - ConcentrationVectorType C1; - ConcentrationVectorType C2; - ConcentrationVectorType odeTimeGrid; - - error_stepper_type stepper; - /** @brief Stepsize. Should be adapted by stepper (runge_kutta_cash_karp54) */ - const double dt = 0.1; - /** @brief perform Step t -> t+dt to calculate approximate value x(t+dt)*/ - - double T = this->m_TimeGrid(timeSteps - 1) + (grid[timeSteps - 1] - grid[timeSteps - 2]); - - for (double t = 0.0; t < T; t += dt) - { - stepper.do_step(ode, x, t, dt); - C1.push_back(x[0]); - C2.push_back(x[1]); - odeTimeGrid.push_back(t); - - } - - /** @brief transfom result of Differential equations back to itk::Array and interpolate to m_TimeGrid (they are calculated on a different grid defined by stepsize of odeint)*/ - ConcentrationCurveType ConcentrationCompartment1 = mitk::convertParameterToArray(C1); - ConcentrationCurveType ConcentrationCompartment2 = mitk::convertParameterToArray(C2); - ConcentrationCurveType rungeKuttaTimeGrid = mitk::convertParameterToArray(odeTimeGrid); - - mitk::ModelBase::ModelResultType C_1 = mitk::InterpolateSignalToNewTimeGrid( - ConcentrationCompartment1, rungeKuttaTimeGrid, m_TimeGrid); - mitk::ModelBase::ModelResultType C_2 = mitk::InterpolateSignalToNewTimeGrid( - ConcentrationCompartment2, rungeKuttaTimeGrid, m_TimeGrid); - - - //Signal that will be returned by ComputeModelFunction - mitk::ModelBase::ModelResultType signal(timeSteps); - signal.fill(0.0); - mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); - mitk::ModelBase::ModelResultType::const_iterator C1Pos = C_1.begin(); - mitk::ModelBase::ModelResultType::const_iterator C2Pos = C_2.begin(); - - - for (AterialInputFunctionType::const_iterator aifpos = aterialInputFunction.begin(); - aifpos != aterialInputFunction.end(); ++aifpos, ++C1Pos, ++C2Pos, ++signalPos) - { - *signalPos = VB * (*aifpos) + (1 - VB) * (*C1Pos + *C2Pos); - } - - return signal; - -} - -itk::LightObject::Pointer mitk::NumericTwoTissueCompartmentModel::InternalClone() const -{ - NumericTwoTissueCompartmentModel::Pointer newClone = NumericTwoTissueCompartmentModel::New(); - - newClone->SetTimeGrid(this->m_TimeGrid); - - return newClone.GetPointer(); -} - -void mitk::NumericTwoTissueCompartmentModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const -{ - Superclass::PrintSelf(os, indent); - - -} - - - - diff --git a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModelFactory.cpp deleted file mode 100644 index d00b9d3370..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModelFactory.cpp +++ /dev/null @@ -1,25 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkNumericTwoTissueCompartmentModelFactory.h" - -#include "mitkNumericTwoTissueCompartmentModelParameterizer.h" -#include "mitkAIFParametrizerHelper.h" - -mitk::NumericTwoTissueCompartmentModelFactory::NumericTwoTissueCompartmentModelFactory() -{ -}; - -mitk::NumericTwoTissueCompartmentModelFactory::~NumericTwoTissueCompartmentModelFactory() -{ -}; - diff --git a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModelParameterizer.cpp deleted file mode 100644 index 32bc61366e..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkNumericTwoTissueCompartmentModelParameterizer.cpp +++ /dev/null @@ -1,35 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkNumericTwoTissueCompartmentModelParameterizer.h" - -mitk::NumericTwoTissueCompartmentModelParameterizer::ParametersType -mitk::NumericTwoTissueCompartmentModelParameterizer::GetDefaultInitialParameterization() const -{ - ParametersType initialParameters; - initialParameters.SetSize(5); - initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_K1] = 0.23; - initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k2] = 0.4; - initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k3] = 0.13; - initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k4] = 0.15; - initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_VB] = 0.03; - - return initialParameters; -}; - -mitk::NumericTwoTissueCompartmentModelParameterizer::NumericTwoTissueCompartmentModelParameterizer() -{ -}; - -mitk::NumericTwoTissueCompartmentModelParameterizer::~NumericTwoTissueCompartmentModelParameterizer() -{ -}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp index a4d455583e..49deb33fac 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp @@ -1,138 +1,141 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkOneTissueCompartmentModel.h" #include "mitkConvolutionHelper.h" #include #include const std::string mitk::OneTissueCompartmentModel::MODEL_DISPLAY_NAME = "One Tissue Compartment Model"; -const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_k1 = "K1"; -const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2 = "k2"; +const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1 = "K_1"; +const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2 = "k_2"; -const std::string mitk::OneTissueCompartmentModel::UNIT_PARAMETER_k1 = "1/min"; +const std::string mitk::OneTissueCompartmentModel::UNIT_PARAMETER_K1 = "1/min"; const std::string mitk::OneTissueCompartmentModel::UNIT_PARAMETER_k2 = "1/min"; -const unsigned int mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k1 = 0; +const unsigned int mitk::OneTissueCompartmentModel::POSITION_PARAMETER_K1 = 0; const unsigned int mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k2 = 1; const unsigned int mitk::OneTissueCompartmentModel::NUMBER_OF_PARAMETERS = 2; +const std::string mitk::OneTissueCompartmentModel::MODEL_TYPE = "Dynamic.PET"; + std::string mitk::OneTissueCompartmentModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::OneTissueCompartmentModel::GetModelType() const { - return "Dynamic.PET"; + return MODEL_TYPE; }; mitk::OneTissueCompartmentModel::OneTissueCompartmentModel() { } mitk::OneTissueCompartmentModel::~OneTissueCompartmentModel() { } mitk::OneTissueCompartmentModel::ParameterNamesType mitk::OneTissueCompartmentModel::GetParameterNames() const { ParameterNamesType result; - result.push_back(NAME_PARAMETER_k1); + result.push_back(NAME_PARAMETER_K1); result.push_back(NAME_PARAMETER_k2); return result; } mitk::OneTissueCompartmentModel::ParametersSizeType mitk::OneTissueCompartmentModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::OneTissueCompartmentModel::ParamterUnitMapType mitk::OneTissueCompartmentModel::GetParameterUnits() const { ParamterUnitMapType result; - result.insert(std::make_pair(NAME_PARAMETER_k1, UNIT_PARAMETER_k1)); + result.insert(std::make_pair(NAME_PARAMETER_K1, UNIT_PARAMETER_K1)); result.insert(std::make_pair(NAME_PARAMETER_k2, UNIT_PARAMETER_k2)); return result; }; + mitk::OneTissueCompartmentModel::ModelResultType mitk::OneTissueCompartmentModel::ComputeModelfunction( const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters - double K1 = (double) parameters[POSITION_PARAMETER_k1] / 60.0; + double K1 = (double) parameters[POSITION_PARAMETER_K1] / 60.0; double k2 = (double) parameters[POSITION_PARAMETER_k2] / 60.0; mitk::ModelBase::ModelResultType convolution = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, k2); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); for (mitk::ModelBase::ModelResultType::const_iterator res = convolution.begin(); res != convolution.end(); ++res, ++signalPos) { *signalPos = K1 * (*res); } return signal; } itk::LightObject::Pointer mitk::OneTissueCompartmentModel::InternalClone() const { OneTissueCompartmentModel::Pointer newClone = OneTissueCompartmentModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; void mitk::OneTissueCompartmentModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp index b9c28d3295..5a2b2c9d1e 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp @@ -1,46 +1,46 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkOneTissueCompartmentModelFactory.h" #include #include #include mitk::ConstraintCheckerBase::Pointer mitk::OneTissueCompartmentModelFactory::CreateDefaultConstraints() const { SimpleBarrierConstraintChecker::Pointer constraints = SimpleBarrierConstraintChecker::New(); - constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k1, 0.0); + constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_K1, 0.0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k2, 0.0); - constraints->SetUpperBarrier (ModelType::POSITION_PARAMETER_k1, 1.0); + constraints->SetUpperBarrier (ModelType::POSITION_PARAMETER_K1, 1.0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k2, 1.0); return constraints.GetPointer(); }; mitk::ModelParameterizerBase::ParametersType mitk::OneTissueCompartmentModelFactory::GetDefaultInitialParameterization() const { return OneTissueCompartmentModelParameterizer::New()->GetDefaultInitialParameterization(); }; mitk::OneTissueCompartmentModelFactory::OneTissueCompartmentModelFactory() { }; mitk::OneTissueCompartmentModelFactory::~OneTissueCompartmentModelFactory() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp index 017db227a0..1dc058f326 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp @@ -1,32 +1,32 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkOneTissueCompartmentModelParameterizer.h" mitk::OneTissueCompartmentModelParameterizer::ParametersType mitk::OneTissueCompartmentModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(2); - initialParameters[mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k1] = 0.5; + initialParameters[mitk::OneTissueCompartmentModel::POSITION_PARAMETER_K1] = 0.5; initialParameters[mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k2] = 0.5; return initialParameters; }; mitk::OneTissueCompartmentModelParameterizer::OneTissueCompartmentModelParameterizer() { }; mitk::OneTissueCompartmentModelParameterizer::~OneTissueCompartmentModelParameterizer() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkStandardToftsModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkStandardToftsModel.cpp index 99600b4559..2dcc396a01 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkStandardToftsModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkStandardToftsModel.cpp @@ -1,168 +1,178 