diff --git a/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/DicomView.cpp b/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/DicomView.cpp index c07ece2100..4da36f5c4e 100644 --- a/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/DicomView.cpp +++ b/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/DicomView.cpp @@ -1,109 +1,110 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "DicomView.h" #include "org_mitk_example_gui_customviewer_views_Activator.h" #include "mitkIDataStorageService.h" #include "mitkDicomSeriesReader.h" +#include "mitkImage.h" #include #include #include #include "QDockWidget" const std::string DicomView::VIEW_ID = "org.mitk.customviewer.views.dicomview"; DicomView::DicomView() : m_Parent(0) { } DicomView::~DicomView() { } // //! [DicomViewCreatePartControl] void DicomView::CreateQtPartControl(QWidget *parent) { // create GUI widgets m_Parent = parent; m_Controls.setupUi(parent); //remove unused widgets QPushButton* downloadButton = parent->findChild("downloadButton"); downloadButton->setVisible(false); QDockWidget* searchWidget = parent->findChild("ExternalSearchDockWidget"); searchWidget->setVisible(false); connect(m_Controls.importButton, SIGNAL(clicked()), m_Controls.widget, SLOT(OnFolderCDImport())); connect(m_Controls.widget, SIGNAL(SignalDicomToDataManager(const QStringList&)), this, SLOT(AddDataNodeFromDICOM(const QStringList&))); m_Parent->setEnabled(true); } // //! [DicomViewCreatePartControl] // //! [DicomViewCreateAddDataNodeInformation] void DicomView::AddDataNodeFromDICOM(const QStringList& Properties) { QString seriesUID = Properties.at(3); QString path = Properties.at(5); // //! [DicomViewCreateAddDataNodeInformation] // //! [DicomViewCreateAddDataNodeLoadSeries] mitk::DicomSeriesReader::StringContainer seriesToLoad; std::size_t found; mitk::DicomSeriesReader::FileNamesGrouping dicomSeriesMap = mitk::DicomSeriesReader::GetSeries(path.toStdString(),false); mitk::DicomSeriesReader::FileNamesGrouping::const_iterator qualifiedSeriesInstanceUIDIterator; for(qualifiedSeriesInstanceUIDIterator = dicomSeriesMap.begin(); qualifiedSeriesInstanceUIDIterator != dicomSeriesMap.end(); ++qualifiedSeriesInstanceUIDIterator) { found = qualifiedSeriesInstanceUIDIterator->second.GetSeriesInstanceUID().find(seriesUID.toStdString()); if(found != std::string::npos) { seriesToLoad = qualifiedSeriesInstanceUIDIterator->second.GetFilenames(); } } mitk::DataNode::Pointer node = mitk::DicomSeriesReader::LoadDicomSeries(seriesToLoad); // //! [DicomViewCreateAddDataNodeLoadSeries] if (node.IsNull()) { MITK_ERROR << "Could not load series: " << seriesUID.toStdString(); } else { // //! [DicomViewCreateAddDataNode] this->GetDataStorage()->Add(node); // //! [DicomViewCreateAddDataNode] mitk::RenderingManager::GetInstance()->SetDataStorage(this->GetDataStorage()); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // //! [DicomViewCreateAddDataNodeActivatePersp] berry::IWorkbenchWindow::Pointer window = this->GetSite()->GetWorkbenchWindow(); std::string perspectiveId = "org.mitk.example.viewerperspective"; window->GetWorkbench()->ShowPerspective(perspectiveId, berry::IWorkbenchWindow::Pointer(window)); // //! [DicomViewCreateAddDataNodeActivatePersp] } } void DicomView::SetFocus () { } diff --git a/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/SimpleRenderWindowView.cpp b/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/SimpleRenderWindowView.cpp index e9117b6532..ca55121a45 100644 --- a/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/SimpleRenderWindowView.cpp +++ b/Examples/Plugins/org.mitk.example.gui.customviewer.views/src/internal/SimpleRenderWindowView.cpp @@ -1,212 +1,213 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "SimpleRenderWindowView.h" #include #include #include #include #include #include #include #include "org_mitk_example_gui_customviewer_views_Activator.h" #include +#include /** * \brief Helper class adapted from QmitkAbstractRenderEditor by defining the correct plugin context. * * This helper class adapted from QmitkAbstractRenderEditor provides the rendering manager interface. */ // //! [SimpleRenderWindowViewHelper] class AbstractRenderWindowViewPrivate { public: AbstractRenderWindowViewPrivate() : m_RenderingManagerInterface(mitk::MakeRenderingManagerInterface(mitk::RenderingManager::GetInstance())) , m_PrefServiceTracker(org_mitk_example_gui_customviewer_views_Activator::GetPluginContext()) // //! [SimpleRenderWindowViewHelper] { m_PrefServiceTracker.open(); } ~AbstractRenderWindowViewPrivate() { delete m_RenderingManagerInterface; } mitk::IRenderingManager* m_RenderingManagerInterface; ctkServiceTracker m_PrefServiceTracker; berry::IBerryPreferences::Pointer m_Prefs; }; const std::string SimpleRenderWindowView::VIEW_ID = "org.mitk.customviewer.views.simplerenderwindowview"; SimpleRenderWindowView::SimpleRenderWindowView() : m_RenderWindow(0), d(new AbstractRenderWindowViewPrivate) { } SimpleRenderWindowView::~SimpleRenderWindowView() { } QmitkRenderWindow *SimpleRenderWindowView::GetActiveQmitkRenderWindow() const { return m_RenderWindow; } QHash SimpleRenderWindowView::GetRenderWindows() const { QHash wnds; wnds.insert("transversal", m_RenderWindow); return wnds; } QHash SimpleRenderWindowView::GetQmitkRenderWindows() const { QHash wnds; wnds.insert("transversal", m_RenderWindow); return wnds; } QmitkRenderWindow *SimpleRenderWindowView::GetRenderWindow(const QString &id) const { if (id == "transversal") { return m_RenderWindow; } return 0; } QmitkRenderWindow *SimpleRenderWindowView::GetQmitkRenderWindow(const QString &id) const { if (id == "transversal") { return m_RenderWindow; } return 0; } mitk::Point3D SimpleRenderWindowView::GetSelectedPosition(const QString & /*id*/) const { const mitk::PlaneGeometry* pg = m_RenderWindow->GetSliceNavigationController()->GetCurrentPlaneGeometry(); if (pg) { return pg->GetCenter(); } else { return mitk::Point3D(); } } void SimpleRenderWindowView::SetSelectedPosition(const mitk::Point3D &pos, const QString &/*id*/) { // create a PositionEvent with the given position and // tell the slice navigation controller to move there mitk::Point2D p2d; mitk::PositionEvent event( m_RenderWindow->GetRenderer(), 0, 0, 0, mitk::Key_unknown, p2d, pos ); mitk::StateEvent stateEvent(mitk::EIDLEFTMOUSEBTN, &event); mitk::StateEvent stateEvent2(mitk::EIDLEFTMOUSERELEASE, &event); m_RenderWindow->GetSliceNavigationController()->HandleEvent( &stateEvent ); // just in case SNCs will develop something that depends on the mouse // button being released again m_RenderWindow->GetSliceNavigationController()->HandleEvent( &stateEvent2 ); // update displays //mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void SimpleRenderWindowView::EnableDecorations(bool enable, const QStringList &decorations) { if (decorations.isEmpty() || decorations.contains(DECORATION_MENU)) { m_RenderWindow->ActivateMenuWidget(enable); } } bool SimpleRenderWindowView::IsDecorationEnabled(const QString &decoration) const { if (decoration == DECORATION_MENU) { return m_RenderWindow->GetActivateMenuWidgetFlag(); } return false; } QStringList SimpleRenderWindowView::GetDecorations() const { QStringList decorations; decorations << DECORATION_MENU; return decorations; } void SimpleRenderWindowView::SetFocus() { m_RenderWindow->setFocus(); } // //! [SimpleRenderWindowViewCreatePartControl] void SimpleRenderWindowView::CreateQtPartControl(QWidget* parent) { QVBoxLayout* layout = new QVBoxLayout(parent); layout->setContentsMargins(0,0,0,0); m_RenderWindow = new QmitkRenderWindow(parent); layout->addWidget(m_RenderWindow); mitk::DataStorage::Pointer ds = this->GetDataStorage(); m_RenderWindow->GetRenderer()->SetDataStorage(ds); this->RequestUpdate(); } // //! [SimpleRenderWindowViewCreatePartControl] mitk::IRenderingManager* SimpleRenderWindowView::GetRenderingManager() const { // we use the global rendering manager here. This should maybe replaced // by a local one, managing only the render windows specific for the view return d->m_RenderingManagerInterface; } void SimpleRenderWindowView::RequestUpdate(mitk::RenderingManager::RequestType requestType) { if (GetRenderingManager()) GetRenderingManager()->RequestUpdateAll(requestType); } void SimpleRenderWindowView::ForceImmediateUpdate(mitk::RenderingManager::RequestType requestType) { if (GetRenderingManager()) GetRenderingManager()->ForceImmediateUpdateAll(requestType); } mitk::SliceNavigationController* SimpleRenderWindowView::GetTimeNavigationController() const { if (GetRenderingManager()) return GetRenderingManager()->GetTimeNavigationController(); return 0; } diff --git a/Examples/Plugins/org.mitk.example.gui.regiongrowing/src/internal/QmitkRegionGrowingView.h b/Examples/Plugins/org.mitk.example.gui.regiongrowing/src/internal/QmitkRegionGrowingView.h index 2f5c998088..3f8ebb81aa 100644 --- a/Examples/Plugins/org.mitk.example.gui.regiongrowing/src/internal/QmitkRegionGrowingView.h +++ b/Examples/Plugins/org.mitk.example.gui.regiongrowing/src/internal/QmitkRegionGrowingView.h @@ -1,97 +1,98 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkRegionGrowingView_h #define QmitkRegionGrowingView_h #include #include #include "ui_QmitkRegionGrowingViewControls.h" //! [includes] #include "mitkPointSet.h" #include "mitkIRenderWindowPartListener.h" +#include class QmitkPointListWidget; //! [includes] /** \brief QmitkRegionGrowingView \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 QmitkRegionGrowingView : 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; QmitkRegionGrowingView(); protected slots: /// \brief Called when the user clicks the GUI button void DoImageProcessing(); protected: virtual void CreateQtPartControl(QWidget *parent); virtual void SetFocus(); /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( berry::IWorkbenchPart::Pointer source, const QList& nodes ); //! [render-window-part-listener] void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart); void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart); //! [render-window-part-listener] Ui::QmitkRegionGrowingViewControls m_Controls; private: //! [itkimageprocessing] /** \brief ITK image processing function This function is templated like an ITK image. The MITK-Macro AccessByItk determines the actual pixel type and dimensionality of a given MITK image and calls this function for further processing (in our case region growing) */ template < typename TPixel, unsigned int VImageDimension > void ItkImageProcessing( itk::Image< TPixel, VImageDimension >* itkImage, mitk::Geometry3D* imageGeometry ); //! [itkimageprocessing] //! [members] /// \brief This is the actual seed point data object mitk::PointSet::Pointer m_PointSet; QmitkPointListWidget* m_PointListWidget; //! [members] }; #endif // QmitkRegionGrowingView_h diff --git a/Examples/Tutorial/Step4/Step4.cpp b/Examples/Tutorial/Step4/Step4.cpp index 3b6a5cffbd..8460245239 100644 --- a/Examples/Tutorial/Step4/Step4.cpp +++ b/Examples/Tutorial/Step4/Step4.cpp @@ -1,186 +1,187 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkRegisterClasses.h" #include "QmitkRenderWindow.h" #include "QmitkSliceWidget.h" #include "mitkDataNodeFactory.h" #include "mitkProperties.h" #include "mitkRenderingManager.h" #include "mitkStandaloneDataStorage.h" #include "mitkNodePredicateDataType.h" #include #include #include +#include //##Documentation //## @brief Use several views to explore data //## //## As in Step2 and Step3, load one or more data sets (many image, //## surface and other formats), but create 3 views on the data. //## The QmitkRenderWindow is used for displaying a 3D view as in Step3, //## but without volume-rendering. //## Furthermore, we create two 2D views for slicing through the data. //## We use the class QmitkSliceWidget, which is based on the class //## QmitkRenderWindow, but additionally provides sliders //## to slice through the data. We create two instances of //## QmitkSliceWidget, one for axial and one for sagittal slicing. //## The two slices are also shown at their correct position in 3D as //## well as intersection-line, each in the other 2D view. int main(int argc, char* argv[]) { QApplication qtapplication( argc, argv ); if(argc<2) { fprintf( stderr, "Usage: %s [filename1] [filename2] ...