diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt index fc47284c90..594bbfb70e 100644 --- a/Applications/Diffusion/CMakeLists.txt +++ b/Applications/Diffusion/CMakeLists.txt @@ -1,96 +1,97 @@ project(MitkDiffusion) set(DIFFUSIONAPP_NAME MitkDiffusion) set(_app_options) if(MITK_SHOW_CONSOLE_WINDOW) list(APPEND _app_options SHOW_CONSOLE) endif() # Create a cache entry for the provisioning file which is used to export # the file name in the MITKConfig.cmake file. This will keep external projects # which rely on this file happy. set(DIFFUSIONIMAGINGAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${DIFFUSIONAPP_NAME}.provisioning" CACHE INTERNAL "${DIFFUSIONAPP_NAME} provisioning file" FORCE) # should be identical to the list in /CMake/mitkBuildConfigurationmitkDiffusion.cmake # remember to set plugins which should be automatically toggled in target_libraries.cmake set(_plugins org.commontk.configadmin org.commontk.eventadmin org.blueberry.core.runtime org.blueberry.core.expressions org.blueberry.core.commands org.blueberry.ui.qt org.blueberry.ui.qt.log org.blueberry.ui.qt.help org.mitk.core.services org.mitk.gui.common org.mitk.planarfigure org.mitk.core.ext org.mitk.gui.qt.application org.mitk.gui.qt.ext org.mitk.gui.qt.diffusionimagingapp org.mitk.gui.qt.common org.mitk.gui.qt.stdmultiwidgeteditor org.mitk.gui.qt.common.legacy org.mitk.gui.qt.datamanager org.mitk.gui.qt.measurementtoolbox org.mitk.gui.qt.segmentation org.mitk.gui.qt.volumevisualization org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.diffusionimaging.connectomics org.mitk.gui.qt.diffusionimaging.fiberfox org.mitk.gui.qt.diffusionimaging.fiberprocessing org.mitk.gui.qt.diffusionimaging.ivim org.mitk.gui.qt.diffusionimaging.odfpeaks org.mitk.gui.qt.diffusionimaging.preprocessing org.mitk.gui.qt.diffusionimaging.reconstruction org.mitk.gui.qt.diffusionimaging.tractography - org.mitk.gui.qt.matchpoint.algorithm.browser - org.mitk.gui.qt.matchpoint.algorithm.control - org.mitk.gui.qt.matchpoint.mapper + org.mitk.gui.qt.diffusionimaging.registration +# org.mitk.gui.qt.matchpoint.algorithm.browser +# org.mitk.gui.qt.matchpoint.algorithm.control +# org.mitk.gui.qt.matchpoint.mapper org.mitk.gui.qt.imagenavigator org.mitk.gui.qt.moviemaker org.mitk.gui.qt.basicimageprocessing org.mitk.gui.qt.properties org.mitk.gui.qt.viewnavigator ) # Plug-ins listed below will not be # - added as a build-time dependency to the executable # - listed in the provisioning file for the executable # - installed if they are external plug-ins set(_exclude_plugins org.blueberry.test org.blueberry.uitest org.mitk.gui.qt.coreapplication org.mitk.gui.qt.extapplication ) set(_src_files MitkDiffusion.cpp ) qt5_add_resources(_src_files splashscreen.qrc) mitkFunctionCreateBlueBerryApplication( NAME ${DIFFUSIONAPP_NAME} DESCRIPTION "MITK Diffusion" PLUGINS ${_plugins} EXCLUDE_PLUGINS ${_exclude_plugins} SOURCES ${_src_files} ${_app_options} ) mitk_use_modules(TARGET ${DIFFUSIONAPP_NAME} MODULES MitkAppUtil) # Add meta dependencies (e.g. on auto-load modules from depending modules) if(TARGET ${CMAKE_PROJECT_NAME}-autoload) add_dependencies(${DIFFUSIONAPP_NAME} ${CMAKE_PROJECT_NAME}-autoload) endif() # Add a build time dependency to legacy BlueBerry bundles. if(MITK_MODULES_ENABLED_PLUGINS) add_dependencies(${DIFFUSIONAPP_NAME} ${MITK_MODULES_ENABLED_PLUGINS}) endif() diff --git a/Applications/Diffusion/target_libraries.cmake b/Applications/Diffusion/target_libraries.cmake index 347d5fbc04..fa0fefc01e 100644 --- a/Applications/Diffusion/target_libraries.cmake +++ b/Applications/Diffusion/target_libraries.cmake @@ -1,32 +1,33 @@ # A list of plug-in targets which should be automatically enabled # (or be available in external projects) for this application set(target_libraries org_blueberry_ui_qt org_blueberry_ui_qt_help org_mitk_planarfigure org_mitk_gui_qt_diffusionimagingapp org_mitk_gui_qt_common_legacy org_mitk_gui_qt_ext org_mitk_gui_qt_datamanager org_mitk_gui_qt_segmentation org_mitk_gui_qt_volumevisualization org_mitk_gui_qt_diffusionimaging org_mitk_gui_qt_diffusionimaging_connectomics org_mitk_gui_qt_diffusionimaging_fiberfox org_mitk_gui_qt_diffusionimaging_fiberprocessing org_mitk_gui_qt_diffusionimaging_ivim org_mitk_gui_qt_diffusionimaging_odfpeaks org_mitk_gui_qt_diffusionimaging_preprocessing org_mitk_gui_qt_diffusionimaging_reconstruction org_mitk_gui_qt_diffusionimaging_tractography + org_mitk_gui_qt_diffusionimaging_registration org_mitk_gui_qt_matchpoint_algorithm_browser org_mitk_gui_qt_matchpoint_algorithm_control org_mitk_gui_qt_matchpoint_mapper org_mitk_gui_qt_imagenavigator org_mitk_gui_qt_moviemaker org_mitk_gui_qt_measurementtoolbox org_mitk_gui_qt_basicimageprocessing org_mitk_gui_qt_viewnavigator ) diff --git a/Modules/MatchPointRegistration/algorithms/mitkMultiModalRigidDefaultRegistrationAlgorithm.h b/Modules/MatchPointRegistration/algorithms/mitkMultiModalRigidDefaultRegistrationAlgorithm.h index 48d312c47c..750fecde0a 100644 --- a/Modules/MatchPointRegistration/algorithms/mitkMultiModalRigidDefaultRegistrationAlgorithm.h +++ b/Modules/MatchPointRegistration/algorithms/mitkMultiModalRigidDefaultRegistrationAlgorithm.h @@ -1,134 +1,134 @@ /*=================================================================== 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 mitkMultiModalRigidDefaultRegistrationAlgorithm_h #define mitkMultiModalRigidDefaultRegistrationAlgorithm_h #include "mapDiscreteElements.h" #include "mapITKEuler3DMattesMIMultiResRegistrationAlgorithmTemplate.h" #include "mapConfigure.h" #include "mitkMultiModalRigidDefaultRegistrationAlgorithm_ProfileResource.h" namespace mitk { /** \class MultiModalRigidDefaultRegistrationAlgorithm * Algorithm is used as default solution for multimodal rigid problem statements in DIPP. * Uses 3 Resolution levels. By default initializes via image centers */ template class MultiModalRigidDefaultRegistrationAlgorithm : - public map::algorithm::boxed::ITKEuler3DMattesMIMultiResRegistrationAlgorithm >, map::algorithm::itk::NoComponentInitializationPolicy> + public ::map::algorithm::boxed::ITKEuler3DMattesMIMultiResRegistrationAlgorithm >, ::map::algorithm::itk::NoComponentInitializationPolicy> { public: typedef MultiModalRigidDefaultRegistrationAlgorithm Self; - typedef map::algorithm::boxed::ITKEuler3DMattesMIMultiResRegistrationAlgorithm >, map::algorithm::itk::NoComponentInitializationPolicy> + typedef ::map::algorithm::boxed::ITKEuler3DMattesMIMultiResRegistrationAlgorithm >, ::map::algorithm::itk::NoComponentInitializationPolicy> Superclass; typedef ::itk::SmartPointer Pointer; typedef ::itk::SmartPointer ConstPointer; itkTypeMacro(MultiModalRigidDefaultRegistrationAlgorithm, ITKEuler3DMattesMIMultiResRegistrationAlgorithm); mapNewAlgorithmMacro(Self); protected: MultiModalRigidDefaultRegistrationAlgorithm() { }; virtual ~MultiModalRigidDefaultRegistrationAlgorithm() { }; void configureAlgorithm() { Superclass::configureAlgorithm(); this->setResolutionLevels(3); this->_preInitialize = true; this->_useCenterOfGravity = false; //optimizer typename Superclass::ConcreteOptimizerType::ScalesType scales(6); scales[0] = 1.0; scales[1] = 1.0; scales[2] = 1.0; scales[3] = 1.0 / 1000; scales[4] = 1.0 / 1000; scales[5] = 1.0 / 1000; this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetScales(scales); this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetMaximumStepLength(3.00); this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetMinimumStepLength(0.5); this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetNumberOfIterations(200); this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetRelaxationFactor(0.8); this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetGradientMagnitudeTolerance(1e-4); //metric this->getConcreteMetricControl()->getConcreteMetric()->SetNumberOfHistogramBins(30); this->getConcreteMetricControl()->getConcreteMetric()->SetUseAllPixels(true); this->getConcreteMetricControl()->getConcreteMetric()->ReinitializeSeed(); this->getConcreteMetricControl()->getConcreteMetric()->UseExplicitPDFDerivativesOn(); } void doInterLevelSetup() { Superclass::doInterLevelSetup(); if (this->getCurrentLevel() == 0) { typename Superclass::OptimizerBaseType::SVNLOptimizerBaseType::ScalesType scales(6); scales[0] = 10.0; scales[1] = 10.0; scales[2] = 10.0; scales[3] = 1.0 / 10000; scales[4] = 1.0 / 10000; scales[5] = 1.0 / 10000; this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetScales(scales); } else { this->getConcreteMetricControl()->getConcreteMetric()->SetUseAllPixels(false); typename Superclass::OptimizerBaseType::SVNLOptimizerBaseType::ScalesType scales(6); scales[0] = 1.0; scales[1] = 1.0; scales[2] = 1.0; scales[3] = 1.0 / 1000; scales[4] = 1.0 / 1000; scales[5] = 1.0 / 1000; this->getConcreteOptimizerControl()->getConcreteOptimizer()->SetScales(scales); unsigned int nrOfSmpl = ::itk::Math::Round (this->getMovingImage()->GetLargestPossibleRegion().GetNumberOfPixels() * 0.15); this->getConcreteMetricControl()->getConcreteMetric()->SetNumberOfSpatialSamples(nrOfSmpl); } }; private: MultiModalRigidDefaultRegistrationAlgorithm(const Self& source); //purposely not implemented void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/MatchPointRegistration/mitkMAPRegistrationWrapper.h b/Modules/MatchPointRegistration/mitkMAPRegistrationWrapper.h index 3bc49d990e..62a93c5108 100644 --- a/Modules/MatchPointRegistration/mitkMAPRegistrationWrapper.h +++ b/Modules/MatchPointRegistration/mitkMAPRegistrationWrapper.h @@ -1,272 +1,272 @@ /*=================================================================== 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 mitkMAPRegistrationWrapper_h #define mitkMAPRegistrationWrapper_h //MITK #include #include //MatchPoint #include #include #include #include //MITK #include "MitkMatchPointRegistrationExports.h" namespace mitk { /*! \brief MAPRegistrationWrapper Wrapper class to allow the handling of MatchPoint registration objects as mitk data (e.g. in the data explorer). */ class MITKMATCHPOINTREGISTRATION_EXPORT MAPRegistrationWrapper: public mitk::BaseData { public: mitkClassMacro( MAPRegistrationWrapper, BaseData ); itkNewMacro( Self ); /** * Empty implementation, since the MAPRegistrationWrapper doesn't * support the requested region concept */ virtual void SetRequestedRegionToLargestPossibleRegion(); /** * Empty implementation, since the MAPRegistrationWrapper doesn't * support the requested region concept */ virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); /** * Empty implementation, since the MAPRegistrationWrapper doesn't * support the requested region concept */ virtual bool VerifyRequestedRegion(); /** * Empty implementation, since the MAPRegistrationWrapper doesn't * support the requested region concept */ virtual void SetRequestedRegion(const itk::DataObject*); /*! @brief Gets the number of moving dimensions @pre valid registration instance must be set. */ virtual unsigned int GetMovingDimensions() const; /*! @brief Gets the number of target dimensions @pre valid registration instance must be set. */ virtual unsigned int GetTargetDimensions() const; /*! typedefs used for the TagMap */ typedef ::map::core::RegistrationBase::TagType TagType; typedef ::map::core::RegistrationBase::ValueType ValueType; typedef ::map::core::RegistrationBase::TagMapType TagMapType; /*! @brief returns the tags associated with this registration @pre valid registration instance must be set. @return a TagMapType containing tags */ const TagMapType& GetTags() const; /*! @brief returns the tag value for a specific tag @pre valid registration instance must be set. @return the success of the operation */ bool GetTagValue(const TagType & tag, ValueType & value) const; /*! Indicates @pre valid registration instance must be set. @return is the target representation limited @retval true if target representation is limited. Thus it is not guaranteed that all inverse mapping operations will succeed. Transformation(inverse kernel) covers only a part of the target space). @retval false if target representation is not limited. Thus it is guaranteed that all inverse mapping operations will succeed. */ bool HasLimitedTargetRepresentation() const; /*! @pre valid registration instance must be set. @return is the moving representation limited @retval true if moving representation is limited. Thus it is not guaranteed that all direct mapping operations will succeed. Transformation(direct kernel) covers only a part of the moving space). @retval false if moving representation is not limited. Thus it is guaranteed that all direct mapping operations will succeed. */ bool HasLimitedMovingRepresentation() const; /*! Helper function that maps a mitk point (of arbitrary dimension) from moving space to target space. @remarks The operation might fail, if the moving and target dimension of the registration is not equal to the dimensionality of the passed points. @pre valid registration instance must be set. @param inPoint Reference pointer to a MovingPointType @param outPoint pointer to a TargetPointType @return success of operation. @pre direct mapping kernel must be defined */ template bool MapPoint(const ::itk::Point& inPoint, ::itk::Point& outPoint) const { typedef typename ::map::core::continuous::Elements::PointType MAPMovingPointType; typedef typename ::map::core::continuous::Elements::PointType MAPTargetPointType; if (m_spRegistration.IsNull()) { mapDefaultExceptionMacro(<< "Error. Cannot map point. Wrapper points to invalid registration (nullptr). Point: " << inPoint); } bool result = false; if ((this->GetMovingDimensions() == VMovingDim)&&(this->GetTargetDimensions() == VTargetDim)) { MAPMovingPointType tempInP; MAPTargetPointType tempOutP; tempInP.CastFrom(inPoint); - typedef map::core::Registration CastedRegType; + typedef ::map::core::Registration CastedRegType; const CastedRegType* pCastedReg = dynamic_cast(m_spRegistration.GetPointer()); if (!pCastedReg) { mapDefaultExceptionMacro(<< "Error. Cannot map point. Registration has invalid dimension. Point: " << inPoint); } result = pCastedReg->mapPoint(tempInP,tempOutP); if (result) { outPoint.CastFrom(tempOutP); } } return result; }; /*! Helper function that maps a mitk point (of arbitrary dimension) from target space to moving space @remarks The operation might faile, if the moving and target dimension of the registration is not equal to the dimensionalities of the passed points. @pre valid registration instance must be set. @param inPoint pointer to a TargetPointType @param outPoint pointer to a MovingPointType @return success of operation */ template bool MapPointInverse(const ::itk::Point & inPoint, ::itk::Point & outPoint) const { typedef typename ::map::core::continuous::Elements::PointType MAPMovingPointType; typedef typename ::map::core::continuous::Elements::PointType MAPTargetPointType; if (m_spRegistration.IsNull()) { mapDefaultExceptionMacro(<< "Error. Cannot map point. Wrapper points to invalid registration (nullptr). Point: " << inPoint); } bool result = false; if ((this->GetMovingDimensions() == VMovingDim)&&(this->GetTargetDimensions() == VTargetDim)) { MAPTargetPointType tempInP; MAPMovingPointType tempOutP; tempInP.CastFrom(inPoint); - typedef map::core::Registration CastedRegType; + typedef ::map::core::Registration CastedRegType; const CastedRegType* pCastedReg = dynamic_cast(m_spRegistration.GetPointer()); if (!pCastedReg) { mapDefaultExceptionMacro(<< "Error. Cannot map point. Registration has invalid dimension. Point: " << inPoint); } result = pCastedReg->mapPointInverse(tempInP,tempOutP); if (result) { outPoint.CastFrom(tempOutP); } } return result; }; /*! returns the direct FieldRepresentationDescriptor which defines the part of the moving space that is guaranteed to be mapped by the direct mapping kernel. This member converts the internal MatchPoint type into a mitk::Geometry3D. @pre valid registration instance must be set. @return smart pointer to a FieldRepresentationDescriptor for the supported registration space in the moving domain. May be null if the direct registration kernel is global and thus not limited. If there is a limitation, the retun value is not nullptr. @retval nullptr no field representation set/requested by the creating registration algorithm. */ mitk::Geometry3D GetDirectFieldRepresentation() const; /*! returns the inverse FieldRepresentationDescriptor which defines the part of the target space that is guaranteed to be mapped by the inverse mapping kernel. This member converts the internal MatchPoint type into a mitk::Geometry3D. @pre valid registration instance must be set. @return a const FieldRepresentationDescriptor for the supported registration space in the target domain. May be null if the inverse registration kernel is global and thus not limited. If there is a limitation, the retun value is not nullptr. @retval nullptr no field representation set/requested by the creating registration algorithm. */ mitk::Geometry3D GetInverseFieldRepresentation() const; /*! forces kernel to precompute, even if it is a LazyFieldKernel @pre valid registration instance must be set. @todo der LazyFieldBasedRegistrationKernel muss dann die stong guarantee erfllen beim erzeugen des feldes ansonsten ist die garantie dieser methode nicht erfllbar. noch berprfen */ void PrecomputeDirectMapping(); /*! forces kernel to precompute, even if it is a LazyFieldKernel @pre valid registration instance must be set. @todo der LazyFieldBasedRegistrationKernel muss dann die stong guarantee erfllen beim erzeugen des feldes ansonsten ist die garantie dieser methode nicht erfllbar. noch berprfen */ void PrecomputeInverseMapping(); - map::core::RegistrationBase* GetRegistration(); - const map::core::RegistrationBase* GetRegistration() const; + ::map::core::RegistrationBase* GetRegistration(); + const ::map::core::RegistrationBase* GetRegistration() const; - void SetRegistration(map::core::RegistrationBase* pReg); + void SetRegistration(::map::core::RegistrationBase* pReg); protected: virtual void PrintSelf (std::ostream &os, itk::Indent indent) const; MAPRegistrationWrapper(); virtual ~MAPRegistrationWrapper(); - map::core::RegistrationBase::Pointer m_spRegistration; + ::map::core::RegistrationBase::Pointer m_spRegistration; private: MAPRegistrationWrapper& operator = (const MAPRegistrationWrapper&); MAPRegistrationWrapper(const MAPRegistrationWrapper&); }; } #endif diff --git a/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegistrationJob.h b/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegistrationJob.h index a1ffdd634b..cfbf51d556 100644 --- a/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegistrationJob.h +++ b/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegistrationJob.h @@ -1,105 +1,105 @@ /*=================================================================== 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 __QMITK_REGISTRATION_JOB_H #define __QMITK_REGISTRATION_JOB_H // QT #include #include // ITK #include // MITK #include "mitkUIDHelper.h" #include #include #include // MatchPoint #include #include #include #include #include #include class MITKMATCHPOINTREGISTRATIONUI_EXPORT QmitkRegistrationJob : public QObject, public QRunnable { // 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: - QmitkRegistrationJob(map::algorithm::RegistrationAlgorithmBase *pAlgorithm); + QmitkRegistrationJob(::map::algorithm::RegistrationAlgorithmBase *pAlgorithm); ~QmitkRegistrationJob(); void run(); signals: void Finished(); void Error(QString err); void RegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob *pJob); void AlgorithmIterated(QString info, bool hasIterationCount, unsigned long currentIteration); void LevelChanged(QString info, bool hasLevelCount, unsigned long currentLevel); void AlgorithmStatusChanged(QString info); void AlgorithmInfo(QString info); public: // Inputs mitk::BaseData::ConstPointer m_spTargetData; mitk::BaseData::ConstPointer m_spMovingData; mitk::Image::ConstPointer m_spTargetMask; mitk::Image::ConstPointer m_spMovingMask; // job settings bool m_MapEntity; bool m_StoreReg; bool m_ErrorOccured; std::string m_JobName; mitk::NodeUIDType m_TargetDataUID; mitk::NodeUIDType m_MovingDataUID; mitk::NodeUIDType m_TargetMaskDataUID; mitk::NodeUIDType m_MovingMaskDataUID; - const map::algorithm::RegistrationAlgorithmBase *GetLoadedAlgorithm() const; + const ::map::algorithm::RegistrationAlgorithmBase *GetLoadedAlgorithm() const; protected: - typedef map::algorithm::facet::IterativeAlgorithmInterface IIterativeAlgorithm; - typedef map::algorithm::facet::MultiResRegistrationAlgorithmInterface IMultiResAlgorithm; + typedef ::map::algorithm::facet::IterativeAlgorithmInterface IIterativeAlgorithm; + typedef ::map::algorithm::facet::MultiResRegistrationAlgorithmInterface IMultiResAlgorithm; // Result registration. - map::core::RegistrationBase::Pointer m_spResultRegistration; + ::map::core::RegistrationBase::Pointer m_spResultRegistration; mitk::DataNode::Pointer m_spRegNode; // mapped image. May be null if m_MapEntity is false. mitk::DataNode::Pointer m_spMappedImageNode; ::itk::MemberCommand::Pointer m_spCommand; unsigned long m_ObserverID; - map::algorithm::RegistrationAlgorithmBase::Pointer m_spLoadedAlgorithm; + ::map::algorithm::RegistrationAlgorithmBase::Pointer m_spLoadedAlgorithm; // Helper functions const mitk::Image *GetTargetDataAsImage() const; const mitk::Image *GetMovingDataAsImage() const; void OnMapAlgorithmEvent(::itk::Object *, const itk::EventObject &event); }; #endif diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake index 074d5c67ef..c410e854d2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake @@ -1,5 +1,5 @@ -set(Plugin-Name "MITK Fiber Processing") +set(Plugin-Name "MITK IVIM") set(Plugin-Version "1.0.0") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common.legacy org.mitk.gui.qt.common) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake index 074d5c67ef..d9d2df538c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake @@ -1,5 +1,5 @@ -set(Plugin-Name "MITK Fiber Processing") +set(Plugin-Name "MITK ODF Peaks") set(Plugin-Version "1.0.0") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common.legacy org.mitk.gui.qt.common) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake index 074d5c67ef..dbf79c0d1e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake @@ -1,5 +1,5 @@ -set(Plugin-Name "MITK Fiber Processing") +set(Plugin-Name "MITK Partial Volume Analysis") set(Plugin-Version "1.0.0") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common.legacy org.mitk.gui.qt.common) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake index 074d5c67ef..b9885bba96 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake @@ -1,5 +1,5 @@ -set(Plugin-Name "MITK Fiber Processing") +set(Plugin-Name "MITK Preprocessing") set(Plugin-Version "1.0.0") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common.legacy org.mitk.gui.qt.common) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp index 6675188dbf..26310fa9ab 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp @@ -1,1963 +1,1962 @@ /*=================================================================== 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 MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" #include "itkB0ImageExtractionImageFilter.h" #include "itkB0ImageExtractionToSeparateImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "itkVectorContainer.h" #include #include #include #include #include #include // Multishell includes #include // Multishell Functors #include #include #include #include // mitk includes #include "QmitkDataStorageComboBox.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkTransferFunction.h" #include "mitkTransferFunctionProperty.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.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 #include #include #include #include const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.preprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkAbstractView(), m_Controls(nullptr) { } QmitkPreprocessingView::~QmitkPreprocessingView() { } void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkPreprocessingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_MeasurementFrameTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_MeasurementFrameTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch); } } void QmitkPreprocessingView::SetFocus() { m_Controls->m_MirrorGradientToHalfSphereButton->setFocus(); } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { m_Controls->m_NormalizationMaskBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_SelctedImageComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MergeDwiBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_AlignImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isOdf, isDti); mitk::NodePredicateAnd::Pointer noDiffusionImage = mitk::NodePredicateAnd::New(isMitkImage, mitk::NodePredicateNot::New(isDiffusionImage)); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer binaryNoDiffusionImage = mitk::NodePredicateAnd::New(noDiffusionImage, isBinaryPredicate); m_Controls->m_NormalizationMaskBox->SetPredicate(binaryNoDiffusionImage); m_Controls->m_SelctedImageComboBox->SetPredicate(isMitkImage); m_Controls->m_MergeDwiBox->SetPredicate(isMitkImage); m_Controls->m_AlignImageBox->SetPredicate(isMitkImage); m_Controls->m_ExtractBrainMask->setVisible(false); m_Controls->m_BrainMaskIterationsBox->setVisible(false); m_Controls->m_ResampleIntFrame->setVisible(false); connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) ); connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) ); connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) ); connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) ); connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) ); connect( (QObject*)(m_Controls->m_MergeDwisButton), SIGNAL(clicked()), this, SLOT(MergeDwis()) ); connect( (QObject*)(m_Controls->m_ProjectSignalButton), SIGNAL(clicked()), this, SLOT(DoProjectSignal()) ); connect( (QObject*)(m_Controls->m_B_ValueMap_Rounder_SpinBox), SIGNAL(valueChanged(int)), this, SLOT(UpdateDwiBValueMapRounder(int))); connect( (QObject*)(m_Controls->m_CreateLengthCorrectedDwi), SIGNAL(clicked()), this, SLOT(DoLengthCorrection()) ); connect( (QObject*)(m_Controls->m_NormalizeImageValuesButton), SIGNAL(clicked()), this, SLOT(DoDwiNormalization()) ); connect( (QObject*)(m_Controls->m_ResampleImageButton), SIGNAL(clicked()), this, SLOT(DoResampleImage()) ); connect( (QObject*)(m_Controls->m_ResampleTypeBox), SIGNAL(currentIndexChanged(int)), this, SLOT(DoUpdateInterpolationGui(int)) ); connect( (QObject*)(m_Controls->m_CropImageButton), SIGNAL(clicked()), this, SLOT(DoCropImage()) ); connect( (QObject*)(m_Controls->m_RemoveGradientButton), SIGNAL(clicked()), this, SLOT(DoRemoveGradient()) ); connect( (QObject*)(m_Controls->m_ExtractGradientButton), SIGNAL(clicked()), this, SLOT(DoExtractGradient()) ); connect( (QObject*)(m_Controls->m_FlipAxis), SIGNAL(clicked()), this, SLOT(DoFlipAxis()) ); connect( (QObject*)(m_Controls->m_FlipGradientsButton), SIGNAL(clicked()), this, SLOT(DoFlipGradientDirections()) ); connect( (QObject*)(m_Controls->m_ClearRotationButton), SIGNAL(clicked()), this, SLOT(DoClearRotationOfGradients()) ); connect( (QObject*)(m_Controls->m_ModifyHeader), SIGNAL(clicked()), this, SLOT(DoApplyHeader()) ); connect( (QObject*)(m_Controls->m_AlignImageButton), SIGNAL(clicked()), this, SLOT(DoAlignImages()) ); connect( (QObject*)(m_Controls->m_SelctedImageComboBox), SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnImageSelectionChanged()) ); m_Controls->m_NormalizationMaskBox->SetZeroEntryText("--"); } } void QmitkPreprocessingView::DoAlignImages() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::DataNode::Pointer target_node = m_Controls->m_AlignImageBox->GetSelectedNode(); if (target_node.IsNull()) { return; } mitk::Image::Pointer target_image = dynamic_cast(target_node->GetData()); if ( target_image == nullptr ) { return; } target_image->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::RenderingManager::GetInstance()->InitializeViews( target_image->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoFlipAxis() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) ); if (isDiffusionImage) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); itk::FixedArray flipAxes; flipAxes[0] = m_Controls->m_FlipX->isChecked(); flipAxes[1] = m_Controls->m_FlipY->isChecked(); flipAxes[2] = m_Controls->m_FlipZ->isChecked(); itk::FlipImageFilter< ItkDwiType >::Pointer flipper = itk::FlipImageFilter< ItkDwiType >::New(); flipper->SetInput(itkVectorImagePointer); flipper->SetFlipAxes(flipAxes); flipper->Update(); GradProp::GradientDirectionsContainerType::Pointer oldGradients = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); GradProp::GradientDirectionsContainerType::Pointer newGradients = GradProp::GradientDirectionsContainerType::New(); for (unsigned int i=0; iSize(); i++) { GradProp::GradientDirectionType g = oldGradients->GetElement(i); GradProp::GradientDirectionType newG = g; if (flipAxes[0]) { newG[0] *= -1; } if (flipAxes[1]) { newG[1] *= -1; } if (flipAxes[2]) { newG[2] *= -1; } newGradients->InsertElement(i, newG); } mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( newGradients ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_flipped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if( image->GetPixelType().GetNumberOfComponents() == 1 ) { AccessFixedDimensionByItk(image, TemplatedFlipAxis,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedFlipAxis(itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } itk::FixedArray flipAxes; flipAxes[0] = m_Controls->m_FlipX->isChecked(); flipAxes[1] = m_Controls->m_FlipY->isChecked(); flipAxes[2] = m_Controls->m_FlipZ->isChecked(); typename itk::FlipImageFilter< itk::Image >::Pointer flipper = itk::FlipImageFilter< itk::Image >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() ); newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_flipped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoRemoveGradient() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } std::vector< unsigned int > channelsToRemove; channelsToRemove.push_back(m_Controls->m_RemoveGradientBox->value()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); itk::RemoveDwiChannelFilter< short >::Pointer filter = itk::RemoveDwiChannelFilter< short >::New(); filter->SetInput(itkVectorImagePointer); filter->SetChannelIndices(channelsToRemove); filter->SetDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetNewDirections() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_removedgradients").