diff --git a/Examples/Plugins/PluginList.cmake b/Examples/Plugins/PluginList.cmake index a5d1494e10..5cc18b92e2 100644 --- a/Examples/Plugins/PluginList.cmake +++ b/Examples/Plugins/PluginList.cmake @@ -1,26 +1,26 @@ # Plug-ins must be ordered according to their dependencies set(MITK_EXAMPLE_PLUGINS org.mitk.example.gui.minimalapplication:ON org.mitk.example.gui.customviewer:ON org.mitk.example.gui.customviewer.views:ON org.mitk.example.gui.multipleperspectives:ON org.mitk.example.gui.selectionserviceqt:ON org.mitk.example.gui.selectionservicemitk:ON org.mitk.example.gui.selectionservicemitk.views:ON org.mitk.example.gui.extensionpointdefinition:ON org.mitk.example.gui.extensionpointcontribution:ON org.mitk.example.gui.regiongrowing:ON org.mitk.example.gui.qmlapplication:ON - + org.mitk.example.gui.pcaexample:ON org.mitk.example.gui.imaging:ON ) if(MITK_USE_OpenCV) list(APPEND MITK_EXAMPLE_PLUGINS org.mitk.example.gui.opencv:ON) else() list(APPEND MITK_EXAMPLE_PLUGINS org.mitk.example.gui.opencv:OFF) endif() diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/CMakeLists.txt b/Examples/Plugins/org.mitk.example.gui.pcaexample/CMakeLists.txt new file mode 100644 index 0000000000..413b21feed --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/CMakeLists.txt @@ -0,0 +1,7 @@ +project(org_mitk_example_gui_pcaexample) + +mitk_create_plugin( + EXPORT_DIRECTIVE PCAEXAMPLE_EXPORT + EXPORTED_INCLUDE_SUFFIXES src + MODULE_DEPENDS MitkQtWidgetsExt +) diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox new file mode 100644 index 0000000000..e754d42a76 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/Manual.dox @@ -0,0 +1,17 @@ +/** +\page org_mitk_example_gui_pcaexample The Pcaexample + +\imageMacro{icon.png,"Icon of Pcaexample",2.00} + +\tableofcontents + +\section org_mitk_example_gui_pcaexampleOverview Overview +Describe the features of your awesome plugin here + + +*/ diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/icon.xpm b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/icon.xpm new file mode 100644 index 0000000000..9057c20bc6 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/UserManual/icon.xpm @@ -0,0 +1,21 @@ +/* XPM */ +static const char * icon_xpm[] = { +"16 16 2 1", +" c #FF0000", +". c #000000", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" "}; diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/doxygen/modules.dox b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/doxygen/modules.dox new file mode 100644 index 0000000000..244d3df107 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/documentation/doxygen/modules.dox @@ -0,0 +1,16 @@ +/** + \defgroup org_mitk_example_gui_pcaexample org.mitk.example.gui.pcaexample + \ingroup MITKPlugins + + \brief Describe your plugin here. + +*/ + +/** + \defgroup org_mitk_example_gui_pcaexample_internal Internal + \ingroup org_mitk_example_gui_pcaexample + + \brief This subcategory includes the internal classes of the org.mitk.example.gui.pcaexample plugin. Other + plugins must not rely on these classes. They contain implementation details and their interface + may change at any time. We mean it. +*/ diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/files.cmake b/Examples/Plugins/org.mitk.example.gui.pcaexample/files.cmake new file mode 100644 index 0000000000..3a72da1a47 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/files.cmake @@ -0,0 +1,42 @@ +set(SRC_CPP_FILES + +) + +set(INTERNAL_CPP_FILES + org_mitk_example_gui_pcaexample_Activator.cpp + PCAExample.cpp +) + +set(UI_FILES + src/internal/PCAExampleControls.ui +) + +set(MOC_H_FILES + src/internal/org_mitk_example_gui_pcaexample_Activator.h + src/internal/PCAExample.h +) + +# list of resource files which can be used by the plug-in +# system without loading the plug-ins shared library, +# for example the icon used in the menu and tabs for the +# plug-in views in the workbench +set(CACHED_RESOURCE_FILES + resources/icon.xpm + plugin.xml +) + +# list of Qt .qrc files which contain additional resources +# specific to this plugin +set(QRC_FILES + +) + +set(CPP_FILES ) + +foreach(file ${SRC_CPP_FILES}) + set(CPP_FILES ${CPP_FILES} src/${file}) +endforeach(file ${SRC_CPP_FILES}) + +foreach(file ${INTERNAL_CPP_FILES}) + set(CPP_FILES ${CPP_FILES} src/internal/${file}) +endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/manifest_headers.cmake b/Examples/Plugins/org.mitk.example.gui.pcaexample/manifest_headers.cmake new file mode 100644 index 0000000000..f37383eaa4 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/manifest_headers.cmake @@ -0,0 +1,5 @@ +set(Plugin-Name "Pcaexample") +set(Plugin-Version "0.1") +set(Plugin-Vendor "DKFZ") +set(Plugin-ContactAddress "") +set(Require-Plugin org.mitk.gui.qt.common) diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/plugin.xml b/Examples/Plugins/org.mitk.example.gui.pcaexample/plugin.xml new file mode 100644 index 0000000000..8a6998e8a6 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/plugin.xml @@ -0,0 +1,11 @@ + + + + + + + + diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/resources/icon.xpm b/Examples/Plugins/org.mitk.example.gui.pcaexample/resources/icon.xpm new file mode 100644 index 0000000000..04cb367f0b --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/resources/icon.xpm @@ -0,0 +1,69 @@ +/* XPM */ +static char * icon_xpm[] = { +"64 64 2 1", +" c None", +". c #000000", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" .... ", +" ............. .......... ...... ", +" .............. ............ ...... ", +" ............... .............. ...... ", +" ................ ...... ....... ........ ", +" ..... ..... ...... ...... ........ ", +" ..... ...... ..... ..... ........ ", +" ..... ..... ..... ..... ......... ", +" ..... ..... ..... ..... .......... ", +" ..... ..... ..... .... ..... ", +" ..... ..... ..... .... .... ", +" ..... ...... ..... ..... .... ", +" ..... ..... ..... ..... ..... ", +" ................ ..... .... ..... ", +" ............... ..... .... .... ", +" .............. ..... ..... .... ", +" ............. ..... ..... ..... ", +" .......... ..... .............. ", +" ..... ..... .............. ", +" ..... ..... ..... ................ ", +" ..... ..... ..... ................ ", +" ..... ..... ..... ..... ..... ", +" ..... ...... ...... ..... ..... ", +" ..... .............. ..... ..... ", +" ..... .............. ..... ..... ", +" ..... ............ ..... ..... ", +" ..... ........ ..... ..... ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" ", +" .. .. ", +" . . ", +" .. .. ... .... ", +" .. .. .... ..... ", +" .. .. .. . .. .. ", +" .. .. ..... .. .. ", +" .. .. .. .. .. ", +" .. .. .. . . ..... . ", +" . . .... .. ..... .. ", +" .. .. . ", +" .... ", +" .. ", +" ", +" ", +" ", +" "}; diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp new file mode 100644 index 0000000000..a4a939d8dc --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp @@ -0,0 +1,167 @@ +/*=================================================================== + +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 + +// Qmitk +#include "PCAExample.h" + +// Qt +#include + +// mitk image +#include + +const std::string PCAExample::VIEW_ID = "org.mitk.views.pcaexample"; + +void PCAExample::SetFocus() +{ + m_Controls.buttonPerformImageProcessing->setFocus(); +} + +void PCAExample::CreateQtPartControl(QWidget *parent) +{ + // create GUI widgets from the Qt Designer's .ui file + m_Controls.setupUi(parent); + connect(m_Controls.buttonPerformImageProcessing, SIGNAL(clicked()), this, SLOT(BtnPerfomPCAClicked())); + + //initialize point set widget and point set node + mitk::DataNode::Pointer PointSetNode = mitk::DataNode::New(); + PointSetNode->SetName("PCA Example Pointset"); + mitk::PointSet::Pointer newPtSet = mitk::PointSet::New(); + PointSetNode->SetData(newPtSet); + m_Controls.m_pointSetWidget->SetPointSetNode(PointSetNode); + this->GetDataStorage()->Add(PointSetNode); +} + +PCAExample::PCAExample() +{ + +} + +PCAExample::~PCAExample() +{ + //clean up + mitk::DataNode::Pointer ptSetNode = m_Controls.m_pointSetWidget->GetPointSetNode(); + m_Controls.m_pointSetWidget->SetPointSetNode(NULL); + this->GetDataStorage()->Remove(ptSetNode); + this->GetDataStorage()->Remove(m_Axis1Node); + this->GetDataStorage()->Remove(m_Axis2Node); + this->GetDataStorage()->Remove(m_Axis3Node); +} + +void PCAExample::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, + const QList &nodes) +{ + // iterate all selected objects, adjust warning visibility + foreach (mitk::DataNode::Pointer node, nodes) + { + if (node.IsNotNull() && dynamic_cast(node->GetData())) + { + m_Controls.buttonPerformImageProcessing->setEnabled(true); + return; + } + } + +} + +void PCAExample::BtnPerfomPCAClicked() +{ + std::vector eigenVectors; + std::vector eigenValues; + mitk::Vector3D mean; + bool success = comutePCA(m_Controls.m_pointSetWidget->GetPointSet(), eigenVectors, eigenValues, mean); + this->showEigenvectors(eigenVectors, eigenValues, mean); + MITK_INFO << "PCA: " << success; +} + +bool PCAExample::comutePCA(mitk::PointSet::Pointer input, std::vector &eigenVectors, std::vector &eigenValues, mitk::Vector3D &pointsMean) +{ +//Step 1: Construct data matrix +vnl_matrix dataMatrix(3, input->GetSize(), 0.0); +int size = input->GetSize(); +for (int i=0; iGetPoint(i)[0]; + dataMatrix[1][i] = input->GetPoint(i)[1]; + dataMatrix[2][i] = input->GetPoint(i)[2]; +} + +//Step 2: Remove average for each row (Mittelwertbefreiung) +mitk::Vector3D mean; +for (int i = 0; i < size; i++) { mean += mitk::Vector3D(dataMatrix.get_column(i)); } +mean /= size; +for (int i = 0; i covMatrix = (1.0 / (size - 1.0)) * dataMatrix * dataMatrix.transpose(); + +//Step 4: Singular value composition +vnl_svd svd(covMatrix); + +//Store results and print them to the console +MITK_INFO << "DataMatrix: " << "\n" << dataMatrix; +MITK_INFO << "CovMatrix: " << "\n" << covMatrix; +for (int i = 0; i < 3; i++) +{ + eigenVectors.push_back(svd.U().get_column(i)); + eigenValues.push_back(sqrt(svd.W(i))); + MITK_INFO << "Eigenvector " << i << ": " << eigenVectors.at(i); + MITK_INFO << "Eigenvalue " << i << ": " << eigenValues.at(i); +} + +//Compute center of points +for (int i = 0; i < size; i++) { pointsMean += input->GetPoint(i).GetVectorFromOrigin(); } +pointsMean /= size; + +return true; +} + +void PCAExample::showEigenvectors(std::vector eigenVectors, std::vector eigenValues, mitk::Vector3D center) +{ + m_Axis1Node = mitk::DataNode::New(); + m_Axis1Node->SetName("Eigenvector 1"); + mitk::PointSet::Pointer axis1 = mitk::PointSet::New(); + axis1->InsertPoint(0, center); + axis1->InsertPoint(1, (center + eigenVectors.at(0)*eigenValues.at(0))); + m_Axis1Node->SetData(axis1); + m_Axis1Node->SetBoolProperty("show contour", true); + m_Axis1Node->SetColor(1, 0, 0); + this->GetDataStorage()->Add(m_Axis1Node); + + m_Axis2Node = mitk::DataNode::New(); + m_Axis2Node->SetName("Eigenvector 2"); + mitk::PointSet::Pointer axis2 = mitk::PointSet::New(); + axis2->InsertPoint(0, center); + axis2->InsertPoint(1, (center + eigenVectors.at(1)*eigenValues.at(1))); + m_Axis2Node->SetData(axis2); + m_Axis2Node->SetBoolProperty("show contour", true); + m_Axis2Node->SetColor(1, 0, 0); + this->GetDataStorage()->Add(m_Axis2Node); + + m_Axis3Node = mitk::DataNode::New(); + m_Axis3Node->SetName("Eigenvector 3"); + mitk::PointSet::Pointer axis3 = mitk::PointSet::New(); + axis3->InsertPoint(0, center); + axis3->InsertPoint(1, (center + eigenVectors.at(2)*eigenValues.at(2))); + m_Axis3Node->SetData(axis3); + m_Axis3Node->SetBoolProperty("show contour", true); + m_Axis3Node->SetColor(1, 0, 0); + this->GetDataStorage()->Add(m_Axis3Node); +} \ No newline at end of file diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.h b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.h new file mode 100644 index 0000000000..0f43ea36e6 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.h @@ -0,0 +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 PCAExample_h +#define PCAExample_h + +#include + +#include + +#include "ui_PCAExampleControls.h" + +/** + \brief PCAExample + + \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 PCAExample : public QmitkAbstractView +{ + // this is needed for all Qt objects that should