\n\n", itksys::SystemTools::GetFilenameName(argv[0]).c_str() ); return 1; } // Register Qmitk-dependent global instances QmitkRegisterClasses(); //************************************************************************* // Part I: Basic initialization //************************************************************************* // Create a DataStorage mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New(); //************************************************************************* // Part II: Create some data by reading files //************************************************************************* int i; for(i=1; iSetFileName(filename); nodeReader->Update(); //********************************************************************* //Part III: Put the data into the datastorage //********************************************************************* // Since the DataNodeFactory directly creates a node, // use the datastorage to add the read node mitk::DataNode::Pointer node = nodeReader->GetOutput(); ds->Add(node); } catch(...) { fprintf( stderr, "Could not open file %s \n\n", filename ); exit(2); } } //************************************************************************* // Part IV: Create windows and pass the tree to it //************************************************************************* // Create toplevel widget with horizontal layout QWidget toplevelWidget; QHBoxLayout layout; layout.setSpacing(2); layout.setMargin(0); toplevelWidget.setLayout(&layout); //************************************************************************* // Part IVa: 3D view //************************************************************************* // Create a renderwindow QmitkRenderWindow renderWindow(&toplevelWidget); layout.addWidget(&renderWindow); // Tell the renderwindow which (part of) the datastorage to render renderWindow.GetRenderer()->SetDataStorage(ds); // Use it as a 3D view renderWindow.GetRenderer()->SetMapperID(mitk::BaseRenderer::Standard3D); // ******************************************************* // ****************** START OF NEW PART ****************** // ******************************************************* //************************************************************************* // Part IVb: 2D view for slicing axially //************************************************************************* // Create QmitkSliceWidget, which is based on the class // QmitkRenderWindow, but additionally provides sliders QmitkSliceWidget view2(&toplevelWidget); layout.addWidget(&view2); view2.SetLevelWindowEnabled(true); // Tell the QmitkSliceWidget which (part of) the tree to render. // By default, it slices the data axially view2.SetDataStorage(ds); // Get the image from the data storage. A predicate (mitk::NodePredicateBase) // is used to get only nodes of the type mitk::Image. mitk::DataStorage::SetOfObjects::ConstPointer rs = ds->GetSubset(mitk::TNodePredicateDataType::New()); view2.SetData(rs->Begin(),mitk::SliceNavigationController::Axial); // We want to see the position of the slice in 2D and the // slice itself in 3D: add it to the datastorage! ds->Add(view2.GetRenderer()->GetCurrentWorldGeometry2DNode()); //************************************************************************* // Part IVc: 2D view for slicing sagitally //************************************************************************* // Create QmitkSliceWidget, which is based on the class // QmitkRenderWindow, but additionally provides sliders QmitkSliceWidget view3(&toplevelWidget); layout.addWidget(&view3); view3.SetDataStorage(ds); // Tell the QmitkSliceWidget which (part of) the datastorage to render // and to slice sagitally view3.SetData(rs->Begin(), mitk::SliceNavigationController::Sagittal); // We want to see the position of the slice in 2D and the // slice itself in 3D: add it to the datastorage! ds->Add(view3.GetRenderer()->GetCurrentWorldGeometry2DNode()); // ******************************************************* // ******************* END OF NEW PART ******************* // ******************************************************* //************************************************************************* // Part V: Qt-specific initialization //************************************************************************* toplevelWidget.show(); // for testing #include "QtTesting.h" if(strcmp(argv[argc-1], "-testing")!=0) return qtapplication.exec(); else return QtTesting(); } /** \example Step4.cpp */ diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.cpp b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.cpp index 367d83497f..1207043f54 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.cpp +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkCmdLineModuleGui.cpp @@ -1,274 +1,275 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) University College London (UCL). All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkCmdLineModuleGui.h" #include "QmitkUiLoader.h" #include #include #include #include #include #include #include #include #include #include #include #include #include "mitkDataStorage.h" +#include //----------------------------------------------------------------------------- struct QmitkCmdLineModuleGuiPrivate { QmitkCmdLineModuleGuiPrivate(const mitk::DataStorage* dataStorage) : m_DataStorage(dataStorage), m_Loader(NULL), m_Transform(NULL), m_TopLevelWidget(NULL) { } const mitk::DataStorage* m_DataStorage; mutable QScopedPointer m_Loader; mutable QScopedPointer m_Transform; mutable QScopedPointer m_TopLevelWidget; }; //----------------------------------------------------------------------------- QmitkCmdLineModuleGui::QmitkCmdLineModuleGui(const mitk::DataStorage* dataStorage, const ctkCmdLineModuleReference& moduleRef) : ctkCmdLineModuleFrontendQtGui(moduleRef) , d(new QmitkCmdLineModuleGuiPrivate(dataStorage)) { qRegisterMetaType(); } //----------------------------------------------------------------------------- QmitkCmdLineModuleGui::~QmitkCmdLineModuleGui() { } //----------------------------------------------------------------------------- QUiLoader* QmitkCmdLineModuleGui::uiLoader() const { // Here we are creating a QUiLoader locally, so when this method // is called, it overrides the one in the base class, so the base // class one is never constructed, and this one is constructed as // a replacement. if (d->m_Loader == NULL) { d->m_Loader.reset(new QmitkUiLoader(d->m_DataStorage)); } return d->m_Loader.data(); } //----------------------------------------------------------------------------- ctkCmdLineModuleXslTransform* QmitkCmdLineModuleGui::xslTransform() const { // This is a virtual getter, overriding the one in the base class. // However, we want to use the transform in the base class, and just append to it. // So we call the base class one, modify it by adding some stuff, and then return // the pointer to the one in the base class. ctkCmdLineModuleXslTransform *transform = ctkCmdLineModuleFrontendQtGui::xslTransform(); if (transform != NULL) { transform->bindVariable("imageInputWidget", QVariant(QString("QmitkDataStorageComboBoxWithSelectNone"))); transform->bindVariable("imageInputValueProperty", "currentValue"); transform->bindVariable("imageInputSetProperty", ""); // Don't need this, as we are connected to DataStorage. } return transform; } //----------------------------------------------------------------------------- QVariant QmitkCmdLineModuleGui::value(const QString ¶meter, int role) const { if (role == UserRole) { ctkCmdLineModuleParameter param = this->moduleReference().description().parameter(parameter); if (param.channel() == "input" && param.tag() == "image") { return this->customValue(parameter, "SelectedNode"); } return QVariant(); } return ctkCmdLineModuleFrontendQtGui::value(parameter, role); } //----------------------------------------------------------------------------- void QmitkCmdLineModuleGui::setValue(const QString& parameter, const QVariant& value, int role) { if (role == UserRole) { ctkCmdLineModuleParameter param = this->moduleReference().description().parameter(parameter); if (param.channel() == "input" && param.tag() == "image") { this->setCustomValue(parameter, value, "SelectedNode"); } else { ctkCmdLineModuleFrontendQtGui::setValue(parameter, value, role); } } else { ctkCmdLineModuleFrontendQtGui::setValue(parameter, value, role); } } //----------------------------------------------------------------------------- QWidget* QmitkCmdLineModuleGui::getGui() { if (!d->m_TopLevelWidget) { // Construct additional widgets to contain full GUI. QWidget *aboutBoxContainerWidget = new QWidget(); ctkCollapsibleGroupBox *aboutBox = new ctkCollapsibleGroupBox(aboutBoxContainerWidget); aboutBox->setTitle("About"); QTextBrowser *aboutBrowser = new QTextBrowser(aboutBox); aboutBrowser->setReadOnly(true); aboutBrowser->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred); aboutBrowser->setOpenExternalLinks(true); aboutBrowser->setOpenLinks(true); QVBoxLayout *aboutLayout = new QVBoxLayout(aboutBox); aboutLayout->addWidget(aboutBrowser); QVBoxLayout *aboutBoxContainerWidgetLayout = new QVBoxLayout(aboutBoxContainerWidget); aboutBoxContainerWidgetLayout->addWidget(aboutBox); QWidget *helpBoxContainerWidget = new QWidget(); ctkCollapsibleGroupBox *helpBox = new ctkCollapsibleGroupBox(); helpBox->setTitle("Help"); QTextBrowser *helpBrowser = new QTextBrowser(helpBox); helpBrowser->setReadOnly(true); helpBrowser->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred); helpBrowser->setOpenExternalLinks(true); helpBrowser->setOpenLinks(true); QVBoxLayout *helpLayout = new QVBoxLayout(helpBox); helpLayout->addWidget(helpBrowser); QVBoxLayout *helpBoxContainerWidgetLayout = new QVBoxLayout(helpBoxContainerWidget); helpBoxContainerWidgetLayout->addWidget(helpBox); QObject* guiHandle = this->guiHandle(); QWidget* generatedGuiWidgets = qobject_cast(guiHandle); QWidget *topLevelWidget = new QWidget(); QGridLayout *topLevelLayout = new QGridLayout(topLevelWidget); topLevelLayout->setContentsMargins(0,0,0,0); topLevelLayout->setSpacing(0); topLevelLayout->addWidget(aboutBoxContainerWidget, 0, 0); topLevelLayout->addWidget(helpBoxContainerWidget, 1, 0); topLevelLayout->addWidget(generatedGuiWidgets, 2, 0); ctkCmdLineModuleDescription description = this->moduleReference().description(); QString helpString = ""; if (!description.title().isEmpty()) { QString titleHtml = "

