diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake index 207ffc1166..c53a565007 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake @@ -1,205 +1,207 @@ set(SRC_CPP_FILES QmitkODFDetailsWidget.cpp QmitkODFRenderWidget.cpp QmitkPartialVolumeAnalysisWidget.cpp QmitkIVIMWidget.cpp QmitkTbssRoiAnalysisWidget.cpp QmitkResidualAnalysisWidget.cpp QmitkResidualViewWidget.cpp QmitkTensorModelParametersWidget.cpp QmitkZeppelinModelParametersWidget.cpp QmitkStickModelParametersWidget.cpp QmitkDotModelParametersWidget.cpp QmitkBallModelParametersWidget.cpp QmitkAstrosticksModelParametersWidget.cpp QmitkPrototypeSignalParametersWidget.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkQBallReconstructionView.cpp QmitkPreprocessingView.cpp QmitkDiffusionDicomImportView.cpp QmitkDiffusionQuantificationView.cpp QmitkTensorReconstructionView.cpp QmitkControlVisualizationPropertiesView.cpp QmitkODFDetailsView.cpp QmitkGibbsTrackingView.cpp QmitkStochasticFiberTrackingView.cpp QmitkStreamlineTrackingView.cpp QmitkFiberProcessingView.cpp # QmitkFiberBundleDeveloperView.cpp QmitkPartialVolumeAnalysisView.cpp QmitkIVIMView.cpp QmitkTractbasedSpatialStatisticsView.cpp QmitkTbssTableModel.cpp QmitkTbssMetaTableModel.cpp QmitkTbssSkeletonizationView.cpp Connectomics/QmitkConnectomicsDataView.cpp Connectomics/QmitkConnectomicsNetworkOperationsView.cpp Connectomics/QmitkConnectomicsStatisticsView.cpp Connectomics/QmitkNetworkHistogramCanvas.cpp Connectomics/QmitkRandomParcellationView.cpp QmitkDwiSoftwarePhantomView.cpp QmitkOdfMaximaExtractionView.cpp QmitkFiberfoxView.cpp QmitkFiberExtractionView.cpp QmitkFieldmapGeneratorView.cpp QmitkDiffusionRegistrationView.cpp QmitkDenoisingView.cpp Perspectives/QmitkFiberProcessingPerspective.cpp Perspectives/QmitkDiffusionImagingAppPerspective.cpp Perspectives/QmitkGibbsTractographyPerspective.cpp Perspectives/QmitkStreamlineTractographyPerspective.cpp Perspectives/QmitkProbabilisticTractographyPerspective.cpp Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp Perspectives/QmitkDIAppIVIMPerspective.cpp + Perspectives/QmitkDiffusionDefaultPerspective.cpp ) set(UI_FILES src/internal/QmitkQBallReconstructionViewControls.ui src/internal/QmitkPreprocessingViewControls.ui src/internal/QmitkDiffusionDicomImportViewControls.ui src/internal/QmitkDiffusionQuantificationViewControls.ui src/internal/QmitkTensorReconstructionViewControls.ui src/internal/QmitkControlVisualizationPropertiesViewControls.ui src/internal/QmitkODFDetailsViewControls.ui src/internal/QmitkGibbsTrackingViewControls.ui src/internal/QmitkStochasticFiberTrackingViewControls.ui src/internal/QmitkStreamlineTrackingViewControls.ui src/internal/QmitkFiberProcessingViewControls.ui # src/internal/QmitkFiberBundleDeveloperViewControls.ui src/internal/QmitkPartialVolumeAnalysisViewControls.ui src/internal/QmitkIVIMViewControls.ui src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui src/internal/QmitkTbssSkeletonizationViewControls.ui src/internal/Connectomics/QmitkConnectomicsDataViewControls.ui src/internal/Connectomics/QmitkConnectomicsNetworkOperationsViewControls.ui src/internal/Connectomics/QmitkConnectomicsStatisticsViewControls.ui src/internal/Connectomics/QmitkRandomParcellationViewControls.ui src/internal/QmitkDwiSoftwarePhantomViewControls.ui src/internal/QmitkOdfMaximaExtractionViewControls.ui src/internal/QmitkFiberfoxViewControls.ui src/internal/QmitkFiberExtractionViewControls.ui src/QmitkTensorModelParametersWidgetControls.ui src/QmitkZeppelinModelParametersWidgetControls.ui src/QmitkStickModelParametersWidgetControls.ui src/QmitkDotModelParametersWidgetControls.ui src/QmitkBallModelParametersWidgetControls.ui src/QmitkAstrosticksModelParametersWidgetControls.ui src/QmitkPrototypeSignalParametersWidgetControls.ui src/internal/QmitkFieldmapGeneratorViewControls.ui src/internal/QmitkDiffusionRegistrationViewControls.ui src/internal/QmitkDenoisingViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkQBallReconstructionView.h src/internal/QmitkPreprocessingView.h src/internal/QmitkDiffusionDicomImportView.h src/internal/QmitkDiffusionQuantificationView.h src/internal/QmitkTensorReconstructionView.h src/internal/QmitkControlVisualizationPropertiesView.h src/internal/QmitkODFDetailsView.h src/QmitkODFRenderWidget.h src/QmitkODFDetailsWidget.h src/internal/QmitkGibbsTrackingView.h src/internal/QmitkStochasticFiberTrackingView.h