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoExtractGradient() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); unsigned int channel = m_Controls->m_ExtractGradientBox->value(); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(channel); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_direction-"+QString::number(channel)).toStdString().c_str() ); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } void QmitkPreprocessingView::DoCropImage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( isDiffusionImage ) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); itk::CropImageFilter< ItkDwiType, ItkDwiType >::Pointer cropper = itk::CropImageFilter< ItkDwiType, ItkDwiType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput( itkVectorImagePointer ); cropper->Update(); ItkDwiType::Pointer itkOutImage = cropper->GetOutput(); ItkDwiType::DirectionType dir = itkOutImage->GetDirection(); itk::Point origin = itkOutImage->GetOrigin(); itk::Point t; t[0] = lower[0]*itkOutImage->GetSpacing()[0]; t[1] = lower[1]*itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2]; t= dir*t; origin[0] += t[0]; origin[1] += t[1]; origin[2] += t[2]; itkOutImage->SetOrigin(origin); mitk::Image::Pointer newimage = mitk::GrabItkImageMemory( itkOutImage ); PropHelper::CopyProperties(image, newimage, false); PropHelper propertyHelper( newimage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newimage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if( image->GetPixelType().GetNumberOfComponents() ) { AccessFixedDimensionByItk(image, TemplatedCropImage,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedCropImage( itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); typedef itk::Image ImageType; typename itk::CropImageFilter< ImageType, ImageType >::Pointer cropper = itk::CropImageFilter< ImageType, ImageType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput(itkImage); cropper->Update(); typename ImageType::Pointer itkOutImage = cropper->GetOutput(); typename ImageType::DirectionType dir = itkOutImage->GetDirection(); itk::Point origin = itkOutImage->GetOrigin(); itk::Point t; t[0] = lower[0]*itkOutImage->GetSpacing()[0]; t[1] = lower[1]*itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2]; t= dir*t; origin[0] += t[0]; origin[1] += t[1]; origin[2] += t[2]; itkOutImage->SetOrigin(origin); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( itkOutImage.GetPointer() ); image->SetVolume( itkOutImage->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoUpdateInterpolationGui(int i) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } switch (i) { case 0: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); break; } case 1: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); mitk::BaseGeometry* geom = image->GetGeometry(); m_Controls->m_ResampleDoubleX->setValue(geom->GetSpacing()[0]); m_Controls->m_ResampleDoubleY->setValue(geom->GetSpacing()[1]); m_Controls->m_ResampleDoubleZ->setValue(geom->GetSpacing()[2]); break; } case 2: { m_Controls->m_ResampleIntFrame->setVisible(true); m_Controls->m_ResampleDoubleFrame->setVisible(false); mitk::BaseGeometry* geom = image->GetGeometry(); m_Controls->m_ResampleIntX->setValue(geom->GetExtent(0)); m_Controls->m_ResampleIntY->setValue(geom->GetExtent(1)); m_Controls->m_ResampleIntZ->setValue(geom->GetExtent(2)); break; } default: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); } } } void QmitkPreprocessingView::DoExtractBrainMask() { } void QmitkPreprocessingView::DoResampleImage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( isDiffusionImage ) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); typedef itk::ResampleDwiImageFilter< short > ResampleFilter; ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput( itkVectorImagePointer ); switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > samplingFactor; samplingFactor[0] = m_Controls->m_ResampleDoubleX->value(); samplingFactor[1] = m_Controls->m_ResampleDoubleY->value(); samplingFactor[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetSamplingFactor(samplingFactor); break; } case 1: { itk::Vector< double, 3 > newSpacing; newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetNewSpacing(newSpacing); break; } case 2: { itk::ImageRegion<3> newRegion; newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); resampler->SetNewImageSize(newRegion); break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; break; } case 1: { resampler->SetInterpolation(ResampleFilter::Interpolate_Linear); outAdd = "Linear"; break; } case 2: { resampler->SetInterpolation(ResampleFilter::Interpolate_BSpline); outAdd = "BSpline"; break; } case 3: { resampler->SetInterpolation(ResampleFilter::Interpolate_WindowedSinc); outAdd = "WindowedSinc"; break; } default: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( resampler->GetOutput() ); PropHelper::CopyProperties(image, newImage, false); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); imageNode->SetVisibility(false); GetDataStorage()->Add(imageNode, node); } else if( image->GetPixelType().GetNumberOfComponents() ) { AccessFixedDimensionByItk(image, TemplatedResampleImage,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedResampleImage( itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } itk::Vector< double, 3 > newSpacing; itk::ImageRegion<3> newRegion; switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > sampling; sampling[0] = m_Controls->m_ResampleDoubleX->value(); sampling[1] = m_Controls->m_ResampleDoubleY->value(); sampling[2] = m_Controls->m_ResampleDoubleZ->value(); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 1: { newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); itk::Vector< double, 3 > oldSpacing = itkImage->GetSpacing(); itk::Vector< double, 3 > sampling; sampling[0] = oldSpacing[0]/newSpacing[0]; sampling[1] = oldSpacing[1]/newSpacing[1]; sampling[2] = oldSpacing[2]/newSpacing[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 2: { newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); itk::ImageRegion<3> oldRegion = itkImage->GetLargestPossibleRegion(); itk::Vector< double, 3 > sampling; sampling[0] = (double)newRegion.GetSize(0)/oldRegion.GetSize(0); sampling[1] = (double)newRegion.GetSize(1)/oldRegion.GetSize(1); sampling[2] = (double)newRegion.GetSize(2)/oldRegion.GetSize(2); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } itk::Point origin = itkImage->GetOrigin(); origin[0] -= itkImage->GetSpacing()[0]/2; origin[1] -= itkImage->GetSpacing()[1]/2; origin[2] -= itkImage->GetSpacing()[2]/2; origin[0] += newSpacing[0]/2; origin[1] += newSpacing[1]/2; origin[2] += newSpacing[2]/2; typedef itk::Image ImageType; typename ImageType::Pointer outImage = ImageType::New(); outImage->SetSpacing( newSpacing ); outImage->SetOrigin( origin ); outImage->SetDirection( itkImage->GetDirection() ); outImage->SetLargestPossibleRegion( newRegion ); outImage->SetBufferedRegion( newRegion ); outImage->SetRequestedRegion( newRegion ); outImage->Allocate(); typedef itk::ResampleImageFilter ResampleFilter; typename ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput(itkImage); resampler->SetOutputParametersFromImage(outImage); QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; break; } case 1: { typename itk::LinearInterpolateImageFunction::Pointer interp = itk::LinearInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "Linear"; break; } case 2: { typename itk::BSplineInterpolateImageFunction::Pointer interp = itk::BSplineInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "BSpline"; break; } case 3: { typename itk::WindowedSincInterpolateImageFunction::Pointer interp = itk::WindowedSincInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "WindowedSinc"; break; } default: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( resampler->GetOutput() ); image->SetVolume( resampler->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::DoApplyHeader() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); bool isDti = false; bool isOdf = false; bool isPeak = false; if (!isDiffusionImage) { if ( dynamic_cast(node->GetData()) ) isDti = true; else if ( dynamic_cast(node->GetData()) ) isOdf = true; else if ( dynamic_cast(node->GetData()) ) isPeak = true; } mitk::Image::Pointer newImage = image->Clone(); mitk::Vector3D spacing; spacing[0] = m_Controls->m_HeaderSpacingX->value(); spacing[1] = m_Controls->m_HeaderSpacingY->value(); spacing[2] = m_Controls->m_HeaderSpacingZ->value(); newImage->GetGeometry()->SetSpacing( spacing ); mitk::Point3D origin; origin[0] = m_Controls->m_HeaderOriginX->value(); origin[1] = m_Controls->m_HeaderOriginY->value(); origin[2] = m_Controls->m_HeaderOriginZ->value(); newImage->GetGeometry()->SetOrigin(origin); vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->SetElement(0,3,newImage->GetGeometry()->GetOrigin()[0]); matrix->SetElement(1,3,newImage->GetGeometry()->GetOrigin()[1]); matrix->SetElement(2,3,newImage->GetGeometry()->GetOrigin()[2]); for (int r=0; r<3; r++) { for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); if (!item) continue; matrix->SetElement(r,c,item->text().toDouble()); } } newImage->GetGeometry()->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(matrix); if ( isDiffusionImage ) { vnl_matrix_fixed< double, 3, 3 > mf; for (int r=0; r<3; r++) { for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); if (!item) continue; mf[r][c] = item->text().toDouble(); } } newImage->GetPropertyList()->ReplaceProperty( PropHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mf ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); } mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); if (isOdf) { mitk::OdfImage::ItkOdfImageType::Pointer itk_img = mitk::OdfImage::ItkOdfImageType::New(); mitk::CastToItkImage(newImage, itk_img); mitk::Image::Pointer odfImage = dynamic_cast(mitk::OdfImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, odfImage); odfImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( odfImage ); } else if (isDti) { mitk::TensorImage::ItkTensorImageType::Pointer itk_img = mitk::ImageToItkImage(newImage); mitk::Image::Pointer tensorImage = dynamic_cast(mitk::TensorImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, tensorImage); tensorImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( tensorImage ); } else if (isPeak) { mitk::PeakImage::ItkPeakImageType::Pointer itk_img = mitk::ImageToItkImage(newImage); mitk::Image::Pointer peakImage = dynamic_cast(mitk::PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, peakImage); peakImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( peakImage ); } else imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_newheader").