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkStandardToftsModel.h" #include "mitkConvolutionHelper.h" #include #include const std::string mitk::StandardToftsModel::MODEL_DISPLAY_NAME = "Standard Tofts Model"; -const std::string mitk::StandardToftsModel::NAME_PARAMETER_Ktrans = "KTrans"; -const std::string mitk::StandardToftsModel::NAME_PARAMETER_ve = "ve"; +const std::string mitk::StandardToftsModel::NAME_PARAMETER_Ktrans = "K^trans"; +const std::string mitk::StandardToftsModel::NAME_PARAMETER_ve = "v_e"; const std::string mitk::StandardToftsModel::UNIT_PARAMETER_Ktrans = "ml/min/100ml"; const std::string mitk::StandardToftsModel::UNIT_PARAMETER_ve = "ml/ml"; const unsigned int mitk::StandardToftsModel::POSITION_PARAMETER_Ktrans = 0; const unsigned int mitk::StandardToftsModel::POSITION_PARAMETER_ve = 1; const unsigned int mitk::StandardToftsModel::NUMBER_OF_PARAMETERS = 2; +const std::string mitk::StandardToftsModel::NAME_DERIVED_PARAMETER_kep = "k_{e->p}"; + +const unsigned int mitk::StandardToftsModel::NUMBER_OF_DERIVED_PARAMETERS = 1; + +const std::string mitk::StandardToftsModel::UNIT_DERIVED_PARAMETER_kep = "1/min"; + +const std::string mitk::StandardToftsModel::MODEL_TYPE = "Perfusion.MR"; + + + std::string mitk::StandardToftsModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::StandardToftsModel::GetModelType() const { - return "Perfusion.MR"; + return MODEL_TYPE; }; mitk::StandardToftsModel::StandardToftsModel() { } mitk::StandardToftsModel::~StandardToftsModel() { } mitk::StandardToftsModel::ParameterNamesType mitk::StandardToftsModel::GetParameterNames() const { ParameterNamesType result; result.push_back(NAME_PARAMETER_Ktrans); result.push_back(NAME_PARAMETER_ve); return result; } mitk::StandardToftsModel::ParametersSizeType mitk::StandardToftsModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::StandardToftsModel::ParamterUnitMapType mitk::StandardToftsModel::GetParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_PARAMETER_Ktrans, UNIT_PARAMETER_Ktrans)); result.insert(std::make_pair(NAME_PARAMETER_ve, UNIT_PARAMETER_ve)); return result; }; mitk::StandardToftsModel::ParameterNamesType mitk::StandardToftsModel::GetDerivedParameterNames() const { ParameterNamesType result; - result.push_back("kep"); + result.push_back(NAME_DERIVED_PARAMETER_kep); return result; }; mitk::StandardToftsModel::ParametersSizeType mitk::StandardToftsModel::GetNumberOfDerivedParameters() const { - return 1; + return NUMBER_OF_DERIVED_PARAMETERS; }; mitk::StandardToftsModel::ParamterUnitMapType mitk::StandardToftsModel::GetDerivedParameterUnits() const { ParamterUnitMapType result; - result.insert(std::make_pair("kep", "1/min")); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_kep, UNIT_DERIVED_PARAMETER_kep)); return result; }; mitk::StandardToftsModel::ModelResultType mitk::StandardToftsModel::ComputeModelfunction( const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters double ktrans = parameters[POSITION_PARAMETER_Ktrans] / 6000.0; double ve = parameters[POSITION_PARAMETER_ve]; double lambda = ktrans / ve; mitk::ModelBase::ModelResultType convolution = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, lambda); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); mitk::ModelBase::ModelResultType::const_iterator res = convolution.begin(); for (AterialInputFunctionType::iterator Cp = aterialInputFunction.begin(); Cp != aterialInputFunction.end(); ++res, ++signalPos, ++Cp) { *signalPos = ktrans * (*res); } return signal; } mitk::ModelBase::DerivedParameterMapType mitk::StandardToftsModel::ComputeDerivedParameters( const mitk::ModelBase::ParametersType& parameters) const { DerivedParameterMapType result; double kep = parameters[POSITION_PARAMETER_Ktrans] / parameters[POSITION_PARAMETER_ve]; - result.insert(std::make_pair("kep", kep)); + result.insert(std::make_pair(NAME_DERIVED_PARAMETER_kep, kep)); return result; }; itk::LightObject::Pointer mitk::StandardToftsModel::InternalClone() const { StandardToftsModel::Pointer newClone = StandardToftsModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; void mitk::StandardToftsModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModel.cpp deleted file mode 100644 index 3c7483f464..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkThreeStepLinearModel.cpp +++ /dev/null @@ -1,275 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkThreeStepLinearModel.h" -#include - - -const std::string mitk::ThreeStepLinearModel::MODEL_DISPLAY_NAME = "Three Step Linear Model"; - -const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_s0 = "Baseline"; -const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_t1 = "Time_point_1"; -const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_t2 = "Time_point_2"; -const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_a1 = "Slope_1"; -const std::string mitk::ThreeStepLinearModel::NAME_PARAMETER_a2 = "Slope_2"; - -// Assuming that Model is calculated on Signal intensities I -const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_s0 = "I"; -const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_t1 = "s"; -const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_t2 = "s"; -const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_a1 = "I/s"; -const std::string mitk::ThreeStepLinearModel::UNIT_PARAMETER_a2 = "I/s"; - -const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_s0 = 0; -const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_t1 = 1; -const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_t2 = 2; -const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_a1 = 3; -const unsigned int mitk::ThreeStepLinearModel::POSITION_PARAMETER_a2 = 4; - -const unsigned int mitk::ThreeStepLinearModel::NUMBER_OF_PARAMETERS = 5; - -std::string mitk::ThreeStepLinearModel::GetModelDisplayName() const -{ - return MODEL_DISPLAY_NAME; -}; - -std::string mitk::ThreeStepLinearModel::GetModelType() const -{ - return "Generic"; -}; - -mitk::ThreeStepLinearModel::FunctionStringType mitk::ThreeStepLinearModel::GetFunctionString() const -{ - return "Baseline if t= t1 && x <= t2) - { - signal = a1 * x + b1; - } - else - { - signal = a2 * x + b2; - } - - - return signal; -}; - -mitk::ThreeStepLinearModel::ParamterUnitMapType mitk::ThreeStepLinearModel::GetDerivedParameterUnits() const -{ - ParamterUnitMapType result; - - result.insert(std::make_pair("AUC", "I*s")); - result.insert(std::make_pair("FinalTimePoint", "s")); - result.insert(std::make_pair("FinalUptake", "I")); - result.insert(std::make_pair("Smax", "I")); - result.insert(std::make_pair("y-intercept1", "I")); - result.insert(std::make_pair("y-intercept2", "I")); - - - - - return result; -}; - -mitk::ThreeStepLinearModel::ModelResultType -mitk::ThreeStepLinearModel::ComputeModelfunction(const ParametersType& parameters) const -{ - //Model Parameters - const double s0 = (double) parameters[POSITION_PARAMETER_s0]; - const double t1 = (double) parameters[POSITION_PARAMETER_t1] ; - const double t2 = (double) parameters[POSITION_PARAMETER_t2] ; - const double a1 = (double) parameters[POSITION_PARAMETER_a1] ; - const double a2 = (double) parameters[POSITION_PARAMETER_a2] ; - - double b1 = s0 - a1 * t1; - double b2 = (a1 * t2 + b1) - (a2 * t2); - - ModelResultType signal(m_TimeGrid.GetSize()); - - TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); - - ModelResultType::iterator signalPos = signal.begin(); - - for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd; ++gridPos, ++signalPos) - { - *signalPos = ComputeSignalFromParameters(*gridPos, s0, t1, t2, a1, a2, b1, b2); - } - - return signal; -}; - -mitk::ThreeStepLinearModel::ParameterNamesType mitk::ThreeStepLinearModel::GetStaticParameterNames() const -{ - ParameterNamesType result; - - return result; -} - -mitk::ThreeStepLinearModel::ParametersSizeType mitk::ThreeStepLinearModel::GetNumberOfStaticParameters() const -{ - return 0; -} - -void mitk::ThreeStepLinearModel::SetStaticParameter(const ParameterNameType&, - const StaticParameterValuesType&) -{ - //do nothing -}; - -mitk::ThreeStepLinearModel::StaticParameterValuesType mitk::ThreeStepLinearModel::GetStaticParameterValue( - const ParameterNameType&) const -{ - StaticParameterValuesType result; - - //do nothing - - return result; -}; - -mitk::ModelBase::DerivedParameterMapType mitk::ThreeStepLinearModel::ComputeDerivedParameters( - const mitk::ModelBase::ParametersType& parameters) const -{ - const double s0 = (double) parameters[POSITION_PARAMETER_s0]; - const double t1 = (double) parameters[POSITION_PARAMETER_t1] ; - const double t2 = (double) parameters[POSITION_PARAMETER_t2] ; - const double a1 = (double) parameters[POSITION_PARAMETER_a1] ; - const double a2 = (double) parameters[POSITION_PARAMETER_a2] ; - - const double b1 = s0 - a1 * t1; - const double b2 = (a1 * t2 + b1) - (a2 * t2); - - unsigned int timeSteps = m_TimeGrid.GetSize(); - - const double taq = (m_TimeGrid.empty() == false) ? (m_TimeGrid.GetElement(timeSteps - 1)) : ( mitkThrow() << "An exception occured because time grid is empty, method can't continue."); - - const double sfin = a2 * taq + b2; - - double smax = sfin; - if ((a1 >= 0) && (a2 >= 0)) - smax = sfin; - else if ((a1 < 0) && (a2 < 0)) - smax = s0; - else if ((a1 > 0) && (a2 < 0)) - smax = (a1 * t2 + b1); - else - { - if (abs(a1 * (t2 - t1)) >= abs(a2 * (taq - t2))) - smax = s0; - else smax = sfin; - } - - double auc = 0.0; - TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); - - for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd - 1; ++gridPos) - { - double currentGridPos = *gridPos; - double nextGridPos = *(++gridPos); - double deltaX = nextGridPos - currentGridPos; - double deltaY = ComputeSignalFromParameters(nextGridPos, s0, t1, t2, a1, a2, b1, b2) - ComputeSignalFromParameters(currentGridPos, s0, t1, t2, a1, a2, b1, b2); - double Yi = ComputeSignalFromParameters(currentGridPos, s0, t1, t2, a1, a2, b1, b2 ); - double intI = 0.5 * deltaX * deltaY + Yi * deltaX; - auc += std::abs(intI); - --gridPos; - } - - - DerivedParameterMapType