src/internal/QmitkStreamlineTrackingView.h src/internal/QmitkFiberProcessingView.h # src/internal/QmitkFiberBundleDeveloperView.h src/internal/QmitkPartialVolumeAnalysisView.h src/QmitkPartialVolumeAnalysisWidget.h src/internal/QmitkIVIMView.h src/internal/QmitkTractbasedSpatialStatisticsView.h src/internal/QmitkTbssSkeletonizationView.h src/QmitkTbssRoiAnalysisWidget.h src/QmitkResidualAnalysisWidget.h src/QmitkResidualViewWidget.h src/internal/Connectomics/QmitkConnectomicsDataView.h src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h src/internal/Connectomics/QmitkConnectomicsStatisticsView.h src/internal/Connectomics/QmitkNetworkHistogramCanvas.h src/internal/Connectomics/QmitkRandomParcellationView.h src/internal/QmitkDwiSoftwarePhantomView.h src/internal/QmitkOdfMaximaExtractionView.h src/internal/QmitkFiberfoxView.h src/internal/QmitkFiberExtractionView.h src/QmitkTensorModelParametersWidget.h src/QmitkZeppelinModelParametersWidget.h src/QmitkStickModelParametersWidget.h src/QmitkDotModelParametersWidget.h src/QmitkBallModelParametersWidget.h src/QmitkAstrosticksModelParametersWidget.h src/QmitkPrototypeSignalParametersWidget.h src/internal/QmitkFieldmapGeneratorView.h src/internal/QmitkDiffusionRegistrationView.h src/internal/QmitkDenoisingView.h src/internal/Perspectives/QmitkFiberProcessingPerspective.h src/internal/Perspectives/QmitkDiffusionImagingAppPerspective.h src/internal/Perspectives/QmitkGibbsTractographyPerspective.h src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h src/internal/Perspectives/QmitkProbabilisticTractographyPerspective.h src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h src/internal/Perspectives/QmitkDIAppIVIMPerspective.h + src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h ) set(CACHED_RESOURCE_FILES # 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 plugin.xml resources/preprocessing.png resources/dwiimport.png resources/quantification.png resources/reconodf.png resources/recontensor.png resources/vizControls.png resources/OdfDetails.png resources/GibbsTracking.png resources/FiberBundleOperations.png resources/PartialVolumeAnalysis_24.png resources/IVIM_48.png resources/stochFB.png resources/tbss.png resources/connectomics/QmitkConnectomicsDataViewIcon_48.png resources/connectomics/QmitkConnectomicsNetworkOperationsViewIcon_48.png resources/connectomics/QmitkConnectomicsStatisticsViewIcon_48.png resources/connectomics/QmitkRandomParcellationIcon.png resources/arrow.png resources/qball_peaks.png resources/phantom.png resources/tensor.png resources/qball.png resources/StreamlineTracking.png resources/dwi2.png resources/odf.png resources/refresh.xpm resources/diffusionregistration.png resources/denoisingicon.png resources/syntheticdata.png resources/ivim.png resources/tractography.png ) set(QRC_FILES # uncomment the following line if you want to use Qt resources resources/QmitkDiffusionImaging.qrc #resources/QmitkTractbasedSpatialStatisticsView.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml index cfda0a2210..3f112d95f3 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml @@ -1,359 +1,371 @@ + + + + + Q-Ball reconstruction view Diffusion DICOM data import Calculation of tensor and Q-ball derived measures. Diffusion weighted MRI data simulation tool. This perspective contains all views necessary to post process fibers. + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.cpp new file mode 100644 index 0000000000..6cc83b47ac --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.cpp @@ -0,0 +1,43 @@ +/*=================================================================== + +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 "QmitkDiffusionDefaultPerspective.h" +#include "berryIViewLayout.h" + +void QmitkDiffusionDefaultPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) +{ + ///////////////////////////////////////////////////// + // all di-app perspectives should have the following: + ///////////////////////////////////////////////////// + + std::string editorArea = layout->GetEditorArea(); + + layout->AddStandaloneView("org.mitk.views.viewnavigatorview", false, berry::IPageLayout::LEFT, 0.25f, editorArea); + + layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); + + layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); + + berry::IFolderLayout::Pointer left = + layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); + + layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); + + ///////////////////////////////////////////// + // here goes the perspective specific stuff + ///////////////////////////////////////////// + +} diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h new file mode 100644 index 0000000000..526c83e548 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h @@ -0,0 +1,36 @@ +/*=================================================================== + +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 QmitkDiffusionDefaultPerspective_H_ +#define QmitkDiffusionDefaultPerspective_H_ + +#include + +class QmitkDiffusionDefaultPerspective : public QObject, public berry::IPerspectiveFactory +{ + Q_OBJECT + Q_INTERFACES(berry::IPerspectiveFactory) + +public: + + QmitkDiffusionDefaultPerspective() {} + ~QmitkDiffusionDefaultPerspective() {} + + void CreateInitialLayout(berry::IPageLayout::Pointer layout); +}; + +#endif /* QmitkDiffusionDefaultPerspective_H_ */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp index 4037a8a75b..08127067a6 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp @@ -1,59 +1,60 @@ /*=================================================================== 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 "QmitkFiberProcessingPerspective.h" #include "berryIViewLayout.h" QmitkFiberProcessingPerspective::QmitkFiberProcessingPerspective() { } QmitkFiberProcessingPerspective::QmitkFiberProcessingPerspective(const QmitkFiberProcessingPerspective& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } void QmitkFiberProcessingPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// std::string editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.1f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// left->AddView("org.mitk.views.fiberextraction"); left->AddView("org.mitk.views.fiberprocessing"); + left->AddView("org.mitk.views.segmentation"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp index b027ead130..36f711d20d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp @@ -1,102 +1,104 @@ /*=================================================================== 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 #include "src/internal/Perspectives/QmitkDiffusionImagingAppPerspective.h" #include "src/internal/Perspectives/QmitkDIAppIVIMPerspective.h" #include "src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h" #include "src/internal/Perspectives/QmitkGibbsTractographyPerspective.h" #include "src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h" #include "src/internal/Perspectives/QmitkProbabilisticTractographyPerspective.h" #include "src/internal/Perspectives/QmitkFiberProcessingPerspective.h" +#include "src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h" #include "src/internal/QmitkQBallReconstructionView.h" #include "src/internal/QmitkPreprocessingView.h" #include "src/internal/QmitkDiffusionDicomImportView.h" #include "src/internal/QmitkDiffusionQuantificationView.h" #include "src/internal/QmitkTensorReconstructionView.h" #include "src/internal/QmitkControlVisualizationPropertiesView.h" #include "src/internal/QmitkODFDetailsView.h" #include "src/internal/QmitkGibbsTrackingView.h" #include "src/internal/QmitkStochasticFiberTrackingView.h" #include "src/internal/QmitkFiberProcessingView.h" #include "src/internal/QmitkPartialVolumeAnalysisView.h" #include "src/internal/QmitkIVIMView.h" #include "src/internal/QmitkTractbasedSpatialStatisticsView.h" #include "src/internal/QmitkTbssSkeletonizationView.h" #include "src/internal/QmitkStreamlineTrackingView.h" #include "src/internal/Connectomics/QmitkConnectomicsDataView.h" #include "src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h" #include "src/internal/Connectomics/QmitkConnectomicsStatisticsView.h" #include "src/internal/Connectomics/QmitkRandomParcellationView.h" #include "src/internal/QmitkOdfMaximaExtractionView.h" #include "src/internal/QmitkFiberfoxView.h" #include "src/internal/QmitkFiberExtractionView.h" #include "src/internal/QmitkFieldmapGeneratorView.h" #include "src/internal/QmitkDiffusionRegistrationView.h" #include "src/internal/QmitkDenoisingView.h" namespace mitk { void PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingAppPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTractographyPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTractographyPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkProbabilisticTractographyPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDIAppSyntheticDataGenerationPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDIAppIVIMPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingPerspective, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDefaultPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDicomImport, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkControlVisualizationPropertiesView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkODFDetailsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStochasticFiberTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPartialVolumeAnalysisView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkIVIMView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTractbasedSpatialStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTbssSkeletonizationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsDataView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsNetworkOperationsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkOdfMaximaExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberfoxView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFieldmapGeneratorView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionRegistrationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDenoisingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkRandomParcellationView, context) } void PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) } } Q_EXPORT_PLUGIN2(org_mitk_gui_qt_diffusionimaging, mitk::PluginActivator) diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js index 37c853c483..f5bbf10fc7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js @@ -1,323 +1,323 @@ // If you want to create a new button you have to add some data (strings) to the following five arrays. // Make sure that you add your data at the same position in each array. // The buttons will be generated in order to the array's index. e.g. data at array's index '0' will generate the first button. // enter the name of your module here var moduleNames = new Array("Dicom Import", "IVIM", "Preprocessing", "Quantification", "Tractography", "Connectomics", "Synthetic Data", "Registration", "Image Processing", "Visualization", "Utilities", "MITK Downloads & News"); // add the MITK-link to your module -var moduleLinks = new Array("mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.dicomimport?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.ivim?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.preprocessingreconstruction?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.quantification?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.tractography?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.connectomics?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.syntheticdata?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.registration?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.imageprocessing?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.visualization?clear=false", - "mitk://mitk.perspectives/org.mitk.diffusionimagingapp.perspectives.utility?clear=false", +var moduleLinks = new Array("mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", + "mitk://mitk.perspectives/org.mitk.perspectives.diffusiondefault?clear=false", "http://www.mitk.org"); // add the filename of your icon for the module. Place the picture in subdirectory "pics". // The picture's width should be 136 pixel; the height 123 pixel. var picFilenames = new Array("01dicomimport.png", "07ivim.png", "02preprocessingreconstruction.png", "03quantification.png", "04tractography.png", "06connectomics.png", "10softwarephantoms.png", "12registration.png", "11segmentation.png", "08volumevisualization.png", "13utilities.png", "button_mitk.png"); // if you want to create an animated icon, add the name of your animated gif (placed in subdirectory "pics"). Otherwise enter an empty string "". // The animation's width should be 136 pixel; the height 123 pixel. var aniFilenames = new Array("01adicomimport.png", "07aivim.png", "02apreprocessingreconstruction.png", "03aquantification.png", "04atractography.png", "06aconnectomics.png", "10asoftwarephantoms.png", "12aregistration.png", "11asegmentation.png", "08avolumevisualization.png", "13autilities.png", "button_mitka.png"); // if your module is not stable, you can mark it as experimental. // just set true