" + description.title() + "

"; helpString += titleHtml; } if (!description.description().isEmpty()) { QString descriptionHtml = "

" + description.description() + "

"; helpString += descriptionHtml; } if (!description.documentationURL().isEmpty()) { QString docUrlHtml = "

For more information please see " + description.documentationURL() + "

"; helpString += docUrlHtml; } QString aboutString = ""; if (!description.title().isEmpty()) { QString titleHtml = "

" + description.title() + "

"; aboutString += titleHtml; } if (!description.contributor().isEmpty()) { QString contributorHtml = "

Contributed By

" + description.contributor() + "

"; aboutString += contributorHtml; } if (!description.license().isEmpty()) { QString licenseHtml = "

License

" + description.license() + "

"; aboutString += licenseHtml; } if (!description.acknowledgements().isEmpty()) { QString acknowledgementsHtml = "

Acknowledgements

" + description.acknowledgements() + "

"; aboutString += acknowledgementsHtml; } helpBrowser->clear(); helpBrowser->setHtml(helpString); helpBox->setCollapsed(true); aboutBrowser->clear(); aboutBrowser->setHtml(aboutString); aboutBox->setCollapsed(true); d->m_TopLevelWidget.reset(topLevelWidget); } return d->m_TopLevelWidget.data(); } //----------------------------------------------------------------------------- void QmitkCmdLineModuleGui::copyParameters(QmitkCmdLineModuleGui& another) { // This copies "display" parameter types. // See ctkCmdLineModuleFrontend::DisplayRole this->setValues(another.values()); // For custom types, we must manually copy the values. // In our case, we copy image types manually, to pass across the mitk::DataNode pointer. QList parameters = another.parameters("image", ctkCmdLineModuleFrontend::Input); foreach (ctkCmdLineModuleParameter parameter, parameters) { QString parameterName = parameter.name(); QVariant tmp = another.value(parameterName, ctkCmdLineModuleFrontend::UserRole); mitk::DataNode::Pointer node = tmp.value(); if (node.IsNotNull()) { mitk::Image* image = dynamic_cast(node->GetData()); if (image != NULL) { this->setValue(parameterName, tmp, ctkCmdLineModuleFrontend::UserRole); } } } } diff --git a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.cpp b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.cpp index 39442bdd17..29c165cee3 100644 --- a/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.cpp +++ b/Plugins/org.mitk.gui.qt.cmdlinemodules/src/internal/QmitkUiLoader.cpp @@ -1,65 +1,66 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) University College London (UCL). All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkUiLoader.h" #include "QmitkDataStorageComboBoxWithSelectNone.h" #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateOr.h" +#include "mitkImage.h" //----------------------------------------------------------------------------- QmitkUiLoader::QmitkUiLoader(const mitk::DataStorage* dataStorage, QObject *parent) : ctkCmdLineModuleQtUiLoader(parent) , m_DataStorage(dataStorage) { } //----------------------------------------------------------------------------- QmitkUiLoader::~QmitkUiLoader() { } //----------------------------------------------------------------------------- QStringList QmitkUiLoader::availableWidgets () const { QStringList availableWidgets = ctkCmdLineModuleQtUiLoader::availableWidgets(); availableWidgets << "QmitkDataStorageComboBoxWithSelectNone"; return availableWidgets; } //----------------------------------------------------------------------------- QWidget* QmitkUiLoader::createWidget(const QString& className, QWidget* parent, const QString& name) { QWidget* widget = NULL; if (className == "QmitkDataStorageComboBoxWithSelectNone") { QmitkDataStorageComboBoxWithSelectNone* comboBox = new QmitkDataStorageComboBoxWithSelectNone(parent); comboBox->setObjectName(name); comboBox->SetAutoSelectNewItems(false); comboBox->SetPredicate(mitk::TNodePredicateDataType< mitk::Image >::New()); comboBox->SetDataStorage(const_cast(m_DataStorage)); comboBox->setCurrentIndex(0); widget = comboBox; } else { widget = ctkCmdLineModuleQtUiLoader::createWidget(className, parent, name); } return widget; } diff --git a/Plugins/org.mitk.gui.qt.dicom/src/internal/DicomEventHandler.cpp b/Plugins/org.mitk.gui.qt.dicom/src/internal/DicomEventHandler.cpp index 754f7c8d16..57ec40acb6 100644 --- a/Plugins/org.mitk.gui.qt.dicom/src/internal/DicomEventHandler.cpp +++ b/Plugins/org.mitk.gui.qt.dicom/src/internal/DicomEventHandler.cpp @@ -1,98 +1,98 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPluginActivator.h" #include "DicomEventHandler.h" #include #include #include #include #include #include #include #include #include #include - +#include "mitkImage.h" DicomEventHandler::DicomEventHandler() { } DicomEventHandler::~DicomEventHandler() { } void DicomEventHandler::OnSignalAddSeriesToDataManager(const ctkEvent& ctkEvent) { QStringList listOfFilesForSeries; mitk::DicomSeriesReader::StringContainer seriesToLoad; listOfFilesForSeries = ctkEvent.getProperty("FilesForSeries").toStringList(); if (!listOfFilesForSeries.isEmpty()){ QStringListIterator it(listOfFilesForSeries); while (it.hasNext()) { seriesToLoad.push_back(it.next().toStdString()); } mitk::DataNode::Pointer node = mitk::DicomSeriesReader::LoadDicomSeries(seriesToLoad); if (node.IsNull()) { MITK_ERROR << "Error loading series: " << ctkEvent.getProperty("SeriesName").toString().toStdString() << " id: " <getServiceReference(); mitk::IDataStorageService* storageService = mitk::PluginActivator::getContext()->getService(serviceReference); mitk::DataStorage* dataStorage = storageService->GetDefaultDataStorage().GetPointer()->GetDataStorage(); dataStorage->Add(node); // Initialize the RenderWindow mitk::TimeGeometry::Pointer geometry = dataStorage->ComputeBoundingGeometry3D(dataStorage->GetAll()); mitk::RenderingManager::GetInstance()->InitializeViews(geometry); } } else { MITK_INFO << "There are no files for the current series"; } } void DicomEventHandler::OnSignalRemoveSeriesFromStorage(const ctkEvent& ctkEvent) { } void DicomEventHandler::SubscribeSlots() { ctkServiceReference ref = mitk::PluginActivator::getContext()->getServiceReference(); if (ref) { ctkEventAdmin* eventAdmin = mitk::PluginActivator::getContext()->getService(ref); ctkDictionary properties; properties[ctkEventConstants::EVENT_TOPIC] = "org/mitk/gui/qt/dicom/ADD"; eventAdmin->subscribeSlot(this, SLOT(OnSignalAddSeriesToDataManager(ctkEvent)), properties); properties[ctkEventConstants::EVENT_TOPIC] = "org/mitk/gui/qt/dicom/DELETED"; eventAdmin->subscribeSlot(this, SLOT(OnSignalRemoveSeriesFromStorage(ctkEvent)), properties); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDwiSoftwarePhantomView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDwiSoftwarePhantomView.h index 3787ea9b1a..52395255f1 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDwiSoftwarePhantomView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDwiSoftwarePhantomView.h @@ -1,89 +1,90 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include "ui_QmitkDwiSoftwarePhantomViewControls.h" +#include /*! \brief View for diffusion software phantom generation using binary ROIs. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkDwiSoftwarePhantomView : public QmitkFunctionality { // 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; QmitkDwiSoftwarePhantomView(); virtual ~QmitkDwiSoftwarePhantomView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); typedef itk::Image ItkUcharImgType; typedef itk::Image ItkFloatImgType; typedef itk::Vector GradientType; typedef std::vector GradientListType; protected slots: void GeneratePhantom(); ///< Start image generation void OnSimulateBaselineToggle(int state); ///< change from SNR to noise variance and vice versa protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); /** Generate gradient directions distributed on half sphere (suboptimal distribution but arbitrary number of gradients) **/ GradientListType GenerateHalfShell(int NPoints); /** Generate gradient directions (n-fold icosaedron tesselation) **/ template std::vector > MakeGradientList(); /** Update button activity etc. depending on current datamanager selection **/ void UpdateGui(); Ui::QmitkDwiSoftwarePhantomViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; std::vector< mitk::DataNode::Pointer > m_SignalRegionNodes; ///< contains binary signal region nodes std::vector< ItkUcharImgType::Pointer > m_SignalRegions; ///< contains binary signal region images /** List of gui elements generated dynamically depending on the number of selected signal regions **/ std::vector< QLabel* > m_Labels; std::vector< QDoubleSpinBox* > m_SpinFa; std::vector< QDoubleSpinBox* > m_SpinAdc; std::vector< QDoubleSpinBox* > m_SpinX; std::vector< QDoubleSpinBox* > m_SpinY; std::vector< QDoubleSpinBox* > m_SpinZ; std::vector< QDoubleSpinBox* > m_SpinWeight; }; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFieldmapGeneratorView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFieldmapGeneratorView.cpp index 82b690a657..0632133f09 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFieldmapGeneratorView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFieldmapGeneratorView.cpp @@ -1,298 +1,299 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // MITK #include "QmitkFieldmapGeneratorView.h" #include #include #include #include +#include const std::string QmitkFieldmapGeneratorView::VIEW_ID = "org.mitk.views.fieldmapgenerator"; QmitkFieldmapGeneratorView::QmitkFieldmapGeneratorView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) { } QmitkFieldmapGeneratorView::~QmitkFieldmapGeneratorView() { } void QmitkFieldmapGeneratorView::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::QmitkFieldmapGeneratorViewControls; m_Controls->setupUi( parent ); m_Controls->m_SelectedImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); m_Controls->m_SelectedImageBox->SetPredicate(isMitkImage); connect((QObject*) m_Controls->m_GenerateFieldmap, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFieldmap())); connect((QObject*) m_Controls->m_PlaceFieldSource, SIGNAL(clicked()), (QObject*) this, SLOT(PlaceFieldSource())); connect((QObject*) m_Controls->m_SourceVarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_SourceHeightBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnHeightChanged(double))); } } void QmitkFieldmapGeneratorView::OnVarianceChanged(double value) { if (m_SelectedSource.IsNotNull()) { m_SelectedSource->SetProperty("pointsize", mitk::FloatProperty::New(value)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkFieldmapGeneratorView::OnHeightChanged(double value) { if (m_SelectedSource.IsNotNull()) { m_SelectedSource->SetProperty("color", mitk::ColorProperty::New(0, 0, value/100.0)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkFieldmapGeneratorView::PlaceFieldSource() { if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNull() || !m_MultiWidget) { m_Controls->m_WorldPosLabel->setText("-"); m_Controls->m_IndexLabel->setText("-"); return; } mitk::Point3D index; mitk::Image::Pointer img = dynamic_cast(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData()); mitk::Geometry3D* geom = img->GetGeometry(); if ( geom->IsInside(m_WorldPoint) ) { img->GetGeometry()->WorldToIndex(m_WorldPoint, index); mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(0, m_WorldPoint); mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_Controls->m_SelectedImageBox->GetSelectedNode()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(pointSet); QString name = QString("FieldSource_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetVisibility(true); float