result; - - result.insert(std::make_pair("AUC", auc)); - result.insert(std::make_pair("FinalTimePoint", taq)); - result.insert(std::make_pair("FinalUptake", sfin)); - result.insert(std::make_pair("Smax", smax)); - result.insert(std::make_pair("y-intercept1", b1)); - result.insert(std::make_pair("y-intercept2", b2)); - - - return result; -}; - -itk::LightObject::Pointer mitk::ThreeStepLinearModel::InternalClone() const -{ - ThreeStepLinearModel::Pointer newClone = ThreeStepLinearModel::New(); - - newClone->SetTimeGrid(this->m_TimeGrid); - - return newClone.GetPointer(); -}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoCompartmentExchangeModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoCompartmentExchangeModel.cpp index f59e917bed..18cc53af40 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoCompartmentExchangeModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoCompartmentExchangeModel.cpp @@ -1,180 +1,183 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoCompartmentExchangeModel.h" #include "mitkConvolutionHelper.h" #include -const std::string mitk::TwoCompartmentExchangeModel::MODEL_DISPLAY_NAME = - "Two Compartment Exchange Model"; +const std::string mitk::TwoCompartmentExchangeModel::MODEL_DISPLAY_NAME = "Two Compartment Exchange Model"; -const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_F = "F"; +const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_F = "F_p"; const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_PS = "PS"; -const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_ve = "ve"; -const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_vp = "vp"; +const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_ve = "v_e"; +const std::string mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_vp = "v_p"; const std::string mitk::TwoCompartmentExchangeModel::UNIT_PARAMETER_F = "ml/min/100ml"; const std::string mitk::TwoCompartmentExchangeModel::UNIT_PARAMETER_PS = "ml/min/100ml"; const std::string mitk::TwoCompartmentExchangeModel::UNIT_PARAMETER_ve = "ml/ml"; const std::string mitk::TwoCompartmentExchangeModel::UNIT_PARAMETER_vp = "ml/ml"; const unsigned int mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_F = 0; const unsigned int mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_PS = 1; const unsigned int mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_ve = 2; const unsigned int mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_vp = 3; const unsigned int mitk::TwoCompartmentExchangeModel::NUMBER_OF_PARAMETERS = 4; +const std::string mitk::TwoCompartmentExchangeModel::MODEL_TYPE = "Perfusion.MR"; + + + inline double square(double a) { return a * a; } std::string mitk::TwoCompartmentExchangeModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::TwoCompartmentExchangeModel::GetModelType() const { - return "Perfusion.MR"; + return MODEL_TYPE; }; mitk::TwoCompartmentExchangeModel::TwoCompartmentExchangeModel() { } mitk::TwoCompartmentExchangeModel::~TwoCompartmentExchangeModel() { } mitk::TwoCompartmentExchangeModel::ParameterNamesType mitk::TwoCompartmentExchangeModel::GetParameterNames() const { ParameterNamesType result; result.push_back(NAME_PARAMETER_F); result.push_back(NAME_PARAMETER_PS); result.push_back(NAME_PARAMETER_ve); result.push_back(NAME_PARAMETER_vp); return result; } mitk::TwoCompartmentExchangeModel::ParametersSizeType mitk::TwoCompartmentExchangeModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::TwoCompartmentExchangeModel::ParamterUnitMapType mitk::TwoCompartmentExchangeModel::GetParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_PARAMETER_F, UNIT_PARAMETER_F)); result.insert(std::make_pair(NAME_PARAMETER_PS, UNIT_PARAMETER_PS)); result.insert(std::make_pair(NAME_PARAMETER_vp, UNIT_PARAMETER_vp)); result.insert(std::make_pair(NAME_PARAMETER_ve, UNIT_PARAMETER_ve)); return result; }; mitk::TwoCompartmentExchangeModel::ModelResultType mitk::TwoCompartmentExchangeModel::ComputeModelfunction(const ParametersType& parameters) const { typedef mitk::ModelBase::ModelResultType ConvolutionResultType; if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); //Model Parameters double F = parameters[POSITION_PARAMETER_F] / 6000.0; double PS = parameters[POSITION_PARAMETER_PS] / 6000.0; double ve = parameters[POSITION_PARAMETER_ve]; double vp = parameters[POSITION_PARAMETER_vp]; if(PS != 0) { double Tp = vp/(PS + F); double Te = ve/PS; double Tb = vp/F; double Kp = 0.5 *( 1/Tp + 1/Te + sqrt(( 1/Tp + 1/Te )*( 1/Tp + 1/Te ) - 4 * 1/Te*1/Tb) ); double Km = 0.5 *( 1/Tp + 1/Te - sqrt(( 1/Tp + 1/Te )*( 1/Tp + 1/Te ) - 4 * 1/Te*1/Tb) ); double E = ( Kp - 1/Tb )/( Kp - Km ); ConvolutionResultType expp = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction,Kp); ConvolutionResultType expm = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction,Km); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType::const_iterator exppPos = expp.begin(); mitk::ModelBase::ModelResultType::const_iterator expmPos = expm.begin(); for( mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); signalPos!=signal.end(); ++exppPos,++expmPos, ++signalPos) { *signalPos = F * ( *exppPos + E*(*expmPos - *exppPos) ); } } else { double Kp = F/vp; ConvolutionResultType exp = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction,Kp); mitk::ModelBase::ModelResultType::const_iterator expPos = exp.begin(); for( mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); signalPos!=signal.end(); ++expPos, ++signalPos) { *signalPos = F * ( *expPos ); } } return signal; } itk::LightObject::Pointer mitk::TwoCompartmentExchangeModel::InternalClone() const { TwoCompartmentExchangeModel::Pointer newClone = TwoCompartmentExchangeModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); } void mitk::TwoCompartmentExchangeModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); } diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModel.cpp deleted file mode 100644 index 19191106fa..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModel.cpp +++ /dev/null @@ -1,209 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkTwoStepLinearModel.h" -#include - -const std::string mitk::TwoStepLinearModel::MODELL_NAME = "Two Step Linear Model"; - -const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_y1 = "BaseValue"; -const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_a1 = "Slope_1"; -const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_t = "Change_Point"; -const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_a2 = "Slope_2"; - -const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_y1 = 0; -const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_t = 1; -const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_a1 = 2; -const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_a2 = 3; - -const unsigned int mitk::TwoStepLinearModel::NUMBER_OF_PARAMETERS = 4; - -std::string mitk::TwoStepLinearModel::GetModelDisplayName() const -{ - return MODELL_NAME; -}; - -std::string mitk::TwoStepLinearModel::GetModelType() const -{ - return "Generic"; -}; - -mitk::TwoStepLinearModel::FunctionStringType mitk::TwoStepLinearModel::GetFunctionString() const -{ - return "Slope_1*t+Y_intercept_1 if t= 0) && (a2 >= 0)) - smax = sfin; - else if ((a1 < 0) && (a2 < 0)) - smax = b1; - else if ((a1 > 0) && (a2 < 0)) - smax = (a1 * t + b1); - else - { - if (abs(a1 * t) >= abs(a2 * (taq - t))) - smax = b1; - else smax = sfin; - } - - double auc = 0.0; - TimeGridType::const_iterator timeGridEnd = m_TimeGrid.end(); - for (TimeGridType::const_iterator gridPos = m_TimeGrid.begin(); gridPos != timeGridEnd -1; ++gridPos) - { - double currentGridPos = *gridPos; - double nextGridPos = *(++gridPos); - double deltaX = nextGridPos - currentGridPos; - double deltaY = ComputeSignalFromParameters(nextGridPos, t, a1, a2, b1, b2) - ComputeSignalFromParameters(currentGridPos, t, a1, a2, b1, b2); - double Yi = ComputeSignalFromParameters(currentGridPos, t, a1, a2, b1, b2); - double intI = 0.5 * deltaX * deltaY + Yi * deltaX; - auc += std::abs(intI); - --gridPos; - } - - DerivedParameterMapType result; - - result.insert(std::make_pair("AUC", auc)); - result.insert(std::make_pair("FinalUptake", sfin)); - result.insert(std::make_pair("Smax", smax)); - result.insert(std::make_pair("y-intercept2", b2)); - - return result; -}; - -itk::LightObject::Pointer mitk::TwoStepLinearModel::InternalClone() const -{ - TwoStepLinearModel::Pointer newClone = TwoStepLinearModel::New(); - - newClone->SetTimeGrid(this->m_TimeGrid); - - return newClone.GetPointer(); -}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelTest.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelTest.cpp deleted file mode 100644 index de8b2e160f..0000000000 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelTest.cpp +++ /dev/null @@ -1,66 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - - //Testing -#include "mitkModelTestFixture.h" - -//MITK includes -#include "mitkTwoStepLinearModel.h" - - - class mitkTwoStepLinearModelTestSuite : public mitk::mitkModelTestFixture -{ - CPPUNIT_TEST_SUITE(mitkTwoStepLinearModelTestSuite); - MITK_TEST(GetModelInfoTest); - MITK_TEST(ComputeModelfunctionTest); - MITK_TEST(ComputeDerivedParametersTest); - CPPUNIT_TEST_SUITE_END(); - -private: - mitk::TwoStepLinearModel::Pointer m_testmodel; - - json m_profile_json_obj; - json m_modelValues_json_obj; - -public: - void setUp() override - { - // Parse JSON files - m_profile_json_obj = ParseJSONFile("Pharmacokinetics/mitkTwoStepLinearModelTest_profile.json"); - m_modelValues_json_obj = ParseJSONFile("Pharmacokinetics/mitkTwoStepLinearModelTest_modelValues.json"); - - // Generate test model - m_testmodel = mitk::TwoStepLinearModel::New(); - } - - void tearDown() override - { - } - - void GetModelInfoTest() - { - // comparison of reference and testmodel profile - CompareModelAndReferenceProfile(m_testmodel, m_profile_json_obj); - } - - void ComputeModelfunctionTest() - { - CompareModelAndReferenceSignal(m_testmodel, m_modelValues_json_obj, m_profile_json_obj); - } - - void ComputeDerivedParametersTest() - { - CompareModelAndReferenceDerivedParameters(m_testmodel, m_modelValues_json_obj); - } -}; - -MITK_TEST_SUITE_REGISTRATION(mitkTwoStepLinearModel) diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModel.cpp index c7c36c53b5..d978c4fdad 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModel.cpp @@ -1,155 +1,158 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoTissueCompartmentFDGModel.h" #include "mitkConvolutionHelper.h" #include const std::string mitk::TwoTissueCompartmentFDGModel::MODEL_DISPLAY_NAME = "Two Tissue Compartment Model for FDG (Sokoloff Model)"; -const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_K1 = "K1"; -const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_k2 = "k2"; -const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_k3 = "k3"; -const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_VB = "V_B"; +const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_K1 = "K_1"; +const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_k2 = "k_2"; +const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_k3 = "k_3"; +const std::string mitk::TwoTissueCompartmentFDGModel::NAME_PARAMETER_vb = "v_b"; const std::string mitk::TwoTissueCompartmentFDGModel::UNIT_PARAMETER_K1 = "1/min"; const std::string mitk::TwoTissueCompartmentFDGModel::UNIT_PARAMETER_k2 = "1/min"; const std::string mitk::TwoTissueCompartmentFDGModel::UNIT_PARAMETER_k3 = "1/min"; -const std::string mitk::TwoTissueCompartmentFDGModel::UNIT_PARAMETER_VB = "ml/ml"; +const std::string mitk::TwoTissueCompartmentFDGModel::UNIT_PARAMETER_vb = "ml/ml"; const unsigned int mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_K1 = 0; const unsigned int mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_k2 = 1; const unsigned int mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_k3 = 2; -const unsigned int mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_VB = 3; +const unsigned int mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_vb = 3; const unsigned int mitk::TwoTissueCompartmentFDGModel::NUMBER_OF_PARAMETERS = 4; +const std::string mitk::TwoTissueCompartmentFDGModel::MODEL_TYPE = "Dynamic.PET"; + std::string mitk::TwoTissueCompartmentFDGModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::TwoTissueCompartmentFDGModel::GetModelType() const { - return "Dynamic.PET"; + return MODEL_TYPE; }; mitk::TwoTissueCompartmentFDGModel::TwoTissueCompartmentFDGModel() { } mitk::TwoTissueCompartmentFDGModel::~TwoTissueCompartmentFDGModel() { } mitk::TwoTissueCompartmentFDGModel::ParameterNamesType mitk::TwoTissueCompartmentFDGModel::GetParameterNames() const { ParameterNamesType result; result.push_back(NAME_PARAMETER_K1); result.push_back(NAME_PARAMETER_k2); result.push_back(NAME_PARAMETER_k3); - result.push_back(NAME_PARAMETER_VB); + result.push_back(NAME_PARAMETER_vb); return result; } mitk::TwoTissueCompartmentFDGModel::ParametersSizeType mitk::TwoTissueCompartmentFDGModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } + mitk::TwoTissueCompartmentFDGModel::ParamterUnitMapType mitk::TwoTissueCompartmentFDGModel::GetParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_PARAMETER_K1, UNIT_PARAMETER_K1)); result.insert(std::make_pair(NAME_PARAMETER_k2, UNIT_PARAMETER_k2)); result.insert(std::make_pair(NAME_PARAMETER_k3, UNIT_PARAMETER_k3)); - result.insert(std::make_pair(NAME_PARAMETER_VB, UNIT_PARAMETER_VB)); + result.insert(std::make_pair(NAME_PARAMETER_vb, UNIT_PARAMETER_vb)); return result; }; mitk::TwoTissueCompartmentFDGModel::ModelResultType mitk::TwoTissueCompartmentFDGModel::ComputeModelfunction(const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters - double k1 = (double)parameters[POSITION_PARAMETER_K1] / 60.0; + double K1 = (double)parameters[POSITION_PARAMETER_K1] / 60.0; double k2 = (double)parameters[POSITION_PARAMETER_k2] / 60.0; double k3 = (double)parameters[POSITION_PARAMETER_k3] / 60.0; - double VB = parameters[POSITION_PARAMETER_VB]; + double vb = parameters[POSITION_PARAMETER_vb]; double lambda = k2+k3; mitk::ModelBase::ModelResultType exp = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, lambda); mitk::ModelBase::ModelResultType CA = mitk::convoluteAIFWithConstant(this->m_TimeGrid, aterialInputFunction, k3); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::const_iterator expPos = exp.begin(); mitk::ModelBase::ModelResultType::const_iterator CAPos = CA.begin(); AterialInputFunctionType::const_iterator aifPos = aterialInputFunction.begin(); for (mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); signalPos != signal.end(); ++expPos, ++signalPos, ++aifPos) { - double Ci = k1 * k2 /lambda *(*expPos) + k1*k3/lambda*(*CAPos); - *signalPos = VB * (*aifPos) + (1 - VB) * Ci; + double Ci = K1 * k2 /lambda *(*expPos) + K1*k3/lambda*(*CAPos); + *signalPos = vb * (*aifPos) + (1 - vb) * Ci; } return signal; } itk::LightObject::Pointer mitk::TwoTissueCompartmentFDGModel::InternalClone() const { TwoTissueCompartmentFDGModel::Pointer newClone = TwoTissueCompartmentFDGModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); } void mitk::TwoTissueCompartmentFDGModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); } diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelFactory.cpp index 8ada9c010b..cc2d11d4b7 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelFactory.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelFactory.cpp @@ -1,50 +1,50 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoTissueCompartmentFDGModelFactory.h" #include #include #include mitk::ConstraintCheckerBase::Pointer mitk::TwoTissueCompartmentFDGModelFactory::CreateDefaultConstraints() const { SimpleBarrierConstraintChecker::Pointer constraints = SimpleBarrierConstraintChecker::New(); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_K1, 0.0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k2, 0, 0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k3, 0, 0); - constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_VB, 0, 0); + constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_vb, 0, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_K1, 1.0, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k2, 1.0, 0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k3, 1.0, 0); - constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_VB, 1, 0); + constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_vb, 1, 0); return constraints.GetPointer(); }; mitk::ModelParameterizerBase::ParametersType mitk::TwoTissueCompartmentFDGModelFactory::GetDefaultInitialParameterization() const { return TwoTissueCompartmentFDGModelParameterizer::New()->GetDefaultInitialParameterization(); }; mitk::TwoTissueCompartmentFDGModelFactory::TwoTissueCompartmentFDGModelFactory() { }; mitk::TwoTissueCompartmentFDGModelFactory::~TwoTissueCompartmentFDGModelFactory() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelParameterizer.cpp index 328dfaa4d8..360b1aeab0 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentFDGModelParameterizer.cpp @@ -1,34 +1,34 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoTissueCompartmentFDGModelParameterizer.h" mitk::TwoTissueCompartmentFDGModelParameterizer::ParametersType mitk::TwoTissueCompartmentFDGModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(4); initialParameters[mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_K1] = 0.5; initialParameters[mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_k2] = 0.5; initialParameters[mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_k3] = 0.5; - initialParameters[mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_VB] = 0.5; + initialParameters[mitk::TwoTissueCompartmentFDGModel::POSITION_PARAMETER_vb] = 0.5; return initialParameters; }; mitk::TwoTissueCompartmentFDGModelParameterizer::TwoTissueCompartmentFDGModelParameterizer() { }; mitk::TwoTissueCompartmentFDGModelParameterizer::~TwoTissueCompartmentFDGModelParameterizer() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModel.cpp index a00a006665..9fccbe1f83 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModel.cpp @@ -1,170 +1,173 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoTissueCompartmentModel.h" #include "mitkConvolutionHelper.h" #include const std::string mitk::TwoTissueCompartmentModel::MODEL_DISPLAY_NAME = "Two Tissue Compartment Model"; -const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_K1 = "K1"; -const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k2 = "k2"; -const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k3 = "k3"; -const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k4 = "k4"; -const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_VB = "V_B"; +const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_K1 = "K_1"; +const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k2 = "k_2"; +const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k3 = "k_3"; +const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k4 = "k_4"; +const std::string mitk::TwoTissueCompartmentModel::NAME_PARAMETER_vb = "v_b"; const std::string mitk::TwoTissueCompartmentModel::UNIT_PARAMETER_K1 = "1/min"; const std::string mitk::TwoTissueCompartmentModel::UNIT_PARAMETER_k2 = "1/min"; const std::string mitk::TwoTissueCompartmentModel::UNIT_PARAMETER_k3 = "1/min"; const std::string mitk::TwoTissueCompartmentModel::UNIT_PARAMETER_k4 = "1/min"; -const std::string mitk::TwoTissueCompartmentModel::UNIT_PARAMETER_VB = "ml/ml"; +const std::string mitk::TwoTissueCompartmentModel::UNIT_PARAMETER_vb = "ml/ml"; const unsigned int mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_K1 = 0; const unsigned int mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k2 = 1; const unsigned int mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k3 = 2; const unsigned int mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k4 = 3; -const unsigned int mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_VB = 4; +const unsigned int mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_vb = 4; const unsigned int mitk::TwoTissueCompartmentModel::NUMBER_OF_PARAMETERS = 5; +const std::string mitk::TwoTissueCompartmentModel::MODEL_TYPE = "Dynamic.PET"; + inline double square(double a) { return a * a; } std::string mitk::TwoTissueCompartmentModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::TwoTissueCompartmentModel::GetModelType() const { - return "Dynamic.PET"; + return MODEL_TYPE; }; mitk::TwoTissueCompartmentModel::TwoTissueCompartmentModel() { } mitk::TwoTissueCompartmentModel::~TwoTissueCompartmentModel() { } mitk::TwoTissueCompartmentModel::ParameterNamesType mitk::TwoTissueCompartmentModel::GetParameterNames() const { ParameterNamesType result; result.push_back(NAME_PARAMETER_K1); result.push_back(NAME_PARAMETER_k2); result.push_back(NAME_PARAMETER_k3); result.push_back(NAME_PARAMETER_k4); - result.push_back(NAME_PARAMETER_VB); + result.push_back(NAME_PARAMETER_vb); return result; } mitk::TwoTissueCompartmentModel::ParametersSizeType mitk::TwoTissueCompartmentModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } + mitk::TwoTissueCompartmentModel::ParamterUnitMapType mitk::TwoTissueCompartmentModel::GetParameterUnits() const { ParamterUnitMapType result; result.insert(std::make_pair(NAME_PARAMETER_K1, UNIT_PARAMETER_K1)); result.insert(std::make_pair(NAME_PARAMETER_k2, UNIT_PARAMETER_k2)); result.insert(std::make_pair(NAME_PARAMETER_k3, UNIT_PARAMETER_k3)); result.insert(std::make_pair(NAME_PARAMETER_k4, UNIT_PARAMETER_k4)); - result.insert(std::make_pair(NAME_PARAMETER_VB, UNIT_PARAMETER_VB)); + result.insert(std::make_pair(NAME_PARAMETER_vb, UNIT_PARAMETER_vb)); return result; }; mitk::TwoTissueCompartmentModel::ModelResultType mitk::TwoTissueCompartmentModel::ComputeModelfunction(const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters - double k1 = (double)parameters[POSITION_PARAMETER_K1] / 60.0; + double K1 = (double)parameters[POSITION_PARAMETER_K1] / 60.0; double k2 = (double)parameters[POSITION_PARAMETER_k2] / 60.0; double k3 = (double)parameters[POSITION_PARAMETER_k3] / 60.0; double k4 = (double)parameters[POSITION_PARAMETER_k4] / 60.0; - double VB = parameters[POSITION_PARAMETER_VB]; + double vb = parameters[POSITION_PARAMETER_vb]; double alpha1 = 0.5 * ((k2 + k3 + k4) - sqrt(square(k2 + k3 + k4) - 4 * k2 * k4)); double alpha2 = 0.5 * ((k2 + k3 + k4) + sqrt(square(k2 + k3 + k4) - 4 * k2 * k4)); mitk::ModelBase::ModelResultType exp1 = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, alpha1); mitk::ModelBase::ModelResultType exp2 = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, alpha2); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::const_iterator exp1Pos = exp1.begin(); mitk::ModelBase::ModelResultType::const_iterator exp2Pos = exp2.begin(); AterialInputFunctionType::const_iterator aifPos = aterialInputFunction.begin(); for (mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); signalPos != signal.end(); ++exp1Pos, ++exp2Pos, ++signalPos, ++aifPos) { - double Ci = k1 / (alpha2 - alpha1) * ((k4 - alpha1 + k3) * (*exp1Pos) + (alpha2 - k4 - k3) * + double Ci = K1 / (alpha2 - alpha1) * ((k4 - alpha1 + k3) * (*exp1Pos) + (alpha2 - k4 - k3) * (*exp2Pos)); - *signalPos = VB * (*aifPos) + (1 - VB) * Ci; + *signalPos = vb * (*aifPos) + (1 - vb) * Ci; } return signal; } itk::LightObject::Pointer mitk::TwoTissueCompartmentModel::InternalClone() const { TwoTissueCompartmentModel::Pointer newClone = TwoTissueCompartmentModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); } void mitk::TwoTissueCompartmentModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); } diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModelParameterizer.cpp index e724bb2d1e..7ddb0abd61 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModelParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoTissueCompartmentModelParameterizer.cpp @@ -1,35 +1,35 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkTwoTissueCompartmentModelParameterizer.h" mitk::TwoTissueCompartmentModelParameterizer::ParametersType mitk::TwoTissueCompartmentModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(5); initialParameters[mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_K1] = 0.5; initialParameters[mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k2] = 0.5; initialParameters[mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k3] = 0.5; initialParameters[mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k4] = 0.5; - initialParameters[mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_VB] = 0.5; + initialParameters[mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_vb] = 0.5; return initialParameters; }; mitk::TwoTissueCompartmentModelParameterizer::TwoTissueCompartmentModelParameterizer() { }; mitk::TwoTissueCompartmentModelParameterizer::~TwoTissueCompartmentModelParameterizer() { }; diff --git a/Modules/Pharmacokinetics/test/files.cmake b/Modules/Pharmacokinetics/test/files.cmake index 41a9258c17..0af3ec8b4a 100644 --- a/Modules/Pharmacokinetics/test/files.cmake +++ b/Modules/Pharmacokinetics/test/files.cmake @@ -1,14 +1,12 @@ SET(MODULE_TESTS mitkDescriptivePharmacokineticBrixModelTest.cpp mitkStandardToftsModelTest.cpp mitkTwoCompartmentExchangeModelTest.cpp mitkExtendedToftsModelTest.cpp mitkConvertSignalToConcentrationTest.cpp mitkCurveDescriptiveParametersTest.cpp - mitkTwoStepLinearModelTest.cpp - mitkThreeStepLinearModelTest.cpp mitkOneTissueCompartmentModelTest.cpp mitkExtendedOneTissueCompartmentModelTest.cpp mitkTwoTissueCompartmentModelTest.cpp mitkTwoTissueCompartmentFDGModelTest.cpp ) diff --git a/Modules/QtWidgets/include/QmitkLevelWindowWidget.h b/Modules/QtWidgets/include/QmitkLevelWindowWidget.h index 573165361b..1dce4bebdc 100644 --- a/Modules/QtWidgets/include/QmitkLevelWindowWidget.h +++ b/Modules/QtWidgets/include/QmitkLevelWindowWidget.h @@ -1,37 +1,49 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkLevelWindowWidget_h #define QmitkLevelWindowWidget_h #include - -#include "ui_QmitkLevelWindowWidget.h" +#include #include +// Forward declarations +namespace Ui +{ + class QmitkLevelWindow; +} + /// \ingroup QmitkModule -class MITKQTWIDGETS_EXPORT QmitkLevelWindowWidget : public QWidget, public Ui::QmitkLevelWindow +class MITKQTWIDGETS_EXPORT QmitkLevelWindowWidget : public QWidget { Q_OBJECT public: QmitkLevelWindowWidget(QWidget *parent = nullptr, Qt::WindowFlags f = nullptr); + ~QmitkLevelWindowWidget() override; + mitk::LevelWindowManager *GetManager(); public slots: void SetDataStorage(mitk::DataStorage *ds); protected: // unsigned long m_ObserverTag; mitk::LevelWindowManager::Pointer m_Manager; + +private: + // GUI controls of this plugin + Ui::QmitkLevelWindow* ui; + }; #endif diff --git a/Modules/QtWidgets/include/QmitkNodeSelectionButton.h b/Modules/QtWidgets/include/QmitkNodeSelectionButton.h index 2b400c5900..111c63a34a 100644 --- a/Modules/QtWidgets/include/QmitkNodeSelectionButton.h +++ b/Modules/QtWidgets/include/QmitkNodeSelectionButton.h @@ -1,71 +1,71 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkNodeSelectionButton_h #define QmitkNodeSelectionButton_h #include #include #include #include /** * @class QmitkNodeSelectionButton * @brief Button class that can be used to display information about a given node. * If the given node is a nullptr the node info text will be shown. -* The node info can be formated text (e.g. HTML code; like the tooltip text). +* The node info can be formatted text (e.g. HTML code; like the tooltip text). */ class MITKQTWIDGETS_EXPORT QmitkNodeSelectionButton : public QPushButton { Q_OBJECT public: explicit QmitkNodeSelectionButton(QWidget *parent = nullptr); ~QmitkNodeSelectionButton() override; const mitk::DataNode* GetSelectedNode() const; bool GetSelectionIsOptional() const; public Q_SLOTS: virtual void SetSelectedNode(const mitk::DataNode* node); virtual void SetNodeInfo(QString info); /** Set the widget into an optional mode. Optional means that the selection of no valid node does not mean an invalid state. Thus no node is a valid "node" selection too. The state influences if the info text is handled as an information (optional) or a warning (optiona==false).*/ void SetSelectionIsOptional(bool isOptional); protected: void paintEvent(QPaintEvent *p) override; void changeEvent(QEvent *event) override; void AddNodeObserver(); void RemoveNodeObserver(); void OnNodeModified(const itk::Object * /*caller*/, const itk::EventObject &); mitk::DataNode::ConstPointer m_SelectedNode; QString m_Info; bool m_OutDatedThumbNail; QPixmap m_ThumbNail; itk::ModifiedTimeType m_DataMTime; itk::ModifiedTimeType m_SelectionPropMTime; bool m_IsOptional; unsigned long m_NodeModifiedObserverTag; bool m_NodeObserved; }; #endif diff --git a/Modules/QtWidgets/include/QmitkSingleNodeSelectionWidget.h b/Modules/QtWidgets/include/QmitkSingleNodeSelectionWidget.h index 2ce34485c9..44130cb7e6 100644 --- a/Modules/QtWidgets/include/QmitkSingleNodeSelectionWidget.h +++ b/Modules/QtWidgets/include/QmitkSingleNodeSelectionWidget.h @@ -1,97 +1,97 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSingleNodeSelectionWidget_h #define QmitkSingleNodeSelectionWidget_h #include #include #include #include #include #include #include class QmitkAbstractDataStorageModel; /** * @class QmitkSingleNodeSelectionWidget * @brief Widget that represents a node selection of (max) one node. It acts like a button. Clicking on it * allows to change the selection. * * @remark This class provides a public function 'SetAutoSelectNewNodes' that can be used to enable * the auto selection mode (default is false). * The user of this class calling this function has to make sure that the base-class Q_SIGNAL * 'CurrentSelectionChanged', which will be emitted by this function, is already * connected to a receiving slot, if the initial valid auto selection should not get lost. */ class MITKQTWIDGETS_EXPORT QmitkSingleNodeSelectionWidget : public QmitkAbstractNodeSelectionWidget { Q_OBJECT public: explicit QmitkSingleNodeSelectionWidget(QWidget* parent = nullptr); mitk::DataNode::Pointer