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoProjectSignal() { switch(m_Controls->m_ProjectionMethodBox->currentIndex()) { case 0: DoADCAverage(); break; case 1: DoAKCFit(); break; case 2: DoBiExpFit(); break; default: DoADCAverage(); } } void QmitkPreprocessingView::DoDwiNormalization() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } GradientDirectionContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); int b0Index = -1; for (unsigned int i=0; isize(); i++) { GradientDirectionType g = gradientContainer->GetElement(i); if (g.magnitude()<0.001) { b0Index = i; break; } } if (b0Index==-1) { return; } typedef itk::DwiNormilzationFilter FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetGradientDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->SetNewMean(m_Controls->m_NewMean->value()); filter->SetNewStdev(m_Controls->m_NewStdev->value()); UcharImageType::Pointer itkImage = nullptr; if (m_Controls->m_NormalizationMaskBox->GetSelectedNode().IsNotNull()) { itkImage = UcharImageType::New(); if ( dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()) != nullptr ) { mitk::CastToItkImage( dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()), itkImage ); } filter->SetMaskImage(itkImage); } filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, false); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_normalized").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::DoLengthCorrection() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } typedef itk::DwiGradientLengthCorrectionFilter FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetRoundingValue( m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); filter->SetReferenceBValue( static_cast (image->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); filter->SetReferenceGradientDirectionContainer( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( itkVectorImagePointer.GetPointer() ); newImage->SetImportVolume( itkVectorImagePointer->GetBufferPointer(), 0, 0, mitk::Image::CopyMemory); itkVectorImagePointer->GetPixelContainer()->ContainerManageMemoryOff(); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetOutputGradientDirectionContainer() ) ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( filter->GetNewBValue() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_rounded").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::UpdateDwiBValueMapRounder(int i) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) ); if ( ! isDiffusionImage ) { return; } UpdateBValueTableWidget(i); } void QmitkPreprocessingView:: CallMultishellToSingleShellFilter( itk::DWIVoxelFunctor * functor, mitk::Image::Pointer image, QString imageName, mitk::DataNode* parent ) { typedef itk::RadialMultishellToSingleshellImageFilter FilterType; // filter input parameter const mitk::BValueMapProperty::BValueMap& originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); ItkDwiType* vectorImage = itkVectorImagePointer.GetPointer(); const GradProp::GradientDirectionsContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); const unsigned int& bValue = static_cast (image->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue(); mitk::DataNode::Pointer imageNode = 0; // filter call FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, outImage, true); outImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetTargetGradientDirections() ) ); outImage->GetPropertyList()->ReplaceProperty( PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( m_Controls->m_targetBValueSpinBox->value() ) ); PropHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); imageNode = mitk::DataNode::New(); imageNode->SetData( outImage ); imageNode->SetName(imageName.toStdString().c_str()); GetDataStorage()->Add(imageNode, parent); // if(m_Controls->m_OutputRMSErrorImage->isChecked()){ // // create new Error image // FilterType::ErrorImageType::Pointer errImage = filter->GetErrorImage(); // mitk::Image::Pointer mitkErrImage = mitk::Image::New(); // mitkErrImage->InitializeByItk(errImage); // mitkErrImage->SetVolume(errImage->GetBufferPointer()); // imageNode = mitk::DataNode::New(); // imageNode->SetData( mitkErrImage ); // imageNode->SetName((imageName+"_Error").toStdString().c_str()); // GetDataStorage()->Add(imageNode); // } } void QmitkPreprocessingView::DoBiExpFit() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap& originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while( it != originalShellMap.end() ) { bValueList.put(s++,(it++)->first); } const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_BiExp", node); } void QmitkPreprocessingView::DoAKCFit() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap& originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_AKC", node); } void QmitkPreprocessingView::DoADCFit() { // later } void QmitkPreprocessingView::DoADCAverage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) return; itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap &originalShellMap = static_cast(image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() )->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_ADC", node); } void QmitkPreprocessingView::CleanBValueTableWidget() { m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(1); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); m_Controls->m_B_ValueMap_TableWidget->setItem(0,0,new QTableWidgetItem("-")); m_Controls->m_B_ValueMap_TableWidget->setItem(0,1,new QTableWidgetItem("-")); } void QmitkPreprocessingView::UpdateBValueTableWidget(int) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { CleanBValueTableWidget(); return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage(false); isDiffusionImage = PropHelper::IsDiffusionWeightedImage(image); if ( ! isDiffusionImage ) { CleanBValueTableWidget(); } else { typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator; BValueMapIterator it; BValueMap roundedBValueMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(roundedBValueMap.size() ); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); int i = 0 ; for(it = roundedBValueMap.begin() ;it != roundedBValueMap.end(); it++) { m_Controls->m_B_ValueMap_TableWidget->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); QTableWidgetItem* item = m_Controls->m_B_ValueMap_TableWidget->item(i,0); item->setFlags(item->flags() & ~Qt::ItemIsEditable); m_Controls->m_B_ValueMap_TableWidget->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); i++; } } } void QmitkPreprocessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer , const QList& nodes) { (void) nodes; this->OnImageSelectionChanged(); } void QmitkPreprocessingView::OnImageSelectionChanged() { for (int r=0; r<3; r++) for (int c=0; c<3; c++) { { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item( r, c ); delete item; item = new QTableWidgetItem(); m_Controls->m_MeasurementFrameTable->setItem( r, c, item ); } { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c ); delete item; item = new QTableWidgetItem(); m_Controls->m_DirectionMatrixTable->setItem( r, c, item ); } } bool foundImageVolume = true; mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } bool foundDwiVolume( PropHelper::IsDiffusionWeightedImage( node ) ); mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool multiComponentVolume = (image->GetPixelType().GetNumberOfComponents() > 1); bool threeDplusTVolume = (image->GetTimeSteps() > 1); m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); m_Controls->m_CheckExtractAll->setEnabled(foundDwiVolume); m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume); m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume); m_Controls->m_MergeDwisButton->setEnabled(foundDwiVolume); m_Controls->m_B_ValueMap_Rounder_SpinBox->setEnabled(foundDwiVolume); m_Controls->m_ProjectSignalButton->setEnabled(foundDwiVolume); m_Controls->m_CreateLengthCorrectedDwi->setEnabled(foundDwiVolume); m_Controls->m_targetBValueSpinBox->setEnabled(foundDwiVolume); m_Controls->m_NormalizeImageValuesButton->setEnabled(foundDwiVolume); m_Controls->m_RemoveGradientButton->setEnabled(foundDwiVolume); m_Controls->m_ExtractGradientButton->setEnabled(foundDwiVolume); m_Controls->m_FlipGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ClearRotationButton->setEnabled(foundDwiVolume); m_Controls->m_DirectionMatrixTable->setEnabled(foundImageVolume); m_Controls->m_ModifyHeader->setEnabled(foundImageVolume); m_Controls->m_AlignImageBox->setEnabled(foundImageVolume); // we do not support multi-component and 3D+t images for certain operations bool foundSingleImageVolume = foundDwiVolume || (foundImageVolume && !