minSpacing; if(geom->GetSpacing()[0]GetSpacing()[1] && geom->GetSpacing()[0]GetSpacing()[2]) minSpacing = geom->GetSpacing()[0]; else if (geom->GetSpacing()[1] < geom->GetSpacing()[2]) minSpacing = geom->GetSpacing()[1]; else minSpacing = geom->GetSpacing()[2]; node->SetProperty("pointsize", mitk::FloatProperty::New(minSpacing*5)); node->SetProperty("color", mitk::ColorProperty::New(0, 0, 1)); GetDataStorage()->Add(node, m_Controls->m_SelectedImageBox->GetSelectedNode()); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkFieldmapGeneratorView::GenerateFieldmap() { if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNull()) return; mitk::Image::Pointer img = dynamic_cast(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData()); mitk::Geometry3D* geom = img->GetGeometry(); typedef itk::Image< double, 3 > FieldMapType; itk::Vector spacing; ///< output image spacing mitk::Point3D origin; ///< output image origin itk::FieldmapGeneratorFilter< FieldMapType >::MatrixType directionMatrix; ///< output image rotation itk::FieldmapGeneratorFilter< FieldMapType >::OutputImageRegionType imageRegion; ///< output image size spacing = geom->GetSpacing(); origin = geom->GetOrigin(); imageRegion.SetSize(0, img->GetDimension(0)); imageRegion.SetSize(1, img->GetDimension(1)); imageRegion.SetSize(2, img->GetDimension(2)); for (int r=0; r<3; r++) for (int c=0; c<3; c++) directionMatrix[r][c]=geom->GetMatrixColumn(c)[r]/spacing[c]; std::vector< double > variances; std::vector< double > heights; std::vector< mitk::Point3D > worldPositions; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_Controls->m_SelectedImageBox->GetSelectedNode()); for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) if(dynamic_cast((*it)->GetData())) { float var = 0; (*it)->GetPropertyValue("pointsize", var); variances.push_back(var); float color[3]; (*it)->GetColor(color); heights.push_back(color[2]*100); mitk::PointSet* ps = dynamic_cast((*it)->GetData()); mitk::Point3D point; ps->GetPointIfExists(0, &point); worldPositions.push_back(point); } vnl_vector_fixed< double, 3 > gradient, offset; gradient[0] = m_Controls->m_xGradientBox->value(); gradient[1] = m_Controls->m_yGradientBox->value(); gradient[2] = m_Controls->m_zGradientBox->value(); offset[0] = m_Controls->m_xOffsetBox->value(); offset[1] = m_Controls->m_yOffsetBox->value(); offset[2] = m_Controls->m_zOffsetBox->value(); itk::FieldmapGeneratorFilter< FieldMapType >::Pointer filter = itk::FieldmapGeneratorFilter< FieldMapType >::New(); filter->SetHeights(heights); filter->SetVariances(variances); filter->SetWorldPositions(worldPositions); filter->SetSpacing(spacing); filter->SetOrigin(origin); filter->SetDirectionMatrix(directionMatrix); filter->SetImageRegion(imageRegion); filter->SetGradient(gradient); filter->SetOffset(offset); filter->Update(); mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(filter->GetOutput(0)); image->SetVolume(filter->GetOutput(0)->GetBufferPointer()); resultNode->SetData( image ); resultNode->SetName(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetName()+"_Fieldmap"); GetDataStorage()->Add(resultNode); } void QmitkFieldmapGeneratorView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkFieldmapGeneratorView::OnSliceChanged ); m_SliceObserverTag1 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkFieldmapGeneratorView::OnSliceChanged ); m_SliceObserverTag2 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkFieldmapGeneratorView::OnSliceChanged ); m_SliceObserverTag3 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } } void QmitkFieldmapGeneratorView::StdMultiWidgetNotAvailable() { { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag1 ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag2 ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag3 ); } m_MultiWidget = NULL; } void QmitkFieldmapGeneratorView::OnSelectionChanged( std::vector nodes ) { if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNotNull()) m_Controls->m_SelectedImageBox->GetSelectedNode()->RemoveObserver( m_PropertyObserverTag ); m_Controls->m_InputData->setTitle("Please Select Reference Image"); m_SelectedSource = NULL; // iterate selection for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && (dynamic_cast(node->GetData())) ) { m_Controls->m_SourceNameLabel->setText(node->GetName().c_str()); m_SelectedSource = node; float variance = 0; node->GetPropertyValue("pointsize", variance); m_Controls->m_SourceVarianceBox->setValue(variance); float color[3]; node->GetColor(color); m_Controls->m_SourceHeightBox->setValue(color[2]*100); } } if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNotNull()) { itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkFieldmapGeneratorView::OnSliceChanged ); m_PropertyObserverTag = m_Controls->m_SelectedImageBox->GetSelectedNode()->AddObserver( itk::ModifiedEvent(), command ); m_Controls->m_InputData->setTitle("Reference Image"); } } void QmitkFieldmapGeneratorView::OnSliceChanged(const itk::EventObject& /*e*/) { if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNull() || !m_MultiWidget) { m_Controls->m_WorldPosLabel->setText("-"); m_Controls->m_IndexLabel->setText("-"); return; } m_WorldPoint = m_MultiWidget->GetCrossPosition(); QString posSting = QString::number(m_WorldPoint[0]); posSting += ", "; posSting += QString::number(m_WorldPoint[1]); posSting += ", "; posSting += QString::number(m_WorldPoint[2]); m_Controls->m_WorldPosLabel->setText(posSting.toStdString().c_str()); mitk::Point3D index; mitk::Image::Pointer img = dynamic_cast(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData()); if ( m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData()->GetGeometry()->IsInside(m_WorldPoint) ) { img->GetGeometry()->WorldToIndex(m_WorldPoint, index); posSting = QString::number(index[0]); posSting += ", "; posSting += QString::number(index[1]); posSting += ", "; posSting += QString::number(index[2]); m_Controls->m_IndexLabel->setText(posSting.toStdString().c_str()); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.cpp index c6df504317..77066e4499 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.cpp @@ -1,493 +1,494 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Qmitk #include "QmitkTbssSkeletonizationView.h" #include #include #include #include #include // mitk #include +#include // Qt #include #include //vtk #include #include // Boost #include const std::string QmitkTbssSkeletonizationView::VIEW_ID = "org.mitk.views.tbssskeletonization"; using namespace berry; QmitkTbssSkeletonizationView::QmitkTbssSkeletonizationView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) { } QmitkTbssSkeletonizationView::~QmitkTbssSkeletonizationView() { } void QmitkTbssSkeletonizationView::OnSelectionChanged(std::vector nodes) { //datamanager selection changed if (!this->IsActivated()) return; bool found3dImage = false; bool found4dImage = false; this->m_Controls->m_TubularName->setText(QString("Tubular Structure Mask: ")); this->m_Controls->m_TubularName->setEnabled(false); this->m_Controls->m_MeanLabel->setText(QString("Mean: ")); this->m_Controls->m_MeanLabel->setEnabled(false); this->m_Controls->m_PatientDataLabel->setText(QString("Patient Data: ")); this->m_Controls->m_PatientDataLabel->setEnabled(false); // iterate selection for ( int i=0; iGetData(); std::string name = ""; nodes[i]->GetStringProperty("name", name); if(nodeData) { if(QString("Image").compare(nodeData->GetNameOfClass())==0) { mitk::Image* img = static_cast(nodeData); if(img->GetDimension() == 3) { bool isBinary(false); nodes[i]->GetBoolProperty("binary", isBinary); if(isBinary) { QString label("Tubular Structure Mask: "); label.append(QString(name.c_str())); this->m_Controls->m_TubularName->setText(label); this->m_Controls->m_TubularName->setEnabled(true); } else { found3dImage = true; QString label("Mean: "); label.append(QString(name.c_str())); this->m_Controls->m_MeanLabel->setText(label); this->m_Controls->m_MeanLabel->setEnabled(true); } } else if(img->GetDimension() == 4) { found4dImage = true; QString label("Patient Data: "); label.append(QString(name.c_str())); this->m_Controls->m_PatientDataLabel->setText(label); this->m_Controls->m_PatientDataLabel->setEnabled(true); } } } } this->m_Controls->m_Skeletonize->setEnabled(found3dImage); this->m_Controls->m_Project->setEnabled(found3dImage && found4dImage); this->m_Controls->m_OutputMask->setEnabled(found3dImage && found4dImage); this->m_Controls->m_OutputDistanceMap->setEnabled(found3dImage && found4dImage); } void QmitkTbssSkeletonizationView::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::QmitkTbssSkeletonizationViewControls; m_Controls->setupUi( parent ); this->CreateConnections(); } } void QmitkTbssSkeletonizationView::Activated() { QmitkFunctionality::Activated(); } void QmitkTbssSkeletonizationView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkTbssSkeletonizationView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_Skeletonize), SIGNAL(clicked()), this, SLOT(Skeletonize() )); connect( (QObject*)(m_Controls->m_Project), SIGNAL(clicked()), this, SLOT(Project() )); } } void QmitkTbssSkeletonizationView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkTbssSkeletonizationView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkTbssSkeletonizationView::Skeletonize() { typedef itk::SkeletonizationFilter SkeletonisationFilterType; SkeletonisationFilterType::Pointer skeletonizer = SkeletonisationFilterType::New(); std::vector nodes = this->GetDataManagerSelection(); mitk::Image::Pointer meanImage = mitk::Image::New(); std::string name = ""; for ( int i=0; iGetData(); if(nodeData) { if(QString("Image").compare(nodeData->GetNameOfClass())==0) { bool isBinary(false); nodes[i]->GetBoolProperty("binary", isBinary); mitk::Image* img = static_cast(nodeData); if(img->GetDimension() == 3 && !isBinary) { meanImage = img; name = nodes[i]->GetName(); } } } } // Calculate skeleton FloatImageType::Pointer itkImg = FloatImageType::New(); mitk::CastToItkImage(meanImage, itkImg); skeletonizer->SetInput(itkImg); skeletonizer->Update(); FloatImageType::Pointer output = skeletonizer->GetOutput(); mitk::Image::Pointer mitkOutput = mitk::Image::New(); mitk::CastToMitkImage(output, mitkOutput); name += "_skeleton"; AddToDataStorage(mitkOutput, name); } void QmitkTbssSkeletonizationView::Project() { typedef itk::SkeletonizationFilter SkeletonisationFilterType; typedef itk::ProjectionFilter ProjectionFilterType; typedef itk::DistanceMapFilter DistanceMapFilterType; SkeletonisationFilterType::Pointer skeletonizer = SkeletonisationFilterType::New(); std::vector nodes = this->GetDataManagerSelection(); mitk::Image::Pointer meanImage = mitk::Image::New(); mitk::Image::Pointer subjects = mitk::Image::New(); mitk::Image::Pointer tubular = mitk::Image::New(); for ( int i=0; iGetData(); if(nodeData) { if(QString("Image").compare(nodeData->GetNameOfClass())==0) { mitk::Image* img = static_cast(nodeData); if(img->GetDimension() == 3) { bool isBinary(false); nodes[i]->GetBoolProperty("binary", isBinary); if(isBinary) { tubular = img; } else { meanImage = img; } } else if(img->GetDimension() == 4) { subjects = img; } } } } Float4DImageType::Pointer allFA = ConvertToItk(subjects); // Calculate skeleton FloatImageType::Pointer itkImg = FloatImageType::New(); mitk::CastToItkImage(meanImage, itkImg); skeletonizer->SetInput(itkImg); skeletonizer->Update(); FloatImageType::Pointer output = skeletonizer->GetOutput(); mitk::Image::Pointer mitkOutput = mitk::Image::New(); mitk::CastToMitkImage(output, mitkOutput); AddToDataStorage(mitkOutput, "mean_FA_skeletonised"); // Retrieve direction image needed later by the projection filter DirectionImageType::Pointer directionImg = skeletonizer->GetVectorImage(); // Calculate