GetSelectedNode() const; bool GetAutoSelectNewNodes() const; using NodeList = QmitkAbstractNodeSelectionWidget::NodeList; public Q_SLOTS: void SetCurrentSelectedNode(mitk::DataNode* selectedNode); /** * Sets the auto selection mode (default is false). - * If auto select is true and the following conditions are fullfilled, the widget will + * If auto select is true and the following conditions are fulfilled, the widget will * select a node automatically from the data storage: * - a data storage is set * - data storage contains at least one node that matches the given predicate * - no selection is set * * @remark Enabling the auto selection mode by calling 'SetAutoSelectNewNodes(true)' * will directly emit a 'QmitkSingleNodeSelectionWidget::CurrentSelectionChanged' Q_SIGNAL * if a valid auto selection was made. * If this initial emission should not get lost, auto selection mode needs to be enabled after this * selection widget has been connected via the 'QmitkSingleNodeSelectionWidget::CurrentSelectionChanged' * Q_SIGNAL to a receiving function. */ void SetAutoSelectNewNodes(bool autoSelect); protected Q_SLOTS: virtual void OnClearSelection(); protected: void ReviseSelectionChanged(const NodeList& oldInternalSelection, NodeList& newInternalSelection) override; bool eventFilter(QObject *obj, QEvent *ev) override; void EditSelection(); void UpdateInfo() override; void OnDataStorageChanged() override; void OnNodeAddedToStorage(const mitk::DataNode* node) override; void AutoSelectNodes(); /** Helper function that gets a suitable auto selected node from the datastorage that fits to the predicate settings. - @param ignoreNodes You may pass a list of nodes that must not be choosen as auto selected node. */ + @param ignoreNodes You may pass a list of nodes that must not be chosen as auto selected node. */ mitk::DataNode::Pointer DetermineAutoSelectNode(const NodeList& ignoreNodes = {}); /** See documentation of SetAutoSelectNewNodes for details*/ bool m_AutoSelectNodes; Ui_QmitkSingleNodeSelectionWidget m_Controls; }; #endif diff --git a/Modules/QtWidgets/src/QmitkAbstractMultiWidget.cpp b/Modules/QtWidgets/src/QmitkAbstractMultiWidget.cpp index 851cf60a9e..75cd50eac3 100644 --- a/Modules/QtWidgets/src/QmitkAbstractMultiWidget.cpp +++ b/Modules/QtWidgets/src/QmitkAbstractMultiWidget.cpp @@ -1,416 +1,415 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // mitk qt widgets module #include "QmitkAbstractMultiWidget.h" -#include "QmitkLevelWindowWidget.h" #include "QmitkMultiWidgetLayoutManager.h" #include "QmitkRenderWindowWidget.h" // mitk core #include #include // qt #include // c++ #include struct QmitkAbstractMultiWidget::Impl final { Impl(QmitkAbstractMultiWidget* multiWidget, const QString& multiWidgetName); ~Impl(); void SetDataStorage(mitk::DataStorage* dataStorage) { if (dataStorage == m_DataStorage) { return; } m_DataStorage = dataStorage; // set new data storage for the render window widgets for (const auto& renderWindowWidget : m_RenderWindowWidgets) { renderWindowWidget.second->SetDataStorage(m_DataStorage); } } void InitializeDisplayActionEventHandling() { m_DisplayActionEventBroadcast = mitk::DisplayActionEventBroadcast::New(); m_DisplayActionEventBroadcast->LoadStateMachine("DisplayInteraction.xml"); } mitk::DataStorage::Pointer m_DataStorage; QString m_MultiWidgetName; RenderWindowWidgetMap m_RenderWindowWidgets; RenderWindowWidgetPointer m_ActiveRenderWindowWidget; int m_MultiWidgetRows; int m_MultiWidgetColumns; // interaction unsigned long m_RenderWindowFocusObserverTag; mitk::DisplayActionEventBroadcast::Pointer m_DisplayActionEventBroadcast; std::unique_ptr m_DisplayActionEventHandler; QmitkMultiWidgetLayoutManager* m_LayoutManager; }; QmitkAbstractMultiWidget::Impl::Impl(QmitkAbstractMultiWidget* multiWidget, const QString& multiWidgetName) : m_DataStorage(nullptr) , m_MultiWidgetName(multiWidgetName) , m_MultiWidgetRows(0) , m_MultiWidgetColumns(0) , m_RenderWindowFocusObserverTag(0) , m_DisplayActionEventBroadcast(nullptr) , m_DisplayActionEventHandler(nullptr) , m_LayoutManager(new QmitkMultiWidgetLayoutManager(multiWidget)) { auto command = itk::MemberCommand::New(); command->SetCallbackFunction(multiWidget, &QmitkAbstractMultiWidget::OnFocusChanged); m_RenderWindowFocusObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::FocusChangedEvent(), command); InitializeDisplayActionEventHandling(); } QmitkAbstractMultiWidget::Impl::~Impl() { mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderWindowFocusObserverTag); } QmitkAbstractMultiWidget::QmitkAbstractMultiWidget(QWidget* parent, Qt::WindowFlags f/* = 0*/, const QString& multiWidgetName/* = "multiwidget"*/) : QWidget(parent, f) , m_Impl(std::make_unique(this, multiWidgetName)) { // nothing here } QmitkAbstractMultiWidget::~QmitkAbstractMultiWidget() { } void QmitkAbstractMultiWidget::SetDataStorage(mitk::DataStorage* dataStorage) { m_Impl->SetDataStorage(dataStorage); } mitk::DataStorage* QmitkAbstractMultiWidget::GetDataStorage() const { return m_Impl->m_DataStorage; } int QmitkAbstractMultiWidget::GetRowCount() const { return m_Impl->m_MultiWidgetRows; } int QmitkAbstractMultiWidget::GetColumnCount() const { return m_Impl->m_MultiWidgetColumns; } void QmitkAbstractMultiWidget::SetLayout(int row, int column) { m_Impl->m_MultiWidgetRows = row; m_Impl->m_MultiWidgetColumns = column; SetLayoutImpl(); } void QmitkAbstractMultiWidget::SetInteractionScheme(mitk::InteractionSchemeSwitcher::InteractionScheme scheme) { auto interactionSchemeSwitcher = mitk::InteractionSchemeSwitcher::New(); auto interactionEventHandler = GetInteractionEventHandler(); try { interactionSchemeSwitcher->SetInteractionScheme(interactionEventHandler, scheme); } catch (const mitk::Exception&) { return; } SetInteractionSchemeImpl(); } mitk::InteractionEventHandler* QmitkAbstractMultiWidget::GetInteractionEventHandler() { return m_Impl->m_DisplayActionEventBroadcast.GetPointer(); } void QmitkAbstractMultiWidget::SetDisplayActionEventHandler(std::unique_ptr displayActionEventHandler) { m_Impl->m_DisplayActionEventHandler = std::move(displayActionEventHandler); m_Impl->m_DisplayActionEventHandler->SetObservableBroadcast(m_Impl->m_DisplayActionEventBroadcast); } mitk::DisplayActionEventHandler* QmitkAbstractMultiWidget::GetDisplayActionEventHandler() { return m_Impl->m_DisplayActionEventHandler.get(); } QmitkAbstractMultiWidget::RenderWindowWidgetMap QmitkAbstractMultiWidget::GetRenderWindowWidgets() const { return m_Impl->m_RenderWindowWidgets; } QmitkAbstractMultiWidget::RenderWindowWidgetMap QmitkAbstractMultiWidget::Get2DRenderWindowWidgets() const { RenderWindowWidgetMap renderWindowWidgets2D; auto renderWindowWidgets = GetRenderWindowWidgets(); for (const auto& renderWindowWidget : renderWindowWidgets) { auto renderWindow = renderWindowWidget.second->GetRenderWindow(); if(mitk::BaseRenderer::Standard2D == mitk::BaseRenderer::GetInstance(renderWindow->GetVtkRenderWindow())->GetMapperID()) { renderWindowWidgets2D.insert(std::make_pair(renderWindowWidget.first, renderWindowWidget.second)); } } return renderWindowWidgets2D; } QmitkAbstractMultiWidget::RenderWindowWidgetMap QmitkAbstractMultiWidget::Get3DRenderWindowWidgets() const { RenderWindowWidgetMap renderWindowWidgets3D; auto renderWindowWidgets = GetRenderWindowWidgets(); for (const auto& renderWindowWidget : renderWindowWidgets) { auto renderWindow = renderWindowWidget.second->GetRenderWindow(); if (mitk::BaseRenderer::Standard3D == mitk::BaseRenderer::GetInstance(renderWindow->GetVtkRenderWindow())->GetMapperID()) { renderWindowWidgets3D.insert(std::make_pair(renderWindowWidget.first, renderWindowWidget.second)); } } return renderWindowWidgets3D; } QmitkAbstractMultiWidget::RenderWindowWidgetPointer QmitkAbstractMultiWidget::GetRenderWindowWidget(int row, int column) const { return GetRenderWindowWidget(GetNameFromIndex(row, column)); } QmitkAbstractMultiWidget::RenderWindowWidgetPointer QmitkAbstractMultiWidget::GetRenderWindowWidget(const QString& widgetName) const { RenderWindowWidgetMap::const_iterator it = m_Impl->m_RenderWindowWidgets.find(widgetName); if (it != m_Impl->m_RenderWindowWidgets.end()) { return it->second; } return nullptr; } QmitkAbstractMultiWidget::RenderWindowWidgetPointer QmitkAbstractMultiWidget::GetRenderWindowWidget(const QmitkRenderWindow* renderWindow) const { auto renderWindowWidgets = GetRenderWindowWidgets(); for (const auto& renderWindowWidget : renderWindowWidgets) { if (renderWindowWidget.second->GetRenderWindow() == renderWindow) { return renderWindowWidget.second; } } return nullptr; } QmitkAbstractMultiWidget::RenderWindowHash QmitkAbstractMultiWidget::GetRenderWindows() const { RenderWindowHash result; // create QHash on demand auto renderWindowWidgets = GetRenderWindowWidgets(); for (const auto& renderWindowWidget : renderWindowWidgets) { result.insert(renderWindowWidget.first, renderWindowWidget.second->GetRenderWindow()); } return result; } QmitkRenderWindow* QmitkAbstractMultiWidget::GetRenderWindow(int row, int column) const { return GetRenderWindow(GetNameFromIndex(row, column)); } QmitkRenderWindow* QmitkAbstractMultiWidget::GetRenderWindow(const QString& widgetName) const { RenderWindowWidgetPointer renderWindowWidget = GetRenderWindowWidget(widgetName); if (nullptr != renderWindowWidget) { return renderWindowWidget->GetRenderWindow(); } return nullptr; } void QmitkAbstractMultiWidget::SetActiveRenderWindowWidget(RenderWindowWidgetPointer activeRenderWindowWidget) { m_Impl->m_ActiveRenderWindowWidget = activeRenderWindowWidget; emit ActiveRenderWindowChanged(); } QmitkAbstractMultiWidget::RenderWindowWidgetPointer QmitkAbstractMultiWidget::GetActiveRenderWindowWidget() const { return m_Impl->m_ActiveRenderWindowWidget; } QmitkAbstractMultiWidget::RenderWindowWidgetPointer QmitkAbstractMultiWidget::GetFirstRenderWindowWidget() const { if (!m_Impl->m_RenderWindowWidgets.empty()) { return m_Impl->m_RenderWindowWidgets.begin()->second; } else { return nullptr; } } QmitkAbstractMultiWidget::RenderWindowWidgetPointer