diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h index 4700a41dcd..c7cef4cdb1 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h @@ -1,153 +1,153 @@ /*=================================================================== 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 __itkTractsToDWIImageFilter_h__ #define __itkTractsToDWIImageFilter_h__ // MITK #include #include #include #include // ITK #include #include #include #include #include #include namespace itk { /** * \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. */ template< class PixelType > class TractsToDWIImageFilter : public ImageSource< itk::VectorImage< PixelType, 3 > > { public: typedef TractsToDWIImageFilter Self; typedef ImageSource< itk::VectorImage< PixelType, 3 > > Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef typename Superclass::OutputImageType OutputImageType; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUcharImgType; typedef mitk::FiberBundleX::Pointer FiberBundleType; typedef itk::VectorImage< double, 3 > DoubleDwiType; typedef std::vector< mitk::KspaceArtifact* > KspaceArtifactList; typedef std::vector< mitk::DiffusionSignalModel* > DiffusionModelList; typedef itk::Matrix MatrixType; typedef mitk::DiffusionNoiseModel NoiseModelType; typedef itk::Image< double, 2 > SliceType; typedef itk::VnlForwardFFTImageFilter::OutputImageType ComplexSliceType; itkNewMacro(Self) itkTypeMacro( TractsToDWIImageFilter, ImageToImageFilter ) // input itkSetMacro( SignalScale, double ) itkSetMacro( FiberRadius, double ) itkSetMacro( InterpolationShrink, double ) ///< large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation) itkSetMacro( VolumeAccuracy, unsigned int ) ///< determines fiber sampling density and thereby the accuracy of the fiber volume fraction itkSetMacro( FiberBundle, FiberBundleType ) ///< input fiber bundle itkSetMacro( Spacing, mitk::Vector3D ) ///< output image spacing itkSetMacro( Origin, mitk::Point3D ) ///< output image origin itkSetMacro( DirectionMatrix, MatrixType ) ///< output image rotation itkSetMacro( EnforcePureFiberVoxels, bool ) ///< treat all voxels containing at least one fiber as fiber-only (actually disable non-fiber compartments for this voxel). itkSetMacro( ImageRegion, ImageRegion<3> ) ///< output image size itkSetMacro( NumberOfRepetitions, unsigned int ) ///< number of acquisition repetitions to reduce noise (default is no additional repetition) itkSetMacro( TissueMask, ItkUcharImgType::Pointer ) ///< voxels outside of this binary mask contain only noise (are treated as air) void SetNoiseModel(NoiseModelType* noiseModel){ m_NoiseModel = noiseModel; } ///< generates the noise added to the image values void SetFiberModels(DiffusionModelList modelList){ m_FiberModels = modelList; } ///< generate signal of fiber compartments void SetNonFiberModels(DiffusionModelList modelList){ m_NonFiberModels = modelList; } ///< generate signal of non-fiber compartments void SetKspaceArtifacts(KspaceArtifactList artifactList){ m_KspaceArtifacts = artifactList; } mitk::LevelWindow GetLevelWindow(){ return m_LevelWindow; } itkSetMacro( FrequencyMap, ItkDoubleImgType::Pointer ) itkSetMacro( kOffset, double ) itkSetMacro( tLine, double ) itkSetMacro( tInhom, double ) itkSetMacro( TE, double ) itkSetMacro( UseInterpolation, bool ) itkSetMacro( SimulateEddyCurrents, bool ) itkSetMacro( SimulateRelaxation, bool ) itkSetMacro( EddyGradientStrength, double ) itkSetMacro( Upsampling, double ) // output std::vector< ItkDoubleImgType::Pointer > GetVolumeFractions(){ return m_VolumeFractions; } void GenerateData(); protected: TractsToDWIImageFilter(); virtual ~TractsToDWIImageFilter(); itk::Point GetItkPoint(double point[3]); itk::Vector GetItkVector(double point[3]); vnl_vector_fixed GetVnlVector(double point[3]); vnl_vector_fixed GetVnlVector(Vector< float, 3 >& vector); /** Transform generated image compartment by compartment, channel by channel and slice by slice using FFT and add k-space artifacts. */ DoubleDwiType::Pointer DoKspaceStuff(std::vector< DoubleDwiType::Pointer >& images); // /** Rearrange FFT output to shift low frequencies to the iamge center (correct itk). */ // TractsToDWIImageFilter::ComplexSliceType::Pointer RearrangeSlice(ComplexSliceType::Pointer slice); - itk::Vector m_Spacing; ///< output image spacing - itk::Vector m_UpsampledSpacing; + mitk::Vector3D m_Spacing; ///< output image spacing + itk::Vector m_UpsampledSpacing; mitk::Point3D m_Origin; ///< output image origin MatrixType m_DirectionMatrix; ///< output image rotation ImageRegion<3> m_ImageRegion; ///< output image size ImageRegion<3> m_UpsampledImageRegion; ItkUcharImgType::Pointer m_TissueMask; ///< voxels outside of this binary mask contain only noise (are treated as air) ItkDoubleImgType::Pointer m_FrequencyMap; ///< map of the B0 inhomogeneities double m_kOffset; double m_tLine; double m_TE; double m_tInhom; FiberBundleType m_FiberBundle; ///< input fiber bundle DiffusionModelList m_FiberModels; ///< generate signal of fiber compartments DiffusionModelList m_NonFiberModels; ///< generate signal of non-fiber compartments KspaceArtifactList m_KspaceArtifacts; NoiseModelType* m_NoiseModel; ///< generates the noise added to the image values bool m_CircleDummy; unsigned int m_VolumeAccuracy; double m_Upsampling; ///< causes ringing artifacts unsigned int m_NumberOfRepetitions; bool m_EnforcePureFiberVoxels; double m_InterpolationShrink; double m_FiberRadius; double m_SignalScale; mitk::LevelWindow m_LevelWindow; bool m_UseInterpolation; std::vector< ItkDoubleImgType::Pointer > m_VolumeFractions; ///< one double image for each compartment containing the corresponding volume fraction per