for experimental or false for stable. var experimental = new Array(false, false, false, false, false, false, false, true, false, false, false, false); // add the description for your module. The description is displayed in a PopUp-window. -var moduleDescriptions = new Array("'Dicom Import' supports direct import of Siemens diffusion weighted DICOM files.", - "'IVIM' stands for Intravoxel Incoherent Motion. The technique allows for the estimation of tissue perfusion on basis of diffusion measurements. Several models are supported by this module. Interactive exploration of the data is supported.", - "'Preprocessing & Reconstruction' lets you estimate diffusion tensors or q-balls using different reconstruction methods and calculates scalar indices (FA, GFA, ...). It also includes an ODF Peak Extraction view and preprocessing steps like gradient avaraging or reduction and baseline image extraction.", - "'Quantification' allows partial volume analysis and the evaluation and exploration of Tract Based Spatial Statistic datasets (it does NOT reimplement the TBSS methods available in FSL). The Partial Volume Analysis view provides a very robust method for semi-automatic ROI analysis. It uses EM clustering to probabilistically segment fiber vs. non-fiber vs. partial volume.", - "'Tractography' implements several fiber tractography algorithms (global, probabilistic and streamline). The fiber bundle operations view allows for extraction, join, and substraction of bundles. It also generates a variety of images from given fiber tracts and gives detailed information about the fiberbundle itself.", - "'Connectomics' aims at building graphs (nodes and edges) from a global tractogram and applying graph theory for data analysis. fMRI-data might be incorporated in future.", - "'Synthetic Data' contains the Fiberfox software phantom tool as well as instruments like tract density image or fiber envelope generation.", - "'Registration' provides views for rigid and point based image registration (only non-diffusion!).", - "'Image Processing' provides tools for image segmentation and diffusion unrelated image processing.", - "'Visualization' provides easy to use and fast volume rendering of images, means to capture high resolution screenshots as well as movies of the 3D sceen.", - "'Utilities' provides the property list view to modify the properties of the selected data node as well as a logging view for debugging purposes.", +var moduleDescriptions = new Array("MITK Diffusion supports direct import of Siemens diffusion weighted DICOM files.", + "You can use Intravoxel Incoherent Motion to estimate tissue perfusion on basis of diffusion measurements. Several models and interactive exploration of the data are supported.", + "You can use MITK Diffusion to preprocess diffusion weighted MR Images using techniques like gradient averaging or reduction and baseline image extraction. Then you can estimate diffusion tensors or q-balls using different reconstruction methods and calculates scalar indices (FA, GFA, ...).", + "MITK Diffusion allows partial volume analysis and the evaluation and exploration of Tract Based Spatial Statistic datasets (it does NOT reimplement the TBSS methods available in FSL). The Partial Volume Analysis view provides a very robust method for semi-automatic ROI analysis. It uses EM clustering to probabilistically segment fiber vs. non-fiber vs. partial volume.", + "The tractography components of MITK Diffusion implement several fiber tractography algorithms (global, probabilistic and streamline). The fiber bundle operations view allows for extraction, join, and substraction of bundles. It also generates a variety of images from given fiber tracts and gives detailed information about the fiberbundle itself.", + "Connectomics aims at building graphs (nodes and edges) from a global tractogram and applying graph theory for data analysis.", + "The Fiberfox software phantom tool allows you to create synthetic phantoms easily and with a wide variety of properties and options.", + "Registration views allow for rigid and point based image registration (only non-diffusion!).", + "MITK Diffusion provides tools for image segmentation and diffusion unrelated image processing.", + "In order to visually present your research MITK Diffusion contains fast volume rendering of images, means to capture high resolution screenshots as well as movies of the 