QmitkAbstractMultiWidget::GetLastRenderWindowWidget() const { if (!m_Impl->m_RenderWindowWidgets.empty()) { return m_Impl->m_RenderWindowWidgets.rbegin()->second; } else { return nullptr; } } QString QmitkAbstractMultiWidget::GetNameFromIndex(int row, int column) const { if (0 <= row && m_Impl->m_MultiWidgetRows > row && 0 <= column && m_Impl->m_MultiWidgetColumns > column) { return GetNameFromIndex(row * m_Impl->m_MultiWidgetColumns + column); } return QString(); } QString QmitkAbstractMultiWidget::GetNameFromIndex(size_t index) const { if (index <= m_Impl->m_RenderWindowWidgets.size()) { return m_Impl->m_MultiWidgetName + ".widget" + QString::number(index); } return QString(); } unsigned int QmitkAbstractMultiWidget::GetNumberOfRenderWindowWidgets() const { return m_Impl->m_RenderWindowWidgets.size(); } void QmitkAbstractMultiWidget::RequestUpdate(const QString& widgetName) { RenderWindowWidgetPointer renderWindowWidget = GetRenderWindowWidget(widgetName); if (nullptr != renderWindowWidget) { return renderWindowWidget->RequestUpdate(); } } void QmitkAbstractMultiWidget::RequestUpdateAll() { for (const auto& renderWindowWidget : m_Impl->m_RenderWindowWidgets) { renderWindowWidget.second->RequestUpdate(); } } void QmitkAbstractMultiWidget::ForceImmediateUpdate(const QString& widgetName) { RenderWindowWidgetPointer renderWindowWidget = GetRenderWindowWidget(widgetName); if (nullptr != renderWindowWidget) { renderWindowWidget->ForceImmediateUpdate(); } } void QmitkAbstractMultiWidget::ForceImmediateUpdateAll() { for (const auto& renderWindowWidget : m_Impl->m_RenderWindowWidgets) { renderWindowWidget.second->ForceImmediateUpdate(); } } void QmitkAbstractMultiWidget::ActivateMenuWidget(bool state) { for (const auto& renderWindowWidget : m_Impl->m_RenderWindowWidgets) { auto renderWindow = renderWindowWidget.second->GetRenderWindow(); renderWindow->ActivateMenuWidget(state); } } bool QmitkAbstractMultiWidget::IsMenuWidgetEnabled() const { return m_Impl->m_ActiveRenderWindowWidget->GetRenderWindow()->GetActivateMenuWidgetFlag(); } QmitkMultiWidgetLayoutManager* QmitkAbstractMultiWidget::GetMultiWidgetLayoutManager() const { return m_Impl->m_LayoutManager; } void QmitkAbstractMultiWidget::OnFocusChanged(itk::Object*, const itk::EventObject& event) { auto focusEvent = dynamic_cast(&event); if (nullptr == focusEvent) { return; } auto focusedRenderWindow = mitk::RenderingManager::GetInstance()->GetFocusedRenderWindow(); RenderWindowWidgetMap renderWindowWidgets = this->GetRenderWindowWidgets(); for (const auto& renderWindowWidget : renderWindowWidgets) { const auto vtkRenderWindow = renderWindowWidget.second->GetRenderWindow()->GetVtkRenderWindow(); if (vtkRenderWindow == focusedRenderWindow) { this->SetActiveRenderWindowWidget(renderWindowWidget.second); break; } } } void QmitkAbstractMultiWidget::AddRenderWindowWidget(const QString& widgetName, RenderWindowWidgetPointer renderWindowWidget) { m_Impl->m_RenderWindowWidgets.insert(std::make_pair(widgetName, renderWindowWidget)); } void QmitkAbstractMultiWidget::RemoveRenderWindowWidget() { auto iterator = m_Impl->m_RenderWindowWidgets.find(this->GetNameFromIndex(this->GetNumberOfRenderWindowWidgets() - 1)); if (iterator == m_Impl->m_RenderWindowWidgets.end()) { return; } // disconnect each signal of this render window widget RenderWindowWidgetPointer renderWindowWidgetToRemove = iterator->second; disconnect(renderWindowWidgetToRemove.get(), 0, 0, 0); // erase the render window from the map m_Impl->m_RenderWindowWidgets.erase(iterator); } diff --git a/Modules/QtWidgets/src/QmitkDataStorageSimpleTreeModel.cpp b/Modules/QtWidgets/src/QmitkDataStorageSimpleTreeModel.cpp index fa45000ca7..212a214bcb 100644 --- a/Modules/QtWidgets/src/QmitkDataStorageSimpleTreeModel.cpp +++ b/Modules/QtWidgets/src/QmitkDataStorageSimpleTreeModel.cpp @@ -1,378 +1,382 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include // qt widgets module #include "QmitkCustomVariants.h" #include "QmitkEnums.h" QmitkDataStorageSimpleTreeModel::QmitkDataStorageSimpleTreeModel(QObject *parent) : QmitkAbstractDataStorageModel(parent) , m_Root(nullptr) { ResetTree(); } QmitkDataStorageSimpleTreeModel::~QmitkDataStorageSimpleTreeModel() { m_Root->Delete(); m_Root = nullptr; } void QmitkDataStorageSimpleTreeModel::ResetTree() { mitk::DataNode::Pointer rootDataNode = mitk::DataNode::New(); rootDataNode->SetName("Data Storage"); m_Root = new TreeItem(rootDataNode, nullptr); } void QmitkDataStorageSimpleTreeModel::DataStorageChanged() { if (m_Root) { m_Root->Delete(); } beginResetModel(); ResetTree(); UpdateModelData(); endResetModel(); } void QmitkDataStorageSimpleTreeModel::NodePredicateChanged() { beginResetModel(); ResetTree(); UpdateModelData(); endResetModel(); } void QmitkDataStorageSimpleTreeModel::NodeAdded(const mitk::DataNode *node) { auto dataStorage = m_DataStorage.Lock(); if (node == nullptr || dataStorage.IsNull() || !dataStorage->Exists(node) || m_Root->Find(node) != nullptr) return; if (m_NodePredicate.IsNull() || m_NodePredicate->CheckNode(node)) { this->AddNodeInternal(node); } } void QmitkDataStorageSimpleTreeModel::NodeChanged(const mitk::DataNode *node) { TreeItem *treeItem = m_Root->Find(node); if (treeItem) { TreeItem *parentTreeItem = treeItem->GetParent(); // as the root node should not be removed one should always have a parent item if (!parentTreeItem) return; QModelIndex index = this->createIndex(treeItem->GetIndex(), 0, treeItem); // now emit the dataChanged signal emit dataChanged(index, index); } } void QmitkDataStorageSimpleTreeModel::NodeRemoved(const mitk::DataNode *node) { if (node == nullptr || !m_Root) return; TreeItem *treeItem = m_Root->Find(node); if (!treeItem) return; // return because there is no treeitem containing this node TreeItem *parentTreeItem = treeItem->GetParent(); QModelIndex parentIndex = this->IndexFromTreeItem(parentTreeItem); // emit beginRemoveRows event (QModelIndex is empty because we dont have a tree model) this->beginRemoveRows(parentIndex, treeItem->GetIndex(), treeItem->GetIndex()); // remove node std::vector children = treeItem->GetChildren(); m_TreeItems.remove(treeItem); delete treeItem; //delete in tree if (!children.empty()) { //if not empty we have to rebuild the whole representation, //because the children could be now top level, or at another //source/parent. this->UpdateModelData(); } } QModelIndex QmitkDataStorageSimpleTreeModel::index(int row, int column, const QModelIndex &parent) const { TreeItem *parentItem; if (!parent.isValid() || parent.model() != this) parentItem = m_Root; else parentItem = static_cast(parent.internalPointer()); if (parentItem) { TreeItem *childItem = parentItem->GetChild(row); if (childItem) return createIndex(row, column, childItem); } return QModelIndex(); } QModelIndex QmitkDataStorageSimpleTreeModel::parent(const QModelIndex &child) const { if (!child.isValid() || !m_Root || child.model() != this) return QModelIndex(); TreeItem *childItem = this->TreeItemFromIndex(child); if (!childItem) return QModelIndex(); TreeItem *parentItem = childItem->GetParent(); if (parentItem == m_Root) return QModelIndex(); return this->createIndex(parentItem->GetIndex(), 0, parentItem); } QmitkDataStorageSimpleTreeModel::TreeItem *QmitkDataStorageSimpleTreeModel::TreeItemFromIndex( const QModelIndex &index) const { if (index.isValid() && index.model() == this) { auto item = static_cast(index.internalPointer()); auto finding = std::find(std::begin(m_TreeItems), std::end(m_TreeItems), item); if (finding == std::end(m_TreeItems)) { return nullptr; } return item; } else return m_Root; } int QmitkDataStorageSimpleTreeModel::rowCount(const QModelIndex &parent) const { TreeItem *parentTreeItem = this->TreeItemFromIndex(parent); if (parentTreeItem) return parentTreeItem->GetChildCount(); else return 0; } int QmitkDataStorageSimpleTreeModel::columnCount(const QModelIndex &/*parent*/) const { return 1; } QVariant QmitkDataStorageSimpleTreeModel::data(const QModelIndex &index, int role) const { if (!index.isValid() || index.model() != this) { return QVariant(); } auto treeItem = this->TreeItemFromIndex(index); if (!treeItem) return QVariant(); mitk::DataNode *dataNode = treeItem->GetDataNode(); + // No need to access dataNode if that is pointing to nullptr, it will always give segfault + if (!dataNode) + return QModelIndex(); + QString nodeName = QString::fromStdString(dataNode->GetName()); if (nodeName.isEmpty()) { nodeName = "unnamed"; } if (role == Qt::DisplayRole) return nodeName; else if (role == Qt::ToolTipRole) return nodeName; else if (role == Qt::DecorationRole) { QmitkNodeDescriptor *nodeDescriptor = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(dataNode); return nodeDescriptor->GetIcon(dataNode); } else if (role == QmitkDataNodeRole) { return QVariant::fromValue(mitk::DataNode::Pointer(dataNode)); } else if (role == QmitkDataNodeRawPointerRole) { return QVariant::fromValue(dataNode); } return QVariant(); } bool QmitkDataStorageSimpleTreeModel::setData(const QModelIndex &index, const QVariant &value, int role) { if (!index.isValid() || index.model() != this) return false; auto treeItem = this->TreeItemFromIndex(index); if (!treeItem) return false; mitk::DataNode *dataNode = treeItem->GetDataNode(); if (!dataNode) return false; if (role == Qt::EditRole && !value.toString().isEmpty()) { dataNode->SetName(value.toString().toStdString().c_str()); } else if (role == Qt::CheckStateRole) { // Please note: value.toInt() returns 2, independentely from the actual checkstate of the index element. // Therefore the checkstate is being estimated again here. QVariant qcheckstate = index.data(Qt::CheckStateRole); int checkstate = qcheckstate.toInt(); bool isVisible = bool(checkstate); dataNode->SetVisibility(!isVisible); } // inform listeners about changes emit dataChanged(index, index); return true; } QVariant QmitkDataStorageSimpleTreeModel::headerData(int /*section*/, Qt::Orientation orientation, int role) const { if (orientation == Qt::Horizontal && role == Qt::DisplayRole && m_Root) return QString::fromStdString(m_Root->GetDataNode()->GetName()); return QVariant(); } Qt::ItemFlags QmitkDataStorageSimpleTreeModel::flags(const QModelIndex &index) const { if (index.isValid() && index.model() == this) { auto treeItem = this->TreeItemFromIndex(index); if (!treeItem) return Qt::NoItemFlags; const auto dataNode = treeItem->GetDataNode(); if (m_NodePredicate.IsNull() || m_NodePredicate->CheckNode(dataNode)) { return Qt::ItemIsEnabled | Qt::ItemIsSelectable | Qt::ItemIsEditable; } else { return Qt::NoItemFlags; } } return Qt::NoItemFlags; } mitk::DataNode *QmitkDataStorageSimpleTreeModel::GetParentNode(const mitk::DataNode *node) const { mitk::DataNode *dataNode = nullptr; mitk::DataStorage::SetOfObjects::ConstPointer _Sources = m_DataStorage.Lock()->GetSources(node); if (_Sources->Size() > 0) dataNode = _Sources->front(); return dataNode; } void QmitkDataStorageSimpleTreeModel::AddNodeInternal(const mitk::DataNode *node) { auto dataStorage = m_DataStorage.Lock(); if (node == nullptr || dataStorage.IsNull() || !dataStorage->Exists(node) || m_Root->Find(node) != nullptr) return; // find out if we have a root node TreeItem *parentTreeItem = m_Root; QModelIndex index; mitk::DataNode *parentDataNode = this->GetParentNode(node); if (parentDataNode) // no top level data node { parentTreeItem = m_Root->Find(parentDataNode); // find the corresponding tree item if (!parentTreeItem) { this->NodeAdded(parentDataNode); parentTreeItem = m_Root->Find(parentDataNode); if (!parentTreeItem) return; } // get the index of this parent with the help of the grand parent index = this->createIndex(parentTreeItem->GetIndex(), 0, parentTreeItem); } int firstRowWithASiblingBelow = 0; int nodeLayer = -1; node->GetIntProperty("layer", nodeLayer); for (TreeItem *siblingTreeItem : parentTreeItem->GetChildren()) { int siblingLayer = -1; if (mitk::DataNode *siblingNode = siblingTreeItem->GetDataNode()) { siblingNode->GetIntProperty("layer", siblingLayer); } if (nodeLayer > siblingLayer) { break; } ++firstRowWithASiblingBelow; } beginInsertRows(index, firstRowWithASiblingBelow, firstRowWithASiblingBelow); auto newNode = new TreeItem(const_cast(node)); parentTreeItem->InsertChild(newNode, firstRowWithASiblingBelow); m_TreeItems.push_back(newNode); endInsertRows(); } QModelIndex QmitkDataStorageSimpleTreeModel::IndexFromTreeItem(TreeItem *item) const { if (item == m_Root) return QModelIndex(); else return this->createIndex(item->GetIndex(), 0, item); } void QmitkDataStorageSimpleTreeModel::UpdateModelData() { auto dataStorage = m_DataStorage.Lock(); if (dataStorage.IsNotNull()) { auto nodeset = m_NodePredicate != nullptr ? dataStorage->GetSubset(m_NodePredicate) : dataStorage->GetAll(); for (const auto& node : *nodeset) { this->AddNodeInternal(node); } } } diff --git a/Modules/QtWidgets/src/QmitkLevelWindowWidget.cpp b/Modules/QtWidgets/src/QmitkLevelWindowWidget.cpp index 422c98ccaf..6e04d83594 100644 --- a/Modules/QtWidgets/src/QmitkLevelWindowWidget.cpp +++ b/Modules/QtWidgets/src/QmitkLevelWindowWidget.cpp @@ -1,33 +1,41 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkLevelWindowWidget.h" #include "QmitkSliderLevelWindowWidget.h" -QmitkLevelWindowWidget::QmitkLevelWindowWidget(QWidget *parent, Qt::WindowFlags f) : QWidget(parent, f) +#include + +QmitkLevelWindowWidget::QmitkLevelWindowWidget(QWidget *parent, Qt::WindowFlags f) + : QWidget(parent, f), ui(new Ui::QmitkLevelWindow) { - this->setupUi(this); + ui->setupUi(this); m_Manager = mitk::LevelWindowManager::New(); - SliderLevelWindowWidget->SetLevelWindowManager(m_Manager.GetPointer()); - LineEditLevelWindowWidget->SetLevelWindowManager(m_Manager.GetPointer()); + ui->SliderLevelWindowWidget->SetLevelWindowManager(m_Manager.GetPointer()); + ui->LineEditLevelWindowWidget->SetLevelWindowManager(m_Manager.GetPointer()); +} + +QmitkLevelWindowWidget::~QmitkLevelWindowWidget() +{ + delete ui; } void QmitkLevelWindowWidget::SetDataStorage(mitk::DataStorage *ds) { m_Manager->SetDataStorage(ds); } mitk::LevelWindowManager *QmitkLevelWindowWidget::GetManager() { return m_Manager.GetPointer(); } diff --git a/Modules/Segmentation/Interactions/mitkProcessExecutor.h b/Modules/Segmentation/Interactions/mitkProcessExecutor.h index 56aaed7dde..f67567de25 100644 --- a/Modules/Segmentation/Interactions/mitkProcessExecutor.h +++ b/Modules/Segmentation/Interactions/mitkProcessExecutor.h @@ -1,116 +1,116 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkProcessExecutor_h #define mitkProcessExecutor_h #include #include #include #include namespace mitk { // Class is adapted from MatchPoint ProcessExecutor class ExternalProcessOutputEvent : public itk::AnyEvent { public: typedef ExternalProcessOutputEvent Self; typedef itk::AnyEvent Superclass; explicit ExternalProcessOutputEvent(const std::string &output = "") : m_Output(output) {} ~ExternalProcessOutputEvent() override {} const char *GetEventName() const override { return "ExternalProcessOutputEvent"; } bool CheckEvent(const ::itk::EventObject *e) const override { return dynamic_cast(e); } itk::EventObject *MakeObject() const override { return new Self(m_Output); } std::string GetOutput() const { return m_Output; } private: std::string m_Output; }; #define mitkProcessExecutorEventMacro(classname) \ class classname : public ExternalProcessOutputEvent \ { \ public: \ typedef classname Self; \ typedef ExternalProcessOutputEvent Superclass; \ \ explicit classname(const std::string &output) : Superclass(output) {} \ ~classname() override {} \ \ virtual const char *GetEventName() const { return #classname; } \ virtual bool CheckEvent(const ::itk::EventObject *e) const { return dynamic_cast(e); } \ virtual ::itk::EventObject *MakeObject() const { return new Self(this->GetOutput()); } \ }; mitkProcessExecutorEventMacro(ExternalProcessStdOutEvent); mitkProcessExecutorEventMacro(ExternalProcessStdErrEvent); /** * @brief You may register an observer for an ExternalProcessOutputEvent, ExternalProcessStdOutEvent or * ExternalProcessStdErrEvent in order to get notified of any output. * @remark The events will only be invoked if the pipes are NOT(!) shared. By default the pipes are not shared. * */ class MITKSEGMENTATION_EXPORT ProcessExecutor : public itk::Object { public: using Self = ProcessExecutor; using Superclass = ::itk::Object; using Pointer = ::itk::SmartPointer; using ConstPointer = ::itk::SmartPointer; itkTypeMacro(ProcessExecutor, ::itk::Object); itkFactorylessNewMacro(Self); itkSetMacro(SharedOutputPipes, bool); itkGetConstMacro(SharedOutputPipes, bool); using ArgumentListType = std::vector; bool Execute(const std::string &executionPath, const std::string &executableName, ArgumentListType &argumentList); /** * @brief Executes the process. This version assumes that the executable name is the first argument in the argument * list and has already been converted to its OS dependent name via the static convert function of this class. */ - bool Execute(const std::string &executionPath, const ArgumentListType &argumentList); + virtual bool Execute(const std::string &executionPath, const ArgumentListType &argumentList); int GetExitValue(); static std::string EnsureCorrectOSPathSeparator(const std::string &); static std::string GetOSDependendExecutableName(const std::string &name); void KillProcess(); protected: ProcessExecutor(); ~ProcessExecutor() override; int m_ExitValue; /** * @brief Specifies if the child process should share the output pipes (true) or not (false). * If pipes are not shared the output will be passed by invoking ExternalProcessOutputEvents * @remark The events will only be invoked if the pipes are NOT(!) shared. */ bool m_SharedOutputPipes; private: itksysProcess *m_ProcessID = nullptr; }; } // namespace mitk #endif diff --git a/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp index 9ff48f4df5..77ffb417cd 100644 --- a/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp +++ b/Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp @@ -1,819 +1,842 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkSegWithPreviewTool.h" #include "mitkToolManager.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkLabelSetImage.h" #include "mitkMaskAndCutRoiImageFilter.h" #include "mitkPadImageFilter.h" #include "mitkNodePredicateGeometry.h" #include "mitkSegTool2D.h" mitk::SegWithPreviewTool::SegWithPreviewTool(bool lazyDynamicPreviews): Tool("dummy"), m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = ToolCommand::New(); } mitk::SegWithPreviewTool::SegWithPreviewTool(bool lazyDynamicPreviews, const char* interactorType, const us::Module* interactorModule) : Tool(interactorType, interactorModule), m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = ToolCommand::New(); } mitk::SegWithPreviewTool::~SegWithPreviewTool() { } void mitk::SegWithPreviewTool::SetMergeStyle(MultiLabelSegmentation::MergeStyle mergeStyle) { m_MergeStyle = mergeStyle; this->Modified(); } void mitk::SegWithPreviewTool::SetOverwriteStyle(MultiLabelSegmentation::OverwriteStyle overwriteStyle) { m_OverwriteStyle = overwriteStyle; this->Modified(); } void mitk::SegWithPreviewTool::SetLabelTransferScope(LabelTransferScope labelTransferScope) { m_LabelTransferScope = labelTransferScope; this->Modified(); } void mitk::SegWithPreviewTool::SetLabelTransferMode(LabelTransferMode labelTransferMode) { m_LabelTransferMode = labelTransferMode; this->Modified(); } void mitk::SegWithPreviewTool::SetSelectedLabels(const SelectedLabelVectorType& labelsToTransfer) { m_SelectedLabels = labelsToTransfer; this->Modified(); } bool mitk::SegWithPreviewTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const { if (!Superclass::CanHandle(referenceData, workingData)) return false; if (workingData == nullptr) return false; auto* referenceImage = dynamic_cast(referenceData); if (referenceImage == nullptr) return false; auto* labelSet = dynamic_cast(workingData); if (labelSet != nullptr) return true; auto* workingImage = dynamic_cast

\a Single image operations

\a Dual image operations