voxel bool m_SimulateRelaxation; bool m_SimulateEddyCurrents; double m_EddyGradientStrength; }; } #include "itkTractsToDWIImageFilter.cpp" #endif diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h index 55d920f7dd..d67bfa75d9 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h @@ -1,210 +1,210 @@ /*=================================================================== 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_QmitkFiberfoxViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View for fiber based diffusion software phantoms (Fiberfox). \sa QmitkFunctionality \ingroup Functionalities */ // Forward Qt class declarations using namespace std; class QmitkFiberfoxView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const string VIEW_ID; QmitkFiberfoxView(); virtual ~QmitkFiberfoxView(); virtual void CreateQtPartControl(QWidget *parent); void SetFocus(); typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef vector GradientListType; template vector > MakeGradientList(); protected slots: void LoadParameters(); void SaveParameters(); void OnDrawROI(); ///< adds new ROI, handles interactors etc. void OnAddBundle(); ///< adds new fiber bundle to datastorage void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists void GenerateFibers(); ///< generate fibers from the selected ROIs void GenerateImage(); ///< generate artificial image from the selected fiber bundle void JoinBundles(); ///< merges selcted fiber bundles into one void CopyBundles(); ///< add copy of the selected bundle to the datamanager void ApplyTransform(); ///< rotate and shift selected bundles void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center void Comp1ModelFrameVisibility(int index);///< only show parameters of selected fiber model type void Comp2ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type void Comp3ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type void Comp4ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type void ShowAdvancedOptions(int state); /** update fibers if any parameter changes */ void OnFiberDensityChanged(int value); void OnFiberSamplingChanged(double value); void OnTensionChanged(double value); void OnContinuityChanged(double value); void OnBiasChanged(double value); void OnVarianceChanged(double value); void OnDistributionChanged(int value); void OnAddGibbsRinging(int value); void OnAddNoise(int value); void OnAddGhosts(int value); void OnAddDistortions(int value); void OnAddEddy(int value); void OnConstantRadius(int value); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&); GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere Ui::QmitkFiberfoxViewControls* m_Controls; void UpdateImageParameters(); ///< update iamge generation paaremeter struct void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection void PlanarFigureSelected( itk::Object* object, const itk::EventObject& ); void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts void NodeAdded( const mitk::DataNode* node ); ///< add observers void NodeRemoved(const mitk::DataNode* node); ///< remove observers /** structure to keep track of planar figures and observers */ struct QmitkPlanarFigureData { QmitkPlanarFigureData() : m_Figure(0) , m_EndPlacementObserverTag(0) , m_SelectObserverTag(0) , m_StartInteractionObserverTag(0) , m_EndInteractionObserverTag(0) , m_Flipped(0) { } mitk::PlanarFigure* m_Figure; unsigned int m_EndPlacementObserverTag; unsigned int m_SelectObserverTag; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; unsigned int m_Flipped; }; /** structure storing the image generation parameters */ struct ImageParameters { itk::ImageRegion<3> imageRegion; - itk::Vector imageSpacing; - itk::Point imageOrigin; + mitk::Vector3D imageSpacing; + mitk::Point3D imageOrigin; itk::Matrix imageDirection; unsigned int numGradients; double b_value; unsigned int repetitions; double signalScale; double tEcho; double tLine; double tInhom; double axonRadius; unsigned int interpolationShrink; double kspaceLineOffset; double upsampling; double eddyStrength; double comp3Weight; double comp4Weight; bool doSimulateRelaxation; bool doSimulateEddyCurrents; bool doDisablePartialVolume; mitk::RicianNoiseModel ricianNoiseModel; mitk::DiffusionSignalModel::GradientListType gradientDirections; itk::TractsToDWIImageFilter< short >::DiffusionModelList fiberModelList, nonFiberModelList; itk::TractsToDWIImageFilter< short >::KspaceArtifactList artifactList; QString signalModelString, artifactModelString; ItkDoubleImgType::Pointer frequencyMap; ItkUcharImgType::Pointer tissueMaskImage; mitk::DataNode::Pointer resultNode; }; ImageParameters m_ImageGenParameters; std::map m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData mitk::Image::Pointer m_TissueMask; ///< mask defining which regions of the image should contain signal and which are containing only noise mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse mitk::DataNode::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedDWI; vector< mitk::DataNode::Pointer > m_SelectedBundles; vector< mitk::DataNode::Pointer > m_SelectedBundles2; vector< mitk::DataNode::Pointer > m_SelectedFiducials; vector< mitk::DataNode::Pointer > m_SelectedImages; // intra and inter axonal compartments mitk::StickModel m_StickModel1; mitk::StickModel m_StickModel2; mitk::TensorModel m_ZeppelinModel1; mitk::TensorModel m_ZeppelinModel2; mitk::TensorModel m_TensorModel1; mitk::TensorModel m_TensorModel2; // extra axonal compartment models mitk::BallModel m_BallModel1; mitk::BallModel m_BallModel2; mitk::AstroStickModel m_AstrosticksModel1; mitk::AstroStickModel m_AstrosticksModel2; mitk::DotModel m_DotModel1; mitk::DotModel m_DotModel2; };