distance image DistanceMapFilterType::Pointer distanceMapFilter = DistanceMapFilterType::New(); distanceMapFilter->SetInput(output); distanceMapFilter->Update(); FloatImageType::Pointer distanceMap = distanceMapFilter->GetOutput(); if(m_Controls->m_OutputDistanceMap->isChecked()) { mitk::Image::Pointer mitkDistance = mitk::Image::New(); mitk::CastToMitkImage(distanceMap, mitkDistance); AddToDataStorage(mitkDistance, "distance map"); } // Do projection // Ask a threshold to create a skeleton mask double threshold = -1.0; while(threshold == -1.0) { threshold = QInputDialog::getDouble(m_Controls->m_Skeletonize, tr("Specify the FA threshold"), tr("Threshold:"), QLineEdit::Normal, 0.2); if(threshold < 0.0 || threshold > 1.0) { QMessageBox msgBox; msgBox.setText("Please choose a value between 0 and 1"); msgBox.exec(); threshold = -1.0; } } typedef itk::BinaryThresholdImageFilter ThresholdFilterType; ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New(); thresholder->SetInput(output); thresholder->SetLowerThreshold(threshold); thresholder->SetUpperThreshold(std::numeric_limits::max()); thresholder->SetOutsideValue(0); thresholder->SetInsideValue(1); thresholder->Update(); CharImageType::Pointer thresholdedImg = thresholder->GetOutput(); if(m_Controls->m_OutputMask->isChecked()) { mitk::Image::Pointer mitkThresholded = mitk::Image::New(); mitk::CastToMitkImage(thresholdedImg, mitkThresholded); std::string maskName = "skeleton_mask_at_" + boost::lexical_cast(threshold); AddToDataStorage(mitkThresholded, maskName); } CharImageType::Pointer itkTubular = CharImageType::New(); mitk::CastToItkImage(tubular, itkTubular); ProjectionFilterType::Pointer projectionFilter = ProjectionFilterType::New(); projectionFilter->SetDistanceMap(distanceMap); projectionFilter->SetDirections(directionImg); projectionFilter->SetAllFA(allFA); projectionFilter->SetTube(itkTubular); projectionFilter->SetSkeleton(thresholdedImg); projectionFilter->Project(); Float4DImageType::Pointer projected = projectionFilter->GetProjections(); mitk::Image::Pointer mitkProjections = mitk::Image::New(); mitk::CastToMitkImage(projected, mitkProjections); AddToDataStorage(mitkProjections, "all_FA_projected"); } void QmitkTbssSkeletonizationView::AddToDataStorage(mitk::Image* img, std::string name) { mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetProperty( "name", mitk::StringProperty::New(name) ); result->SetData( img ); // add new image to data storage and set as active to ease further processing GetDefaultDataStorage()->Add( result ); } -Float4DImageType::Pointer QmitkTbssSkeletonizationView::ConvertToItk(mitk::Image::Pointer image) +Float4DImageType::Pointer QmitkTbssSkeletonizationView::ConvertToItk(itk::SmartPointer image) { Float4DImageType::Pointer output = Float4DImageType::New(); mitk::Geometry3D* geo = image->GetGeometry(); mitk::Vector3D mitkSpacing = geo->GetSpacing(); mitk::Point3D mitkOrigin = geo->GetOrigin(); Float4DImageType::SpacingType spacing; spacing[0] = mitkSpacing[0]; spacing[1] = mitkSpacing[1]; spacing[2] = mitkSpacing[2]; spacing[3] = 1.0; // todo: check if spacing has length 4 Float4DImageType::PointType origin; origin[0] = mitkOrigin[0]; origin[1] = mitkOrigin[1]; origin[2] = mitkOrigin[2]; origin[3] = 0; Float4DImageType::SizeType size; size[0] = image->GetDimension(0); size[1] = image->GetDimension(1); size[2] = image->GetDimension(2); size[3] = image->GetDimension(3); Float4DImageType::DirectionType dir; vtkLinearTransform* lin = geo->GetVtkTransform(); vtkMatrix4x4 *m = lin->GetMatrix(); dir.Fill(0.0); for(int x=0; x<3; x++) { for(int y=0; y<3; y++) { dir[x][y] = m->GetElement(x,y); } } dir[3][3] = 1; output->SetSpacing(spacing); output->SetOrigin(origin); output->SetRegions(size); output->SetDirection(dir); output->Allocate(); if(image->GetDimension() == 4) { int timesteps = image->GetDimension(3); try{ // REPLACE THIS METHODE()ConvertToItk) WITH mitk::CastToItk // iterate through the subjects and copy data to output for(int t=0; tGetDimension(0); x++) { for(int y=0; yGetDimension(1); y++) { for(int z=0; zGetDimension(2); z++) { itk::Index<3> ix = {x, y, z}; itk::Index<4> ix4 = {x, y, z, t}; output->SetPixel(ix4, image->GetPixelValueByIndex(ix, t)); } } } } } catch(std::exception & e) { MITK_INFO << e.what(); } } return output; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.h index 683c7bdd1b..7321584b91 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.h @@ -1,95 +1,99 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkTbssSkeletonizationView_h #define QmitkTbssSkeletonizationView_h #include #include "ui_QmitkTbssSkeletonizationViewControls.h" +#include "itkImage.h" +namespace mitk { + class Image; +} typedef itk::Image FloatImageType; typedef itk::Image CharImageType; typedef itk::Image Float4DImageType; typedef itk::CovariantVector VectorType; typedef itk::Image DirectionImageType; /*! * \brief Implementation of the core functionality of TBSS. * This plugin provides the core functionality of TBSS (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024) * It can skeletonize a mean FA image and calculate the projection of all individual subjects to this skeleton. */ class QmitkTbssSkeletonizationView : public QmitkFunctionality { Q_OBJECT public: static const std::string VIEW_ID; QmitkTbssSkeletonizationView(); virtual ~QmitkTbssSkeletonizationView(); virtual void CreateQtPartControl(QWidget *parent); //Creation of the connections of main and control widget virtual void CreateConnections(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); protected slots: /* \brief Perform skeletonization only */ void Skeletonize(); // Perform skeletonization and Projection of subject data to the skeleton void Project(); protected: //brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkTbssSkeletonizationViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; void AddToDataStorage(mitk::Image* img, std::string name); - Float4DImageType::Pointer ConvertToItk(mitk::Image::Pointer image); + Float4DImageType::Pointer ConvertToItk(itk::SmartPointer image); }; #endif // _QMITKTbssSkeletonizationVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkMeasurementView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkMeasurementView.cpp index bef27189bd..4f1ac3fdec 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkMeasurementView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkMeasurementView.cpp @@ -1,890 +1,891 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #define MEASUREMENT_DEBUG MITK_DEBUG("QmitkMeasurementView") << __LINE__ << ": " #include "QmitkMeasurementView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include #include "mitkPluginActivator.h" #include "usModuleRegistry.h" template static T* GetService() { ctkPluginContext* context = mitk::PluginActivator::GetContext(); ctkServiceReference serviceRef = context->getServiceReference(); return serviceRef ? context->getService(serviceRef) : NULL; } struct QmitkPlanarFigureData { QmitkPlanarFigureData() : m_Figure(0), m_EndPlacementObserverTag(0), m_SelectObserverTag(0), m_StartInteractionObserverTag(0), m_EndInteractionObserverTag(0) { } mitk::PlanarFigure* m_Figure; unsigned int m_EndPlacementObserverTag; unsigned int m_SelectObserverTag; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; }; struct QmitkMeasurementViewData { QmitkMeasurementViewData() : m_LineCounter(0), m_PathCounter(0), m_AngleCounter(0), m_FourPointAngleCounter(0), m_EllipseCounter(0), m_DoubleEllipseCounter(0), m_RectangleCounter(0), m_PolygonCounter(0), m_UnintializedPlanarFigure(false) { } // internal vars unsigned int m_LineCounter; unsigned int m_PathCounter; unsigned int m_AngleCounter; unsigned int m_FourPointAngleCounter; unsigned int m_EllipseCounter; unsigned int m_DoubleEllipseCounter; unsigned int m_RectangleCounter; unsigned int m_PolygonCounter; QList m_CurrentSelection; std::map m_DataNodeToPlanarFigureData; mitk::WeakPointer m_SelectedImageNode; bool m_UnintializedPlanarFigure; // WIDGETS QWidget* m_Parent; QLabel* m_SelectedImageLabel; QAction* m_DrawLine; QAction* m_DrawPath; QAction* m_DrawAngle; QAction* m_DrawFourPointAngle; QAction* m_DrawEllipse; QAction* m_DrawDoubleEllipse; QAction* m_DrawRectangle; QAction* m_DrawPolygon; QToolBar* m_DrawActionsToolBar; QActionGroup* m_DrawActionsGroup; QTextBrowser* m_SelectedPlanarFiguresText; QPushButton* m_CopyToClipboard; QGridLayout* m_Layout; }; const std::string QmitkMeasurementView::VIEW_ID = "org.mitk.views.measurement"; QmitkMeasurementView::QmitkMeasurementView() : d( new QmitkMeasurementViewData ) { } QmitkMeasurementView::~QmitkMeasurementView() { this->RemoveAllInteractors(); delete d; } void QmitkMeasurementView::CreateQtPartControl(QWidget* parent) { d->m_Parent = parent; // image label QLabel* selectedImageLabel = new QLabel("Reference Image: "); d->m_SelectedImageLabel = new QLabel; d->m_SelectedImageLabel->setStyleSheet("font-weight: bold;"); d->m_DrawActionsToolBar = new QToolBar; d->m_DrawActionsGroup = new QActionGroup(this); d->m_DrawActionsGroup->setExclusive(true); //# add actions MEASUREMENT_DEBUG << "Draw Line"; QAction* currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/line.png"), "Draw Line"); currentAction->setCheckable(true); d->m_DrawLine = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Path"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/path.png"), "Draw Path"); currentAction->setCheckable(true); d->m_DrawPath = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Angle"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/angle.png"), "Draw Angle"); currentAction->setCheckable(true); d->m_DrawAngle = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Four Point Angle"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/four-point-angle.png"), "Draw Four Point Angle"); currentAction->setCheckable(true); d->m_DrawFourPointAngle = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Circle"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/circle.png"), "Draw Circle"); currentAction->setCheckable(true); d->m_DrawEllipse = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Double Ellipse"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/doubleellipse.png"), "Draw Double Ellipse"); currentAction->setCheckable(true); d->m_DrawDoubleEllipse = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Rectangle"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/rectangle.png"), "Draw Rectangle"); currentAction->setCheckable(true); d->m_DrawRectangle = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); MEASUREMENT_DEBUG << "Draw Polygon"; currentAction = d->m_DrawActionsToolBar->addAction(QIcon(":/measurement/polygon.png"), "Draw Polygon"); currentAction->setCheckable(true); d->m_DrawPolygon = currentAction; d->m_DrawActionsToolBar->addAction(currentAction); d->m_DrawActionsGroup->addAction(currentAction); // planar figure details text d->m_SelectedPlanarFiguresText = new QTextBrowser; // copy to clipboard button d->m_CopyToClipboard = new QPushButton("Copy to Clipboard"); d->m_Layout = new QGridLayout; d->m_Layout->addWidget(selectedImageLabel, 0, 0, 1, 1); d->m_Layout->addWidget(d->m_SelectedImageLabel, 0, 1, 1, 1); d->m_Layout->addWidget(d->m_DrawActionsToolBar, 1, 0, 1, 2); d->m_Layout->addWidget(d->m_SelectedPlanarFiguresText, 2, 0, 1, 2); d->m_Layout->addWidget(d->m_CopyToClipboard, 3, 0, 1, 2); d->m_Parent->setLayout(d->m_Layout); // create connections this->CreateConnections(); // readd interactors and observers this->AddAllInteractors(); } void