(multiComponentVolume || threeDplusTVolume)); m_Controls->m_FlipAxis->setEnabled(foundSingleImageVolume); m_Controls->m_CropImageButton->setEnabled(foundSingleImageVolume); m_Controls->m_ExtractBrainMask->setEnabled(foundSingleImageVolume); m_Controls->m_ResampleImageButton->setEnabled(foundSingleImageVolume); // reset sampling frame to 1 and update all ealted components m_Controls->m_B_ValueMap_Rounder_SpinBox->setValue(1); UpdateBValueTableWidget(m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); DoUpdateInterpolationGui(m_Controls->m_ResampleTypeBox->currentIndex()); m_Controls->m_HeaderSpacingX->setValue(image->GetGeometry()->GetSpacing()[0]); m_Controls->m_HeaderSpacingY->setValue(image->GetGeometry()->GetSpacing()[1]); m_Controls->m_HeaderSpacingZ->setValue(image->GetGeometry()->GetSpacing()[2]); m_Controls->m_HeaderOriginX->setValue(image->GetGeometry()->GetOrigin()[0]); m_Controls->m_HeaderOriginY->setValue(image->GetGeometry()->GetOrigin()[1]); m_Controls->m_HeaderOriginZ->setValue(image->GetGeometry()->GetOrigin()[2]); m_Controls->m_XstartBox->setMaximum(image->GetGeometry()->GetExtent(0)-1); m_Controls->m_YstartBox->setMaximum(image->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZstartBox->setMaximum(image->GetGeometry()->GetExtent(2)-1); m_Controls->m_XendBox->setMaximum(image->GetGeometry()->GetExtent(0)-1); m_Controls->m_YendBox->setMaximum(image->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZendBox->setMaximum(image->GetGeometry()->GetExtent(2)-1); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Direction matrix QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c ); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); double val = image->GetGeometry()->GetVtkMatrix()->GetElement(r,c)/image->GetGeometry()->GetSpacing()[c]; item->setText(QString::number(val)); m_Controls->m_DirectionMatrixTable->setItem( r, c, item ); } if (foundDwiVolume) { m_Controls->m_InputData->setTitle("Input Data"); vnl_matrix_fixed< double, 3, 3 > mf = static_cast (image->GetProperty(PropHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str()).GetPointer() ) ->GetMeasurementFrame(); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Measurement frame QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item( r, c ); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); item->setText(QString::number(mf.get(r,c))); m_Controls->m_MeasurementFrameTable->setItem( r, c, item ); } //calculate target bValue for MultishellToSingleShellfilter const mitk::BValueMapProperty::BValueMap & bValMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = bValMap.begin(); unsigned int targetBVal = 0; while(it != bValMap.end()) { targetBVal += (it++)->first; } targetBVal /= (float)bValMap.size()-1; m_Controls->m_targetBValueSpinBox->setValue(targetBVal); m_Controls->m_RemoveGradientBox->setMaximum(static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer()->Size()-1); m_Controls->m_ExtractGradientBox->setMaximum(static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer()->Size()-1); } } void QmitkPreprocessingView::Activated() { } void QmitkPreprocessingView::Deactivated() { OnImageSelectionChanged(); } void QmitkPreprocessingView::Visible() { OnImageSelectionChanged(); } void QmitkPreprocessingView::Hidden() { } void QmitkPreprocessingView::DoClearRotationOfGradients() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) return; mitk::Image::Pointer image = dynamic_cast(node->GetData()); if (image == nullptr) return; if(!PropHelper::IsDiffusionWeightedImage(image)) return; mitk::Image::Pointer newDwi = image->Clone(); PropHelper propertyHelper( newDwi ); propertyHelper.InitializeImage(); PropHelper::ClearMeasurementFrameAndRotationMatrixFromGradients(newDwi); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_OriginalGradients").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoFlipGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::Image::Pointer newDwi = image->Clone(); GradientDirectionContainerType::Pointer gradientContainer = static_cast ( newDwi->GetProperty(PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); for (unsigned int j=0; jSize(); j++) { if (m_Controls->m_FlipGradBoxX->isChecked()) { gradientContainer->at(j)[0] *= -1; } if (m_Controls->m_FlipGradBoxY->isChecked()) { gradientContainer->at(j)[1] *= -1; } if (m_Controls->m_FlipGradBoxZ->isChecked()) { gradientContainer->at(j)[2] *= -1; } } PropHelper::CopyProperties(image, newDwi, true); newDwi->GetPropertyList()->ReplaceProperty( PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( gradientContainer ) ); PropHelper propertyHelper( newDwi ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_GradientFlip").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::Image::Pointer newDwi = image->Clone(); GradientDirectionContainerType::Pointer gradientContainer = static_cast ( newDwi->GetProperty(PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); for (unsigned int j=0; jSize(); j++) { if (gradientContainer->at(j)[0]<0) { gradientContainer->at(j) = -gradientContainer->at(j); } } PropHelper::CopyProperties(image, newDwi, true); newDwi->GetPropertyList()->ReplaceProperty( PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( gradientContainer ) ); PropHelper propertyHelper( newDwi ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_halfsphere").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoShowGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } int maxIndex = 0; unsigned int maxSize = image->GetDimension(0); if (maxSizeGetDimension(1)) { maxSize = image->GetDimension(1); maxIndex = 1; } if (maxSizeGetDimension(2)) { maxSize = image->GetDimension(2); maxIndex = 2; } mitk::Point3D origin = image->GetGeometry()->GetOrigin(); mitk::PointSet::Pointer originSet = mitk::PointSet::New(); typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator; BValueMap bValMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); GradientDirectionContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); mitk::BaseGeometry::Pointer geometry = image->GetGeometry(); int shellCount = 1; for(BValueMapIterator it = bValMap.begin(); it!=bValMap.end(); ++it) { mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (unsigned int j=0; jsecond.size(); j++) { mitk::Point3D ip; vnl_vector_fixed< double, 3 > v = gradientContainer->at(it->second[j]); if (v.magnitude()>mitk::eps) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*image->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*image->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*image->GetDimension(2)/2; pointset->InsertPoint(j, ip); } else if (originSet->IsEmpty()) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*image->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*image->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*image->GetDimension(2)/2; originSet->InsertPoint(j, ip); } } if ( it->first < mitk::eps ) { continue; } // add shell to datastorage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pointset); QString name = node->GetName().c_str(); name += "_Shell_"; name += QString::number( it->first ); newNode->SetName( name.toStdString().c_str() ); newNode->SetProperty( "pointsize", mitk::FloatProperty::New((float)maxSize / 50) ); int b0 = shellCount % 2; int b1 = 0; int b2 = 0; if (shellCount>4) { b2 = 1; } if (shellCount%4 >= 2) { b1 = 1; } newNode->SetProperty("color", mitk::ColorProperty::New( b2, b1, b0 )); GetDataStorage()->Add( newNode, node ); shellCount++; } // add origin to datastorage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(originSet); QString name = node->GetName().c_str(); name += "_Origin"; newNode->SetName(name.toStdString().c_str()); newNode->SetProperty("pointsize", mitk::FloatProperty::New((float)maxSize/50)); newNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); GetDataStorage()->Add(newNode, node); } void QmitkPreprocessingView::DoReduceGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter FilterType; typedef mitk::BValueMapProperty::BValueMap BValueMap; // GetShellSelection from GUI BValueMap shellSlectionMap; BValueMap originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); std::vector newNumGradientDirections; int shellCounter = 0; QString name = node->GetName().c_str(); for (int i=0; im_B_ValueMap_TableWidget->rowCount(); i++) { double BValue = m_Controls->m_B_ValueMap_TableWidget->item(i,0)->text().toDouble(); shellSlectionMap[BValue] = originalShellMap[BValue]; unsigned int num = m_Controls->m_B_ValueMap_TableWidget->item(i,1)->text().toUInt(); newNumGradientDirections.push_back(num); name += "_"; name += QString::number(num); shellCounter++; } if (newNumGradientDirections.empty()) { return; } GradientDirectionContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(newNumGradientDirections); filter->SetOriginalBValueMap(originalShellMap); filter->SetShellSelectionBValueMap(shellSlectionMap); filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetGradientDirections() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); imageNode->SetName(name.toStdString().c_str()); GetDataStorage()->Add(imageNode, node); // update the b-value widget to remove the modified number of gradients used for extraction this->CleanBValueTableWidget(); this->UpdateBValueTableWidget(0); } void QmitkPreprocessingView::MergeDwis() { typedef GradProp::GradientDirectionsContainerType GradientContainerType; mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } mitk::DataNode::Pointer node2 = m_Controls->m_MergeDwiBox->GetSelectedNode(); if (node2.IsNull()) { return; } mitk::Image::Pointer image2 = dynamic_cast(node2->GetData()); if ( image2 == nullptr ) { return; } typedef itk::VectorImage DwiImageType; typedef std::vector< DwiImageType::Pointer > DwiImageContainerType; typedef std::vector< GradientContainerType::Pointer > GradientListContainerType; DwiImageContainerType imageContainer; GradientListContainerType gradientListContainer; std::vector< double > bValueContainer; QString name = ""; { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); imageContainer.push_back( itkVectorImagePointer ); gradientListContainer.push_back( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); bValueContainer.push_back( static_cast (image->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); name += node->GetName().c_str(); } { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image2, itkVectorImagePointer); imageContainer.push_back( itkVectorImagePointer ); gradientListContainer.push_back( static_cast ( image2->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); bValueContainer.push_back( static_cast (image2->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); name += "+"; name += node2->GetName().c_str(); } typedef itk::MergeDiffusionImagesFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetImageVolumes(imageContainer); filter->SetGradientLists(gradientListContainer); filter->SetBValues(bValueContainer); filter->Update(); vnl_matrix_fixed< double, 3, 3 > mf; mf.set_identity(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetOutputGradients() ) ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mf ) ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( filter->GetB_Value() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); imageNode->SetName(name.toStdString().c_str()); GetDataStorage()->Add(imageNode); } void QmitkPreprocessingView::ExtractB0() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } // call the extraction withou averaging if the check-box is checked if( this->m_Controls->m_CheckExtractAll->isChecked() ) { DoExtractBOWithoutAveraging(); return; } ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer newNode=mitk::DataNode::New(); newNode->SetData( mitkImage ); newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0")); GetDataStorage()->Add(newNode, node); } void QmitkPreprocessingView::DoExtractBOWithoutAveraging() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } // typedefs typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); // Extract image using found index FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer newNode=mitk::DataNode::New(); newNode->SetData( mitkImage ); newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0_ALL")); GetDataStorage()->Add(newNode, node); /*A reinitialization is needed to access the time channels via the ImageNavigationController The Global-Geometry can not recognize the time channel without a re-init. (for a new selection in datamanger a automatically updated of the Global-Geometry should be done - if it contains the time channel)*/ mitk::RenderingManager::GetInstance()->InitializeViews( newNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } void QmitkPreprocessingView::AverageGradients() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) return; mitk::Image::Pointer newDwi = image->Clone(); PropHelper propertyHelper(newDwi); propertyHelper.AverageRedundantGradients(m_Controls->m_Blur->value()); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_averaged").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt index aea4114c8e..ef0bf7b66f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt @@ -1,9 +1,9 @@ # The project name must correspond to the directory name of your plug-in # and must not contain periods. project(org_mitk_gui_qt_diffusionimaging_registration) mitk_create_plugin( EXPORT_DIRECTIVE DIFFUSIONIMAGING_REGISTRATION_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkDiffusionCore + MODULE_DEPENDS MitkDiffusionCore MitkMatchPointRegistration MitkMatchPointRegistrationUI ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkDiffusionImagingRegistration.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkDiffusionImagingRegistration.dox index 771863b4ba..9ee9c72c29 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkDiffusionImagingRegistration.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkDiffusionImagingRegistration.dox @@ -1,16 +1,14 @@ /** -\page org_mitk_views_diffusionregistrationview DWI Registration +\page org_mitk_views_diffusionregistrationview Head-Motion Correction -\section QmitkDiffusionImagingUserManualDWIRegistration DWI Registration - -The DWI registration view allows head-motion and eddy-current correction. First the b=0 images (if more than 1) are registered and averaged. The averaged image then serves as fixed image for the alignment of the remaining (weighted, b>0) images. +This view provides head-motion and eddy-current correction methods. First the b=0 images (if more than 1) are registered and averaged. The averaged image then serves as fixed image for the alignment of the remaining (weighted, b>0) images. \imageMacro{registration_basic.png,"Basic DWI Registration Interface",8.00} In the basic settings, a selected DW image in the Data Manager is marked as Input Data and the Start Head Motion Correction button is enabled. If more than one DW images are selected, they will be processed in a consecutive manner. For larger sets of dw images to be processed, the Advanced settings can be used. \imageMacro{registration_batch.png,"Batch Processing DWI Registration Interface",8.00} Here all valid .dwi data located in the given input folder will be processed through the head motion correction and the output will be stored in the current working directory or in a custom folder if specified in the user interface. The output image will have the _MC postfix attached to the input's name. */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRigidRegistration.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRigidRegistration.dox new file mode 100644 index 0000000000..d98878e5a2 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRigidRegistration.dox @@ -0,0 +1,5 @@ +/** +\page org_mitk_views_simplerigidregistrationview Rigid Registration + +This view enables the simple rigid registration of two images. The registered image will be displayed in transparent blue color overlayed over the fixed image. To regain normal coloring, right-click on the data node and adjust the corresponding settings. +*/ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake index fe5c97e6a5..b20be9d47b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake @@ -1,41 +1,46 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp - + QmitkDiffusionRegistrationView.cpp + QmitkSimpleRigidRegistrationView.cpp + QmitkDwiRegistrationPerspective.cpp ) set(UI_FILES src/internal/QmitkDiffusionRegistrationViewControls.ui + src/internal/QmitkSimpleRigidRegistrationViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkDiffusionRegistrationView.h + src/internal/QmitkSimpleRigidRegistrationView.h + src/internal/QmitkDwiRegistrationPerspective.h ) set(CACHED_RESOURCE_FILES plugin.xml - + resources/diffusionregistration.png ) 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/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake index 074d5c67ef..d54299c5e7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake @@ -1,5 +1,5 @@ -set(Plugin-Name "MITK Fiber Processing") +set(Plugin-Name "MITK dMRI Registration") set(Plugin-Version "1.0.0") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common.legacy org.mitk.gui.qt.common) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml index cc8c81d085..3a030cdea7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml @@ -1,24 +1,52 @@ + + + + + - + + This perspective contains views for rigid image registration and head motion correction. + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkDwiRegistrationPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkDwiRegistrationPerspective.cpp new file mode 100644 index 0000000000..7f1109ce4d --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkDwiRegistrationPerspective.cpp @@ -0,0 +1,49 @@ +/*=================================================================== + +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 "QmitkDwiRegistrationPerspective.h" +#include "berryIViewLayout.h" + +void QmitkDwiRegistrationPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) +{ + ///////////////////////////////////////////////////// + // all di-app perspectives should have the following: + ///////////////////////////////////////////////////// + + QString 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.simplerigidregistrationview"); + left->AddView("org.mitk.views.diffusionregistrationview"); +} diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkDwiRegistrationPerspective.h similarity index 50% copy from Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp copy to Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkDwiRegistrationPerspective.h index 488e20c269..c89a61672e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkDwiRegistrationPerspective.h @@ -1,39 +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. ===================================================================*/ -#include "mitkPluginActivator.h" -#include "src/internal/QmitkDiffusionRegistrationView.h" +#ifndef QmitkDwiRegistrationPerspective_H_ +#define QmitkDwiRegistrationPerspective_H_ +#include -ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; - -ctkPluginContext* mitk::PluginActivator::GetContext() +class QmitkDwiRegistrationPerspective : public QObject, public berry::IPerspectiveFactory { - return m_Context; -} + Q_OBJECT + Q_INTERFACES(berry::IPerspectiveFactory) -void mitk::PluginActivator::start(ctkPluginContext* context) -{ - BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionRegistrationView, context) - m_Context = context; -} +public: -void mitk::PluginActivator::stop(ctkPluginContext* context) -{ - Q_UNUSED(context) - m_Context = nullptr; -} + QmitkDwiRegistrationPerspective() {} + ~QmitkDwiRegistrationPerspective() {} + + void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; +}; + +#endif /* QmitkFiberProcessingPerspective_H_ */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationView.cpp new file mode 100644 index 0000000000..2954bc3839 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationView.cpp @@ -0,0 +1,275 @@ +/*=================================================================== + +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. + +===================================================================*/ + +//misc +#define _USE_MATH_DEFINES +#include + +// Blueberry +#include +#include + +// Qmitk +#include "QmitkSimpleRigidRegistrationView.h" + +// MITK +#include +#include +#include +#include +#include +#include + +// Qt +#include + +#define _USE_MATH_DEFINES +#include + +const std::string QmitkSimpleRigidRegistrationView::VIEW_ID = "org.mitk.views.simplerigidregistrationview"; + +QmitkSimpleRigidRegistrationView::QmitkSimpleRigidRegistrationView() + : QmitkAbstractView() + , m_Controls( 0 ) +{ + +} + +// Destructor +QmitkSimpleRigidRegistrationView::~QmitkSimpleRigidRegistrationView() +{ + +} + +void QmitkSimpleRigidRegistrationView::StartRegistration() +{ + typedef itk::Image< float, 3 > ItkFloatImageType; + mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::New(); + + QmitkRegistrationJob* pJob = new QmitkRegistrationJob(algo); + pJob->setAutoDelete(true); + + m_MovingImageNode = m_Controls->m_MovingImageBox->GetSelectedNode(); + mitk::Image::Pointer movingImage = dynamic_cast(m_MovingImageNode->GetData()); + if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage)) + { + ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); + mitk::CastToItkImage(movingImage, itkVectorImagePointer); + + itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); + filter->SetInput( itkVectorImagePointer); + filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value()); + filter->Update(); + + mitk::Image::Pointer newImage = mitk::Image::New(); + newImage->InitializeByItk( filter->GetOutput() ); + newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); + + pJob->m_spMovingData = newImage; + } + else + pJob->m_spMovingData = movingImage; + + + mitk::Image::Pointer fixedImage = dynamic_cast(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); + if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(fixedImage)) + { + ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); + mitk::CastToItkImage(fixedImage, itkVectorImagePointer); + + itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); + filter->SetInput( itkVectorImagePointer); + filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value()); + filter->Update(); + + mitk::Image::Pointer newImage = mitk::Image::New(); + newImage->InitializeByItk( filter->GetOutput() ); + newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); + + pJob->m_spTargetData = newImage; + } + else + pJob->m_spTargetData = fixedImage; + + pJob->m_TargetDataUID = mitk::EnsureUID(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); + pJob->m_MovingDataUID = mitk::EnsureUID(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData()); + + connect(pJob, SIGNAL(RegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), this, + SLOT(OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), + Qt::BlockingQueuedConnection); + +// connect(pJob, SIGNAL(AlgorithmInfo(QString)), this, SLOT(OnAlgorithmInfo(QString))); +// connect(pJob, SIGNAL(AlgorithmStatusChanged(QString)), this, SLOT(OnAlgorithmStatusChanged(QString))); +// connect(pJob, SIGNAL(AlgorithmIterated(QString, bool, unsigned long)), this, SLOT(OnAlgorithmIterated(QString, bool, unsigned long))); +// connect(pJob, SIGNAL(LevelChanged(QString, bool, unsigned long)), this, SLOT(OnLevelChanged(QString, bool, unsigned long))); + + QThreadPool* threadPool = QThreadPool::globalInstance(); + threadPool->start(pJob); + + m_Controls->m_RegistrationStartButton->setEnabled(false); + m_Controls->m_RegistrationStartButton->setText("Registration in progress ..."); +} + +void QmitkSimpleRigidRegistrationView::OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* ) +{ + mitk::Image::Pointer movingImage = dynamic_cast(m_MovingImageNode->GetData()); + mitk::Image::Pointer image = mitk::ImageMappingHelper::refineGeometry(movingImage, spResultRegistration, true); + + if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image)) + { + mitk::DiffusionPropertyHelper propertyHelper( image ); + propertyHelper.InitializeImage(); + } + + mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); + resultNode->SetData(image); + + if (m_MovingImageNode.IsNotNull()) + { + m_MovingImageNode->SetVisibility(false); + QString name = m_MovingImageNode->GetName().c_str(); + resultNode->SetName((name+"_registered").toStdString().c_str()); + } + else + resultNode->SetName("Registered"); + resultNode->SetOpacity(0.6); + resultNode->SetColor(0.0, 0.0, 1.0); + + GetDataStorage()->Add(resultNode); + + this->GetRenderWindowPart()->RequestUpdate(); + + m_Controls->m_RegistrationStartButton->setEnabled(true); + m_Controls->m_RegistrationStartButton->setText("Start Registration"); + + m_MovingImageNode = nullptr; +} + +void QmitkSimpleRigidRegistrationView::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::QmitkSimpleRigidRegistrationViewControls; + m_Controls->setupUi( parent ); + + m_Controls->m_FixedImageBox->SetDataStorage(this->GetDataStorage()); + m_Controls->m_MovingImageBox->SetDataStorage(this->GetDataStorage()); + + mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); + m_Controls->m_FixedImageBox->SetPredicate(isImagePredicate); + m_Controls->m_MovingImageBox->SetPredicate(isImagePredicate); + + connect( m_Controls->m_FixedImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(FixedImageChanged()) ); + connect( m_Controls->m_MovingImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(MovingImageChanged()) ); + connect( m_Controls->m_RegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartRegistration()) ); + + FixedImageChanged(); + MovingImageChanged(); + } +} + +void QmitkSimpleRigidRegistrationView::FixedImageChanged() +{ + if (m_Controls->m_FixedImageBox->GetSelectedNode().IsNotNull()) + { + mitk::Image::Pointer image = dynamic_cast(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); + int channels = image->GetNumberOfChannels(); + int dims = image->GetDimension(); + int fourth_dim_size = image->GetTimeSteps(); + bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image); + + if (dims==4 || channels>1) + { + m_Controls->m_FixedChannelBox->setEnabled(false); + m_Controls->m_RegistrationStartButton->setEnabled(false); + } + + if (isdiff) + { + m_Controls->m_FixedChannelBox->setEnabled(true); + if (fourth_dim_size>1) + m_Controls->m_FixedChannelBox->setMaximum(fourth_dim_size-1); + else if (isdiff) + m_Controls->m_FixedChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1); + } + else + { + m_Controls->m_FixedChannelBox->setEnabled(false); + } + + m_Controls->m_RegistrationStartButton->setEnabled(true); + } + else + { + m_Controls->m_FixedChannelBox->setEnabled(false); + m_Controls->m_RegistrationStartButton->setEnabled(false); + } +} + +void QmitkSimpleRigidRegistrationView::MovingImageChanged() +{ + if (m_Controls->m_MovingImageBox->GetSelectedNode().IsNotNull()) + { + mitk::Image::Pointer image = dynamic_cast(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData()); + int channels = image->GetNumberOfChannels(); + int dims = image->GetDimension(); + int fourth_dim_size = image->GetTimeSteps(); + bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image); + + if (dims==4 || channels>1) + { + m_Controls->m_MovingChannelBox->setEnabled(false); + m_Controls->m_RegistrationStartButton->setEnabled(false); + } + + if (isdiff) + { + m_Controls->m_MovingChannelBox->setEnabled(true); + if (fourth_dim_size>1) + m_Controls->m_MovingChannelBox->setMaximum(fourth_dim_size-1); + else if (isdiff) + m_Controls->m_MovingChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1); + } + else + { + m_Controls->m_MovingChannelBox->setEnabled(false); + } + + m_Controls->m_RegistrationStartButton->setEnabled(true); + } + else + { + m_Controls->m_MovingChannelBox->setEnabled(false); + m_Controls->m_RegistrationStartButton->setEnabled(false); + } +} + +void QmitkSimpleRigidRegistrationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& ) +{ + FixedImageChanged(); + MovingImageChanged(); +} + + +void QmitkSimpleRigidRegistrationView::SetFocus() +{ + m_Controls->m_RegistrationStartButton->setFocus(); + FixedImageChanged(); + MovingImageChanged(); +} + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationView.h new file mode 100644 index 0000000000..23f278e3f4 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationView.h @@ -0,0 +1,71 @@ +/*=================================================================== + +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 +#include +#include "ui_QmitkSimpleRigidRegistrationViewControls.h" + +#include +#include +#include + +typedef short DiffusionPixelType; + +/*! +\brief View for diffusion image registration / head motion correction +*/ + +// Forward Qt class declarations + +class QmitkSimpleRigidRegistrationView : 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: + + typedef itk::VectorImage< short, 3 > ItkDwiType; + static const std::string VIEW_ID; + + QmitkSimpleRigidRegistrationView(); + virtual ~QmitkSimpleRigidRegistrationView(); + + virtual void CreateQtPartControl(QWidget *parent) override; + void SetFocus() override; + +protected slots: + + void MovingImageChanged(); + void FixedImageChanged(); + void StartRegistration(); + void OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* pRegJob); + +protected: + + /// \brief called by QmitkAbstractView when DataManager's selection has changed + virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; + + Ui::QmitkSimpleRigidRegistrationViewControls* m_Controls; + mitk::DataNode::Pointer m_MovingImageNode; + +private: + +}; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationViewControls.ui new file mode 100644 index 0000000000..e20c3f8dca --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRigidRegistrationViewControls.ui @@ -0,0 +1,118 @@ + + + QmitkSimpleRigidRegistrationViewControls + + + + 0 + 0 + 435 + 744 + + + + Form + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + + + Moving Image: + + + + + + + Fixed Image: + + + + + + + + + + false + + + Select dMRI volume used to calculate transformation. + + + + + + + false + + + Select dMRI volume used to calculate transformation. + + + + + + + + + + false + + + Start DWI registration/Head Motion Correction + + + Start Registration + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + QmitkDataStorageComboBox + QComboBox +
QmitkDataStorageComboBox.h
+ + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp index 488e20c269..581c7cf5d6 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp @@ -1,39 +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 "mitkPluginActivator.h" #include "src/internal/QmitkDiffusionRegistrationView.h" +#include "src/internal/QmitkSimpleRigidRegistrationView.h" +#include "src/internal/QmitkDwiRegistrationPerspective.h" ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; ctkPluginContext* mitk::PluginActivator::GetContext() { return m_Context; } void mitk::PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionRegistrationView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkSimpleRigidRegistrationView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkDwiRegistrationPerspective, context) m_Context = context; } void mitk::PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) m_Context = nullptr; }