3D sceen.", + "Further utilites include the property list view to modify the properties of the selected data node as well as a logging view for debugging purposes.", "Open the MITK website in an external browser."); var bttns = new Array(); var d = document, da = d.all; // holds id of current mouseover-HTML-element var currentTarget; // get the id of current mouseover-HTML-element d.onmouseover = function(o){ var e = da ? event.srcElement : o.target; currentTarget = e.id; } // build-function called by onload-event in HTML-document function createButtons(){ for (i=0; i < moduleNames.length; i++){ bttns[i] = new Button(moduleNames[i],moduleLinks[i], picFilenames[i], aniFilenames[i],moduleDescriptions[i]); bttns[i].createButton(); } for (i=0; i < moduleNames.length; i++){ if(experimental[i]){ setExperimental(i); } } createClearFloat(); } // Class Button function Button(moduleName, moduleLink, picFilename, aniFilename, moduleDescr){ // Properties this.bttnID = "bttn" + moduleName; this.modName = moduleName; this.modLink = moduleLink; this.picPath = "pics/" + picFilename; this.aniPath = "pics/" + aniFilename; this.modDescr = moduleDescr; // Methods this.createButton = function(){ // get DIV-wrapper for Button and append it to HTML-document bttnWrapper = this.createWrapper(); document.getElementById("bttnField").appendChild(bttnWrapper); // get link-element for picture and append it to DIV-wrapper bttnPicLink = this.createPicLink(); bttnWrapper.appendChild(bttnPicLink); // set HTML attributes for button-element bttn = document.createElement("img"); bttn.src = this.picPath; bttn.id = this.bttnID; bttn.className = "modBttn"; bttn.height = 123; bttn.width = 136; bttn.onmouseover = function(){startAni(this.id);}; bttn.onmouseout = function(){stopAni(this.id);}; // append button to link-element bttnPicLink.appendChild(bttn); // create text-link and add it to DIV-wrapper bttnTxtLink = document.createElement("a"); bttnTxtLink.href = this.modLink; bttnTxtLink.className = "txtLink"; bttnTxtLink.appendChild(document.createTextNode(this.modName)); bttnWrapper.appendChild(bttnTxtLink); // create pop-up link for module description bttnPopUpLink = document.createElement("a"); modName = this.modName; modDescr = this.modDescr; bttnPopUpLink.onclick = function(){showPopUpWindow();}; bttnPopUpLink.className = "popUpLink"; bttnPopUpLink.id = "popup" + this.modName; bttnPopUpLink.appendChild(document.createTextNode("more info >>")); bttnWrapper.appendChild(document.createElement("br")); bttnWrapper.appendChild(bttnPopUpLink); return bttn; } this.createWrapper = function(){ bttnWrapper = document.createElement("div"); bttnWrapper.id = "wrapper" + this.modName; bttnWrapper.className = "bttnWrap"; return bttnWrapper; } this.createPicLink = function(){ picLink = document.createElement("a"); picLink.href = this.modLink; picLink.id = "link" + this.modName; return picLink; } } function showPopUpWindow(){ // modules position in array? modulePos = getPos(currentTarget,"popup"); // get reference to anchor-element in HTML-document popUpAnchor = document.getElementById("popupAnchor"); // check if a popUp is open if(popUpAnchor.hasChildNodes()){ // if a popUp is open, remove it! popUpAnchor.removeChild(document.getElementById("popup")); } // create new container for popUp container = document.createElement("div"); container.id = "popup"; container.align = "right"; // append popUp-container to HTML-document popUpAnchor.appendChild(container); // create close-button and append it to popUp-container bttnClose = document.createElement("img"); bttnClose.src = "pics/popup_bttn_close.png"; bttnClose.id = "bttnClose"; bttnClose.onclick = function(){closeInfoWindow();}; container.appendChild(bttnClose); // create container for content-elements contHeadline = document.createElement("div"); contHeadline.id = "contHeadline"; contDescription = document.createElement("div"); contDescription.id = "contDescription"; contModLink = document.createElement("div"); contModLink.id = "contModLink"; // append content-container to popUp-container container.appendChild(contHeadline); container.appendChild(contDescription); container.appendChild(contModLink); // create text-elements with content headline = document.createTextNode(moduleNames[modulePos] + " "); description = document.createTextNode(moduleDescriptions[modulePos]); moduleLink = document.createElement("a"); moduleLink.href = moduleLinks[modulePos] ; moduleLink.className = 'moduleLink'; moduleLinkTxt = document.createTextNode("Click here to open '" + moduleNames[modulePos].toLowerCase() + "'"); moduleLink.appendChild(moduleLinkTxt); // append text-elements to their container contHeadline.appendChild(headline); contDescription.appendChild(description); - contModLink.appendChild(moduleLink); + //contModLink.appendChild(moduleLink); } function getPos(id,prefix){ if(prefix == "popup"){ targetID = id.slice(5); }else{ if(prefix == "bttn"){ targetID = id.slice(4); } } for(i=0; i < moduleNames.length; i++ ){ if(moduleNames[i] == targetID){ return i; } } } function setExperimental(modPos){ linkID = "link" + moduleNames[modPos]; expPic = document.createElement("img"); expPic.src = "pics/experimental.png"; expPic.className = "expPic"; //alert(bttns[modPos].bttnID); expPic.onmouseover = function(){startAni(bttns[modPos].bttnID);changeToHover(bttns[modPos].bttnID);}; expPic.onmouseout = function(){stopAni(bttns[modPos].bttnID);changeToNormal(bttns[modPos].bttnID);}; document.getElementById(linkID).appendChild(expPic); } function changeToHover(targetId){ bttn = document.getElementById(targetId); bttn.className = "modBttnHover"; } function changeToNormal(targetId){ bttn = document.getElementById(targetId); bttn.className = "modBttn"; } // function to close PopUp-window function closeInfoWindow(){ popUpAnchor = document.getElementById("popupAnchor"); popUpAnchor.removeChild(document.getElementById("popup")); } function createClearFloat(){ cf = document.createElement("div"); cf.className = "clearfloat"; document.getElementById("bttnField").appendChild(cf); } startAni = function(targetId){ modulePos = getPos(targetId,"bttn"); if(aniFilenames[modulePos] != ''){ bttn = document.getElementById(targetId); bttn.src = "pics/" + aniFilenames[modulePos]; } } stopAni = function(targetId){ modulePos = getPos(targetId,"bttn"); bttn = document.getElementById(targetId); bttn.src = "pics/" + picFilenames[modulePos]; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html index d050141429..db39343fd2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html @@ -1,37 +1,40 @@ MITK Diffusion Imaging App

Welcome to MITK Diffusion!

This application includes all diffusion imaging modules that were developed at the German Cancer Research Center (DKFZ). The software is developed on the basis of the well established, free open source software toolkit MITK. It is designed to perform tasks like fiber tracking, quantification, group analysis, connectomics, synthetic data generation or other image processing tasks. For more information, please also visit our website www.mitk.org or have a look at the help perspective. -

Instructions:

+
+ Work with MITK Diffusion + +

Features:

diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp index 2f9d8e44fb..1e2a24b0bb 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp @@ -1,204 +1,204 @@ /*=================================================================== 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 "QmitkDiffusionImagingAppIntroPart.h" #include "mitkNodePredicateDataType.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "QmitkDiffusionApplicationPlugin.h" #include "mitkDataStorageEditorInput.h" #include #include "mitkBaseDataIOFactory.h" #include "mitkSceneIO.h" #include "mitkProgressBar.h" #include "mitkDataNodeFactory.h" #include "mitkNodePredicateNot.h" #include "mitkNodePredicateProperty.h" QmitkDiffusionImagingAppIntroPart::QmitkDiffusionImagingAppIntroPart() : m_Controls(NULL) { berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences(); workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, true); workbenchPrefs->Flush(); } QmitkDiffusionImagingAppIntroPart::~QmitkDiffusionImagingAppIntroPart() { // if the workbench is not closing (that means, welcome screen was closed explicitly), set "Show_intro" false if (!this->GetIntroSite()->GetPage()->GetWorkbenchWindow()->GetWorkbench()->IsClosing()) { berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences(); workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, false); workbenchPrefs->Flush(); } else { berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences(); workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, true); workbenchPrefs->Flush(); } // if workbench is not closing (Just welcome screen closing), open last used perspective if (this->GetIntroSite()->GetPage()->GetPerspective()->GetId() == "org.mitk.diffusionimagingapp.perspectives.welcome" && !this->GetIntroSite()->GetPage()->GetWorkbenchWindow()->GetWorkbench()->IsClosing()) { - berry::IPerspectiveDescriptor::Pointer perspective = this->GetIntroSite()->GetWorkbenchWindow()->GetWorkbench()->GetPerspectiveRegistry()->FindPerspectiveWithId("org.mitk.diffusionimagingapp.perspectives.diffusionimagingapp"); + berry::IPerspectiveDescriptor::Pointer perspective = this->GetIntroSite()->GetWorkbenchWindow()->GetWorkbench()->GetPerspectiveRegistry()->FindPerspectiveWithId("org.mitk.perspectives.diffusiondefault"); if (perspective) { this->GetIntroSite()->GetPage()->SetPerspective(perspective); } } } void QmitkDiffusionImagingAppIntroPart::CreateQtPartControl(QWidget* parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkWelcomeScreenViewControls; m_Controls->setupUi(parent); // create a QWebView as well as a QWebPage and QWebFrame within the QWebview m_view = new QWebView(parent); m_view->page()->setLinkDelegationPolicy(QWebPage::DelegateAllLinks); QUrl urlQtResource(QString("qrc:/org.mitk.gui.qt.welcomescreen/mitkdiffusionimagingappwelcomeview.html"), QUrl::TolerantMode ); m_view->load( urlQtResource ); // adds the webview as a widget parent->layout()->addWidget(m_view); this->CreateConnections(); } } void QmitkDiffusionImagingAppIntroPart::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_view->page()), SIGNAL(linkClicked(const QUrl& )), this, SLOT(DelegateMeTo(const QUrl& )) ); } } void QmitkDiffusionImagingAppIntroPart::DelegateMeTo(const QUrl& showMeNext) { QString scheme = showMeNext.scheme(); QByteArray urlHostname = showMeNext.encodedHost(); QByteArray urlPath = showMeNext.encodedPath(); QByteArray dataset = showMeNext.encodedQueryItemValue("dataset"); QByteArray clear = showMeNext.encodedQueryItemValue("clear"); if (scheme.isEmpty()) MITK_INFO << " empty scheme of the to be delegated link" ; // if the scheme is set to mitk, it is to be tested which action should be applied if (scheme.contains(QString("mitk")) ) { if(urlPath.isEmpty() ) MITK_INFO << " mitk path is empty " ; // searching for the perspective keyword within the host name if(urlHostname.contains(QByteArray("perspectives")) ) { // the simplified method removes every whitespace // ( whitespace means any character for which the standard C++ isspace() method returns true) urlPath = urlPath.simplified(); QString tmpPerspectiveId(urlPath.data()); tmpPerspectiveId.replace(QString("/"), QString("") ); std::string perspectiveId = tmpPerspectiveId.toStdString(); // is working fine as long as the perspective id is valid, if not the application crashes GetIntroSite()->GetWorkbenchWindow()->GetWorkbench()->ShowPerspective(perspectiveId, GetIntroSite()->GetWorkbenchWindow() ); // search the Workbench for opened StdMultiWidgets to ensure the focus does not stay on the welcome screen and is switched to // an StdMultiWidget if one available mitk::IDataStorageService::Pointer service = berry::Platform::GetServiceRegistry().GetServiceById(mitk::IDataStorageService::ID); berry::IEditorInput::Pointer editorInput; editorInput = new mitk::DataStorageEditorInput( service->GetActiveDataStorage() ); // the solution is not clean, but the dependency to the StdMultiWidget was removed in order to fix a crash problem // as described in Bug #11715 // This is the correct way : use the static string ID variable // berry::IEditorPart::Pointer editor = GetIntroSite()->GetPage()->FindEditors( editorInput, QmitkStdMultiWidgetEditor::EDITOR_ID ); // QuickFix: we use the same string for an local variable const std::string stdEditorID = "org.mitk.editors.stdmultiwidget"; // search for opened StdMultiWidgetEditors std::vector editorList = GetIntroSite()->GetPage()->FindEditors( editorInput, stdEditorID, 1 ); // if an StdMultiWidgetEditor open was found, give focus to it if(editorList.size()) { GetIntroSite()->GetPage()->Activate( editorList[0]->GetPart(true) ); } } } // if the scheme is set to http, by default no action is performed, if an external webpage needs to be // shown it should be implemented below else if (scheme.contains(QString("http")) ) { QDesktopServices::openUrl(showMeNext); // m_view->load( ) ; } else if(scheme.contains("qrc")) { m_view->load(showMeNext); } } void QmitkDiffusionImagingAppIntroPart::StandbyStateChanged(bool) { } void QmitkDiffusionImagingAppIntroPart::SetFocus() { }