QmitkMeasurementView::CreateConnections() { QObject::connect( d->m_DrawLine, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawLineTriggered(bool) ) ); QObject::connect( d->m_DrawPath, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawPathTriggered(bool) ) ); QObject::connect( d->m_DrawAngle, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawAngleTriggered(bool) ) ); QObject::connect( d->m_DrawFourPointAngle, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawFourPointAngleTriggered(bool) ) ); QObject::connect( d->m_DrawEllipse, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawEllipseTriggered(bool) ) ); QObject::connect( d->m_DrawDoubleEllipse, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawDoubleEllipseTriggered(bool) ) ); QObject::connect( d->m_DrawRectangle, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawRectangleTriggered(bool) ) ); QObject::connect( d->m_DrawPolygon, SIGNAL( triggered(bool) ), this, SLOT( ActionDrawPolygonTriggered(bool) ) ); QObject::connect( d->m_CopyToClipboard, SIGNAL( clicked(bool) ), this, SLOT( CopyToClipboard(bool) ) ); } void QmitkMeasurementView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MEASUREMENT_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer() ); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); // nonConstNode->SetBoolProperty( "planarfigure.isextendable", true ); } else { // just to be sure that the interactor is not added twice // mitk::GlobalInteraction::GetInstance()->RemoveInteractor(figureInteractor); } MEASUREMENT_DEBUG << "adding interactor to globalinteraction"; // mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); MEASUREMENT_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkMeasurementView > SimpleCommandType; SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); initializationCommand->SetCallbackFunction( this, &QmitkMeasurementView::PlanarFigureInitialized ); data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkMeasurementView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkMeasurementView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkMeasurementView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkMeasurementView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); // adding to the map of tracked planarfigures d->m_DataNodeToPlanarFigureData[nonConstNode] = data; } this->CheckForTopMostVisibleImage(); } void QmitkMeasurementView::NodeChanged(const mitk::DataNode* node) { // DETERMINE IF WE HAVE TO RENEW OUR DETAILS TEXT (ANY NODE CHANGED IN OUR SELECTION?) bool renewText = false; for( int i=0; i < d->m_CurrentSelection.size(); ++i ) { if( node == d->m_CurrentSelection.at(i) ) { renewText = true; break; } } if(renewText) { MEASUREMENT_DEBUG << "Selected nodes changed. Refreshing text."; this->UpdateMeasurementText(); } this->CheckForTopMostVisibleImage(); } void QmitkMeasurementView::CheckForTopMostVisibleImage(mitk::DataNode* _NodeToNeglect) { d->m_SelectedImageNode = this->DetectTopMostVisibleImage().GetPointer(); if( d->m_SelectedImageNode.GetPointer() == _NodeToNeglect ) d->m_SelectedImageNode = 0; if( d->m_SelectedImageNode.IsNotNull() && d->m_UnintializedPlanarFigure == false ) { MEASUREMENT_DEBUG << "Reference image found"; d->m_SelectedImageLabel->setText( QString::fromStdString( d->m_SelectedImageNode->GetName() ) ); d->m_DrawActionsToolBar->setEnabled(true); MEASUREMENT_DEBUG << "Updating Measurement text"; } else { MEASUREMENT_DEBUG << "No reference image available. Will disable actions for creating new planarfigures"; if( d->m_UnintializedPlanarFigure == false ) d->m_SelectedImageLabel->setText( "No visible image available." ); d->m_DrawActionsToolBar->setEnabled(false); } } void QmitkMeasurementView::NodeRemoved(const mitk::DataNode* node) { MEASUREMENT_DEBUG << "node removed from data storage"; mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = d->m_DataNodeToPlanarFigureData.find(nonConstNode); bool isFigureFinished = false; bool isPlaced = false; if( it != d->m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); MEASUREMENT_DEBUG << "removing from the list of tracked planar figures"; isFigureFinished = data.m_Figure->GetPropertyList()->GetBoolProperty("initiallyplaced",isPlaced); if (!isFigureFinished) { // if the property does not yet exist or is false, drop the datanode PlanarFigureInitialized(); // normally called when a figure is finished, to reset all buttons } d->m_DataNodeToPlanarFigureData.erase( it ); } mitk::TNodePredicateDataType::Pointer isPlanarFigure = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer nodes = GetDataStorage()->GetDerivations(node,isPlanarFigure); for (unsigned int x = 0; x < nodes->size(); x++) { mitk::PlanarFigure* planarFigure = dynamic_cast (nodes->at(x)->GetData()); if (planarFigure != NULL) { isFigureFinished = planarFigure->GetPropertyList()->GetBoolProperty("initiallyplaced",isPlaced); if (!isFigureFinished) { // if the property does not yet exist or is false, drop the datanode GetDataStorage()->Remove(nodes->at(x)); if( !d->m_DataNodeToPlanarFigureData.empty() ) { std::map::iterator it2 = d->m_DataNodeToPlanarFigureData.find(nodes->at(x)); //check if returned it2 valid if( it2 != d->m_DataNodeToPlanarFigureData.end() ) { d->m_DataNodeToPlanarFigureData.erase( it2 );// removing planar figure from tracked figure list PlanarFigureInitialized(); // normally called when a figure is finished, to reset all buttons EnableCrosshairNavigation(); } } } } } this->CheckForTopMostVisibleImage(nonConstNode); } void QmitkMeasurementView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { MEASUREMENT_DEBUG << "planar figure " << object << " selected"; std::map::iterator it = d->m_DataNodeToPlanarFigureData.begin(); d->m_CurrentSelection.clear(); while( it != d->m_DataNodeToPlanarFigureData.end()) { mitk::DataNode* node = it->first; QmitkPlanarFigureData& data = it->second; if( data.m_Figure == object ) { MITK_DEBUG << "selected node found. enabling selection"; node->SetSelected(true); d->m_CurrentSelection.push_back( node ); } else { node->SetSelected(false); } ++it; } this->UpdateMeasurementText(); this->RequestRenderWindowUpdate(); } void QmitkMeasurementView::PlanarFigureInitialized() { MEASUREMENT_DEBUG << "planar figure initialized"; d->m_UnintializedPlanarFigure = false; d->m_DrawActionsToolBar->setEnabled(true); d->m_DrawLine->setChecked(false); d->m_DrawPath->setChecked(false); d->m_DrawAngle->setChecked(false); d->m_DrawFourPointAngle->setChecked(false); d->m_DrawEllipse->setChecked(false); d->m_DrawDoubleEllipse->setChecked(false); d->m_DrawRectangle->setChecked(false); d->m_DrawPolygon->setChecked(false); } void QmitkMeasurementView::SetFocus() { d->m_SelectedImageLabel->setFocus(); } void QmitkMeasurementView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList &nodes) { MEASUREMENT_DEBUG << "Determine the top most visible image"; MEASUREMENT_DEBUG << "The PlanarFigure interactor will take the currently visible PlaneGeometry from the slice navigation controller"; this->CheckForTopMostVisibleImage(); MEASUREMENT_DEBUG << "refreshing selection and detailed text"; d->m_CurrentSelection = nodes; this->UpdateMeasurementText(); // bug 16600: deselecting all planarfigures by clicking on datamanager when no node is selected if(d->m_CurrentSelection.size() == 0) { mitk::TNodePredicateDataType::Pointer isPlanarFigure = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer planarFigures = this->GetDataStorage()->GetSubset( isPlanarFigure ); // setting all planar figures which are not helper objects not selected for(mitk::DataStorage::SetOfObjects::ConstIterator it=planarFigures->Begin(); it!=planarFigures->End(); it++) { mitk::DataNode* node = it.Value(); bool isHelperObject(false); node->GetBoolProperty("helper object", isHelperObject); if(!isHelperObject) { node->SetSelected(false); } } } for( int i=d->m_CurrentSelection.size()-1; i>= 0; --i) { mitk::DataNode* node = d->m_CurrentSelection.at(i); mitk::PlanarFigure* _PlanarFigure = dynamic_cast (node->GetData()); // the last selected planar figure if (_PlanarFigure && _PlanarFigure->GetGeometry2D()) { QmitkRenderWindow* selectedRenderWindow = 0; bool PlanarFigureInitializedWindow = false; mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart()); if(! linkedRenderWindow ) { return; } QmitkRenderWindow* RenderWindow1 = linkedRenderWindow->GetQmitkRenderWindow( "axial") ; QmitkRenderWindow* RenderWindow2 = linkedRenderWindow->GetQmitkRenderWindow( "sagittal") ; QmitkRenderWindow* RenderWindow3 = linkedRenderWindow->GetQmitkRenderWindow( "coronal") ; QmitkRenderWindow* RenderWindow4 = linkedRenderWindow->GetQmitkRenderWindow( "3d") ; if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow1->GetRenderer())) { selectedRenderWindow = RenderWindow1; } if (!selectedRenderWindow && node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow2->GetRenderer())) { selectedRenderWindow = RenderWindow2; } if (!selectedRenderWindow && node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,RenderWindow3->GetRenderer())) { selectedRenderWindow = RenderWindow3; } if (!selectedRenderWindow && node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow4->GetRenderer())) { selectedRenderWindow = RenderWindow4; } const mitk::PlaneGeometry* _PlaneGeometry = dynamic_cast (_PlanarFigure->GetGeometry2D()); mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl(); mitk::Geometry2D::ConstPointer worldGeometry1 = RenderWindow1->GetRenderer()->GetCurrentWorldGeometry2D(); mitk::PlaneGeometry::ConstPointer _Plane1 = dynamic_cast( worldGeometry1.GetPointer() ); mitk::VnlVector normal1 = _Plane1->GetNormalVnl(); mitk::Geometry2D::ConstPointer worldGeometry2 = RenderWindow2->GetRenderer()->GetCurrentWorldGeometry2D(); mitk::PlaneGeometry::ConstPointer _Plane2 = dynamic_cast( worldGeometry2.GetPointer() ); mitk::VnlVector normal2 = _Plane2->GetNormalVnl(); mitk::Geometry2D::ConstPointer worldGeometry3 = RenderWindow3->GetRenderer()->GetCurrentWorldGeometry2D(); mitk::PlaneGeometry::ConstPointer _Plane3 = dynamic_cast( worldGeometry3.GetPointer() ); mitk::VnlVector normal3 = _Plane3->GetNormalVnl(); normal[0] = fabs(normal[0]); normal[1] = fabs(normal[1]); normal[2] = fabs(normal[2]); normal1[0] = fabs(normal1[0]); normal1[1] = fabs(normal1[1]); normal1[2] = fabs(normal1[2]); normal2[0] = fabs(normal2[0]); normal2[1] = fabs(normal2[1]); normal2[2] = fabs(normal2[2]); normal3[0] = fabs(normal3[0]); normal3[1] = fabs(normal3[1]); normal3[2] = fabs(normal3[2]); double ang1 = angle(normal, normal1); double ang2 = angle(normal, normal2); double ang3 = angle(normal, normal3); if(ang1 < ang2 && ang1 < ang3) { selectedRenderWindow = RenderWindow1; } else { if(ang2 < ang3) { selectedRenderWindow = RenderWindow2; } else { selectedRenderWindow = RenderWindow3; } } // re-orient view if (selectedRenderWindow) { const mitk::Point3D& centerP = _PlaneGeometry->GetOrigin(); selectedRenderWindow->GetSliceNavigationController()->ReorientSlices(centerP, _PlaneGeometry->GetNormal()); } } break; } this->RequestRenderWindowUpdate(); } void QmitkMeasurementView::ActionDrawLineTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarLine::Pointer figure = mitk::PlanarLine::New(); QString qString = QString("Line%1").arg(++d->m_LineCounter); this->AddFigureToDataStorage(figure, qString); MEASUREMENT_DEBUG << "PlanarLine initialized..."; } void QmitkMeasurementView::ActionDrawPathTriggered(bool checked) { Q_UNUSED(checked) mitk::IPropertyFilters* propertyFilters = GetService(); if (propertyFilters != NULL) { mitk::PropertyFilter filter; filter.AddEntry("ClosedPlanarPolygon", mitk::PropertyFilter::Blacklist); propertyFilters->AddFilter(filter, "PlanarPolygon"); } mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOff(); QString qString = QString("Path%1").arg(++d->m_PathCounter); mitk::DataNode::Pointer node = this->AddFigureToDataStorage(figure, qString); mitk::BoolProperty::Pointer closedProperty = mitk::BoolProperty::New( false ); node->SetProperty("ClosedPlanarPolygon", closedProperty); node->SetProperty("planarfigure.isextendable",mitk::BoolProperty::New(true)); MEASUREMENT_DEBUG << "PlanarPath initialized..."; } void QmitkMeasurementView::ActionDrawAngleTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarAngle::Pointer figure = mitk::PlanarAngle::New(); QString qString = QString("Angle%1").arg(++d->m_AngleCounter); this->AddFigureToDataStorage(figure, qString); MEASUREMENT_DEBUG << "PlanarAngle initialized..."; } void QmitkMeasurementView::ActionDrawFourPointAngleTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarFourPointAngle::Pointer figure = mitk::PlanarFourPointAngle::New(); QString qString = QString("Four Point Angle%1").arg(++d->m_FourPointAngleCounter); this->AddFigureToDataStorage(figure, qString); MEASUREMENT_DEBUG << "PlanarFourPointAngle initialized..."; } void QmitkMeasurementView::ActionDrawEllipseTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); QString qString = QString("Circle%1").arg(++d->m_EllipseCounter); this->AddFigureToDataStorage(figure, qString); MEASUREMENT_DEBUG << "PlanarCircle initialized..."; } void QmitkMeasurementView::ActionDrawDoubleEllipseTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarDoubleEllipse::Pointer figure = mitk::PlanarDoubleEllipse::New(); QString qString = QString("DoubleEllipse%1").arg(++d->m_DoubleEllipseCounter); this->AddFigureToDataStorage(figure, qString); MEASUREMENT_DEBUG << "PlanarDoubleEllipse initialized..."; } void QmitkMeasurementView::ActionDrawRectangleTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarRectangle::Pointer figure = mitk::PlanarRectangle::New(); QString qString = QString("Rectangle%1").arg(++d->m_RectangleCounter); this->AddFigureToDataStorage(figure, qString); MEASUREMENT_DEBUG << "PlanarRectangle initialized..."; } void QmitkMeasurementView::ActionDrawPolygonTriggered(bool checked) { Q_UNUSED(checked) mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); QString qString = QString("Polygon%1").arg(++d->m_PolygonCounter); mitk::DataNode::Pointer node = this->AddFigureToDataStorage(figure, qString); node->SetProperty("planarfigure.isextendable",mitk::BoolProperty::New(true)); MEASUREMENT_DEBUG << "PlanarPolygon initialized..."; } void QmitkMeasurementView::CopyToClipboard( bool checked ) { Q_UNUSED(checked) MEASUREMENT_DEBUG << "Copying current Text to clipboard..."; QString clipboardText = d->m_SelectedPlanarFiguresText->toPlainText(); QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard); } mitk::DataNode::Pointer QmitkMeasurementView::AddFigureToDataStorage( mitk::PlanarFigure* figure, const QString& name) { // add as MEASUREMENT_DEBUG << "Adding new figure to datastorage..."; if( d->m_SelectedImageNode.IsNull() ) { MITK_ERROR << "No reference image available"; return 0; } mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); // set as selected newNode->SetSelected( true ); this->GetDataStorage()->Add(newNode, d->m_SelectedImageNode); // set all others in selection as deselected for( int i=0; im_CurrentSelection.size(); ++i) d->m_CurrentSelection.at(i)->SetSelected(false); d->m_CurrentSelection.clear(); d->m_CurrentSelection.push_back( newNode ); this->UpdateMeasurementText(); this->DisableCrosshairNavigation(); d->m_DrawActionsToolBar->setEnabled(false); d->m_UnintializedPlanarFigure = true; return newNode; } void QmitkMeasurementView::UpdateMeasurementText() { d->m_SelectedPlanarFiguresText->clear(); QString infoText; QString plainInfoText; int j = 1; mitk::PlanarFigure* _PlanarFigure = 0; mitk::PlanarAngle* planarAngle = 0; mitk::PlanarFourPointAngle* planarFourPointAngle = 0; mitk::DataNode::Pointer node = 0; for (int i=0; im_CurrentSelection.size(); ++i, ++j) { plainInfoText.clear(); node = d->m_CurrentSelection.at(i); _PlanarFigure = dynamic_cast (node->GetData()); if( !_PlanarFigure ) continue; if(j>1) infoText.append("
"); infoText.append(QString("%1
").arg(QString::fromStdString( node->GetName()))); plainInfoText.append(QString("%1").arg(QString::fromStdString( node->GetName()))); planarAngle = dynamic_cast (_PlanarFigure); if(!planarAngle) { planarFourPointAngle = dynamic_cast (_PlanarFigure); } double featureQuantity = 0.0; for (unsigned int k = 0; k < _PlanarFigure->GetNumberOfFeatures(); ++k) { if ( !_PlanarFigure->IsFeatureActive( k ) ) continue; featureQuantity = _PlanarFigure->GetQuantity(k); if ((planarAngle && k == planarAngle->FEATURE_ID_ANGLE) || (planarFourPointAngle && k == planarFourPointAngle->FEATURE_ID_ANGLE)) featureQuantity = featureQuantity * 180 / vnl_math::pi; infoText.append( QString("%1: %2 %3") .arg(QString( _PlanarFigure->GetFeatureName(k))) .arg(featureQuantity, 0, 'f', 2) .arg(QString(_PlanarFigure->GetFeatureUnit(k)))); plainInfoText.append( QString("\n%1: %2 %3") .arg(QString(_PlanarFigure->GetFeatureName(k))) .arg( featureQuantity, 0, 'f', 2) .arg(QString( _PlanarFigure->GetFeatureUnit(k)))); if(k+1 != _PlanarFigure->GetNumberOfFeatures()) infoText.append("
"); } if (j != d->m_CurrentSelection.size()) infoText.append("
"); } d->m_SelectedPlanarFiguresText->setHtml(infoText); } void QmitkMeasurementView::AddAllInteractors() { MEASUREMENT_DEBUG << "Adding interactors and observers to all planar figures"; mitk::DataStorage::SetOfObjects::ConstPointer planarFigures = this->GetAllPlanarFigures(); for(mitk::DataStorage::SetOfObjects::ConstIterator it=planarFigures->Begin(); it!=planarFigures->End(); it++) { this->NodeAdded( it.Value() ); } } void QmitkMeasurementView::RemoveAllInteractors() { MEASUREMENT_DEBUG << "Removing interactors and observers from all planar figures"; mitk::DataStorage::SetOfObjects::ConstPointer planarFigures = this->GetAllPlanarFigures(); for(mitk::DataStorage::SetOfObjects::ConstIterator it=planarFigures->Begin(); it!=planarFigures->End(); it++) { this->NodeRemoved( it.Value() ); } } mitk::DataNode::Pointer QmitkMeasurementView::DetectTopMostVisibleImage() { // get all images from the data storage which are not a segmentation mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinary = mitk::NodePredicateNot::New( isBinary ); mitk::NodePredicateAnd::Pointer isNormalImage = mitk::NodePredicateAnd::New( isImage, isNotBinary ); mitk::DataStorage::SetOfObjects::ConstPointer Images = this->GetDataStorage()->GetSubset( isNormalImage ); mitk::DataNode::Pointer currentNode; int maxLayer = itk::NumericTraits::min(); // iterate over selection for (mitk::DataStorage::SetOfObjects::ConstIterator sofIt = Images->Begin(); sofIt != Images->End(); ++sofIt) { mitk::DataNode::Pointer node = sofIt->Value(); if ( node.IsNull() ) continue; if (node->IsVisible(NULL) == false) continue; // we also do not want to assign planar figures to helper objects ( even if they are of type image ) if (node->GetProperty("helper object")) continue; int layer = 0; node->GetIntProperty("layer", layer); if ( layer < maxLayer ) { continue; } else { maxLayer = layer; currentNode = node; } } return currentNode; } void QmitkMeasurementView::EnableCrosshairNavigation() { MEASUREMENT_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MEASUREMENT_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); linkedRenderWindow->EnableSlicingPlanes(true); } } void QmitkMeasurementView::DisableCrosshairNavigation() { MEASUREMENT_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MEASUREMENT_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); linkedRenderWindow->EnableSlicingPlanes(false); } } mitk::DataStorage::SetOfObjects::ConstPointer QmitkMeasurementView::GetAllPlanarFigures() const { mitk::TNodePredicateDataType::Pointer isPlanarFigure = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isNotHelperObject = mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(false)); mitk::NodePredicateAnd::Pointer isNotHelperButPlanarFigure = mitk::NodePredicateAnd::New( isPlanarFigure, isNotHelperObject ); return this->GetDataStorage()->GetSubset( isPlanarFigure ); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp index 438fae704b..0a85bb0e1e 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp @@ -1,301 +1,302 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkImageMaskingWidget.h" +#include "mitkImage.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include #include #include #include #include #include #include static const char* const HelpText = "Select a regular image and a binary image"; QmitkImageMaskingWidget::QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls.setupUi(this); m_Controls.dataSelectionWidget->AddDataStorageComboBox(QmitkDataSelectionWidget::ImagePredicate); m_Controls.dataSelectionWidget->AddDataStorageComboBox(QmitkDataSelectionWidget::SegmentationPredicate); m_Controls.dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); connect (m_Controls.rbMaskImage, SIGNAL(toggled(bool)), this, SLOT(OnImageMaskingToggled(bool))); connect (m_Controls.rbMaskSurface, SIGNAL(toggled(bool)), this, SLOT(OnSurfaceMaskingToggled(bool))); connect (m_Controls.btnMaskImage, SIGNAL(pressed()), this, SLOT(OnMaskImagePressed())); connect(m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if( m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { this->OnSelectionChanged( 0, m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkImageMaskingWidget::~QmitkImageMaskingWidget() { } void QmitkImageMaskingWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNull() || node1.IsNull() ) { if( m_Controls.rbMaskImage->isChecked() ) { dataSelectionWidget->SetHelpText(HelpText); } else { dataSelectionWidget->SetHelpText("Select a regular image and a surface"); } this->EnableButtons(false); } else { this->SelectionControl(index, selection); } } void QmitkImageMaskingWidget::SelectionControl(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); //if Image-Masking is enabled, check if image-dimension of reference and binary image is identical if( m_Controls.rbMaskImage->isChecked() ) { if( dataSelectionWidget->GetSelection(0) == dataSelectionWidget->GetSelection(1) ) { dataSelectionWidget->SetHelpText("Select two different images above"); this->EnableButtons(false); return; } else if( node.IsNotNull() && selection ) { mitk::Image::Pointer referenceImage = dynamic_cast ( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Image::Pointer maskImage = dynamic_cast ( dataSelectionWidget->GetSelection(1)->GetData() ); if( referenceImage->GetLargestPossibleRegion().GetSize() != maskImage->GetLargestPossibleRegion().GetSize() ) { dataSelectionWidget->SetHelpText("Different image sizes cannot be masked"); this->EnableButtons(false); return; } } else { dataSelectionWidget->SetHelpText(HelpText); return; } } dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } void QmitkImageMaskingWidget::EnableButtons(bool enable) { m_Controls.btnMaskImage->setEnabled(enable); } void QmitkImageMaskingWidget::OnImageMaskingToggled(bool status) { if (status) { m_Controls.dataSelectionWidget->SetHelpText("Select a regular image and a binary image"); m_Controls.dataSelectionWidget->SetPredicate(1, QmitkDataSelectionWidget::SegmentationPredicate); } } void QmitkImageMaskingWidget::OnSurfaceMaskingToggled(bool status) { if (status) { m_Controls.dataSelectionWidget->SetHelpText("Select a regular image and a surface"); m_Controls.dataSelectionWidget->SetPredicate(1, QmitkDataSelectionWidget::SurfacePredicate); } } void QmitkImageMaskingWidget::OnMaskImagePressed() { //Disable Buttons during calculation and initialize Progressbar this->EnableButtons(false); mitk::ProgressBar::GetInstance()->AddStepsToDo(4); mitk::ProgressBar::GetInstance()->Progress(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; //create