have a Qt meta-object + // (everything that derives from QObject and wants to have signal/slots) + Q_OBJECT + +public: + static const std::string VIEW_ID; + + PCAExample(); + + virtual ~PCAExample(); + +protected slots: + + /// \brief Called when the user clicks the GUI button + void BtnPerfomPCAClicked(); + +protected: + virtual void CreateQtPartControl(QWidget *parent) override; + + virtual void SetFocus() override; + + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, + const QList &nodes) override; + + /** Performs a PCA on a (3D) point set. + * @param input Point set to work on. + * @param[out] eigenVectors Eigenvectors as computed by the PCA. Returns an empty vector + * if PCA failed or did not run before. + * @param[out] eigenValues Eigenvalues as computed by the PCA. Returns an empty vector + * if PCA failed or did not run before. The ID inside the vector + * corresponds to the ID inside the eigenvector vector. For a 3D + * pointset 3 eigenvalues and -vectors will be computed. + * @param[out] pointsMean Returns the mean/center of the pointset + */ + bool comutePCA(mitk::PointSet::Pointer input, std::vector &eigenVectors, std::vector &eigenValues, mitk::Vector3D &pointsMean); + + /** Adds mitk data nodes for all eigenvectors to visualize them in the multi widget. */ + void showEigenvectors(std::vector eigenVectors, std::vector eigenValues, mitk::Vector3D center); + + mitk::DataNode::Pointer m_Axis1Node; + mitk::DataNode::Pointer m_Axis2Node; + mitk::DataNode::Pointer m_Axis3Node; + + Ui::PCAExampleControls m_Controls; +}; + +#endif // PCAExample_h diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExampleControls.ui b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExampleControls.ui new file mode 100644 index 0000000000..a9daab997d --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExampleControls.ui @@ -0,0 +1,72 @@ + + + PCAExampleControls + + + + 0 + 0 + 222 + 688 + + + + + 0 + 0 + + + + QmitkTemplate + + + + + + + 0 + 250 + + + + + + + + Do image processing + + + Perform PCA + + + + + + + Qt::Vertical + + + QSizePolicy::Expanding + + + + 20 + 220 + + + + + + + + + + QmitkPointListWidget + QWidget +
QmitkPointListWidget.h
+ 1 + + + + + diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/org_mitk_example_gui_pcaexample_Activator.cpp b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/org_mitk_example_gui_pcaexample_Activator.cpp new file mode 100644 index 0000000000..76e75338e1 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/org_mitk_example_gui_pcaexample_Activator.cpp @@ -0,0 +1,29 @@ +/*=================================================================== + +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 "org_mitk_example_gui_pcaexample_Activator.h" +#include "PCAExample.h" + +namespace mitk +{ + void org_mitk_example_gui_pcaexample_Activator::start(ctkPluginContext *context) + { + BERRY_REGISTER_EXTENSION_CLASS(PCAExample, context) + } + + void org_mitk_example_gui_pcaexample_Activator::stop(ctkPluginContext *context) { Q_UNUSED(context) } +} diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/org_mitk_example_gui_pcaexample_Activator.h b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/org_mitk_example_gui_pcaexample_Activator.h new file mode 100644 index 0000000000..d80ec16e35 --- /dev/null +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/org_mitk_example_gui_pcaexample_Activator.h @@ -0,0 +1,38 @@ +/*=================================================================== + +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 org_mitk_example_gui_pcaexample_Activator_h +#define org_mitk_example_gui_pcaexample_Activator_h + +#include + +namespace mitk +{ + class org_mitk_example_gui_pcaexample_Activator : public QObject, public ctkPluginActivator + { + Q_OBJECT + Q_PLUGIN_METADATA(IID "org_mitk_example_gui_pcaexample") + Q_INTERFACES(ctkPluginActivator) + + public: + void start(ctkPluginContext *context); + void stop(ctkPluginContext *context); + + }; // org_mitk_example_gui_pcaexample_Activator +} + +#endif // org_mitk_example_gui_pcaexample_Activator_h