result image, get mask node and reference image mitk::Image::Pointer resultImage(0); mitk::DataNode::Pointer maskingNode = dataSelectionWidget->GetSelection(1); mitk::Image::Pointer referenceImage = static_cast(dataSelectionWidget->GetSelection(0)->GetData()); if(referenceImage.IsNull() || maskingNode.IsNull() ) { MITK_ERROR << "Selection does not contain an image"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain an image", QMessageBox::Ok ); m_Controls.btnMaskImage->setEnabled(true); return; } //Do Image-Masking if (m_Controls.rbMaskImage->isChecked()) { mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer maskImage = dynamic_cast ( maskingNode->GetData() ); if(maskImage.IsNull() ) { MITK_ERROR << "Selection does not contain a binary image"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a binary image", QMessageBox::Ok ); this->EnableButtons(); return; } if( referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) { resultImage = this->MaskImage( referenceImage, maskImage ); } } //Do Surface-Masking else { mitk::ProgressBar::GetInstance()->Progress(); //1. convert surface to image mitk::Surface::Pointer surface = dynamic_cast ( maskingNode->GetData() ); //TODO Get 3D Surface of current time step if(surface.IsNull()) { MITK_ERROR << "Selection does not contain a surface"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a surface", QMessageBox::Ok ); this->EnableButtons(); return; } mitk::Image::Pointer maskImage = this->ConvertSurfaceToImage( referenceImage, surface ); //2. mask reference image with mask image if(maskImage.IsNotNull() && referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) { resultImage = this->MaskImage( referenceImage, maskImage ); } } mitk::ProgressBar::GetInstance()->Progress(); if( resultImage.IsNull() ) { MITK_ERROR << "Masking failed"; QMessageBox::information( this, "Image and Surface Masking", "Masking failed. For more information please see logging window.", QMessageBox::Ok ); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(4); return; } //Add result to data storage this->AddToDataStorage( dataSelectionWidget->GetDataStorage(), resultImage, dataSelectionWidget->GetSelection(0)->GetName() + "_" + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(); } mitk::Image::Pointer QmitkImageMaskingWidget::MaskImage(mitk::Image::Pointer referenceImage, mitk::Image::Pointer maskImage ) { mitk::Image::Pointer resultImage(0); mitk::MaskImageFilter::Pointer maskFilter = mitk::MaskImageFilter::New(); maskFilter->SetInput( referenceImage ); maskFilter->SetMask( maskImage ); maskFilter->OverrideOutsideValueOn(); maskFilter->SetOutsideValue( referenceImage->GetStatistics()->GetScalarValueMin() ); try { maskFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return 0; } resultImage = maskFilter->GetOutput(); return resultImage; } mitk::Image::Pointer QmitkImageMaskingWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ) { mitk::ProgressBar::GetInstance()->AddStepsToDo(2); mitk::ProgressBar::GetInstance()->Progress(); mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->MakeOutputBinaryOn(); surfaceToImageFilter->SetInput(surface); surfaceToImageFilter->SetImage(image); try { surfaceToImageFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return 0; } mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer resultImage = mitk::Image::New(); resultImage = surfaceToImageFilter->GetOutput(); return resultImage; } void QmitkImageMaskingWidget::AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent ) { mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); dataNode->SetName(name); dataNode->SetData(segmentation); dataStorage->Add(dataNode, parent); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h index e370cefa40..79fca915ad 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h @@ -1,80 +1,84 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkImageMaskingWidget_h #define QmitkImageMaskingWidget_h #include "../QmitkSegmentationUtilityWidget.h" #include #include +namespace mitk { + class Image; +} + /*! \brief QmitkImageMaskingWidget Tool masks an image with a binary image or a surface. The Method requires an image and a binary image mask or a surface. The input image and the binary image mask must be of the same size. Masking with a surface creates first a binary image of the surface and then use this for the masking of the input image. */ class QmitkImageMaskingWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ explicit QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = NULL); /** @brief Defaul destructor. */ ~QmitkImageMaskingWidget(); private slots: /** @brief This slot is called if the selection in the workbench is changed. */ void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); /** @brief This slot is called if user activates the radio button for masking an image with a binary image mask. */ void OnImageMaskingToggled(bool); /** @brief This slot is called if user activates the radio button for masking an image with a surface. */ void OnSurfaceMaskingToggled(bool); /** @brief This slot is called if user activates the button to mask an image. */ void OnMaskImagePressed(); private: /** @brief Check if selections is valid. */ void SelectionControl( unsigned int index, const mitk::DataNode* selection); /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Mask an image with a given binary mask. Note that the input image and the mask image must be of the same size. */ - mitk::Image::Pointer MaskImage(mitk::Image::Pointer referenceImage, mitk::Image::Pointer maskImage ); + itk::SmartPointer MaskImage(itk::SmartPointer referenceImage, itk::SmartPointer maskImage ); /** @brief Convert a surface into an binary image. */ - mitk::Image::Pointer ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ); + itk::SmartPointer ConvertSurfaceToImage( itk::SmartPointer image, mitk::Surface::Pointer surface ); /** @brief Adds a new data object to the DataStorage.*/ - void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, + void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, itk::SmartPointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = NULL); Ui::QmitkImageMaskingWidgetControls m_Controls; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp index 02fe54b911..93304e5ef6 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp @@ -1,156 +1,158 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkSurfaceToImageWidget.h" #include #include #include #include #include +#include +#include #include static const char* const HelpText = "Select a regular image and a surface"; QmitkSurfaceToImageWidget::QmitkSurfaceToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls.setupUi(this); m_Controls.dataSelectionWidget->AddDataStorageComboBox(QmitkDataSelectionWidget::ImagePredicate); m_Controls.dataSelectionWidget->AddDataStorageComboBox(QmitkDataSelectionWidget::SurfacePredicate); m_Controls.dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); connect (m_Controls.btnSurface2Image, SIGNAL(pressed()), this, SLOT(OnSurface2ImagePressed())); connect(m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if( m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { this->OnSelectionChanged( 0, m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkSurfaceToImageWidget::~QmitkSurfaceToImageWidget() { } void QmitkSurfaceToImageWidget::EnableButtons(bool enable) { m_Controls.btnSurface2Image->setEnabled(enable); } void QmitkSurfaceToImageWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer surfaceNode = dataSelectionWidget->GetSelection(1); if (imageNode.IsNull() || surfaceNode.IsNull() ) { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } else { mitk::Image::Pointer image = dynamic_cast( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Surface::Pointer surface = dynamic_cast( dataSelectionWidget->GetSelection(1)->GetData() ); if( image->GetTimeSteps() != surface->GetTimeSteps() ) { dataSelectionWidget->SetHelpText("Image and surface are of different size"); this->EnableButtons(false); } else { dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } } } void QmitkSurfaceToImageWidget::OnSurface2ImagePressed() { this->EnableButtons(false); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::Image::Pointer image = dynamic_cast( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Surface::Pointer surface = dynamic_cast( dataSelectionWidget->GetSelection(1)->GetData() ); if( image.IsNull() || surface.IsNull()) { MITK_ERROR << "Selection does not contain an image and/or a surface"; QMessageBox::information( this, "Surface To Image", "Selection does not contain an image and/or a surface", QMessageBox::Ok ); this->EnableButtons(); return; } mitk::Image::Pointer resultImage(0); resultImage = this->ConvertSurfaceToImage( image, surface ); if( resultImage.IsNull() ) { MITK_ERROR << "Convert Surface to binary image failed"; QMessageBox::information( this, "Surface To Image", "Convert Surface to binary image failed", QMessageBox::Ok ); this->EnableButtons(); return; } //create name for result node std::string nameOfResultImage = dataSelectionWidget->GetSelection(0)->GetName(); nameOfResultImage.append("_"); nameOfResultImage.append(dataSelectionWidget->GetSelection(1)->GetName()); //create data node and add to data storage mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); resultNode->SetData( resultImage ); resultNode->SetProperty("name", mitk::StringProperty::New(nameOfResultImage) ); resultNode->SetProperty("binary", mitk::BoolProperty::New(true) ); dataSelectionWidget->GetDataStorage()->Add(resultNode, dataSelectionWidget->GetSelection(0)); this->EnableButtons(); } mitk::Image::Pointer QmitkSurfaceToImageWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ) { mitk::ProgressBar::GetInstance()->AddStepsToDo(2); mitk::ProgressBar::GetInstance()->Progress(); mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->MakeOutputBinaryOn(); surfaceToImageFilter->SetInput(surface); surfaceToImageFilter->SetImage(image); try { surfaceToImageFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return 0; } mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer resultImage = surfaceToImageFilter->GetOutput(); return resultImage; } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h index c773313ae6..ca3c7b9df8 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h @@ -1,64 +1,67 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkSurfaceToImageWidget_h #define QmitkSurfaceToImageWidget_h #include "../QmitkSegmentationUtilityWidget.h" #include -#include +namespace mitk { + class Surface; + class Image; +} /*! \brief QmitkSurfaceToImageWidget The Tool converts a surface to a binary image. The Method requires a surface and an image, which header information defines the output image. The resulting binary image has the same dimension, size, and Geometry3D as the input image. */ class QmitkSurfaceToImageWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ explicit QmitkSurfaceToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = NULL); /** @brief Defaul destructor. */ ~QmitkSurfaceToImageWidget(); private slots: /** @brief This slot is called if the selection in the workbench is changed. */ void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); /** @brief This slot is called if user activates the button to convert a surface into a binary image. */ void OnSurface2ImagePressed(); private: /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Convert a surface into an binary image. */ - mitk::Image::Pointer ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ); + itk::SmartPointer ConvertSurfaceToImage( itk::SmartPointer image, itk::SmartPointer surface ); Ui::QmitkSurfaceToImageWidgetControls m_Controls; }; #endif