diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp index ff74d07c12..90a392188d 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp @@ -1,246 +1,231 @@ /*=================================================================== 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. ===================================================================*/ /* * mitkFiberBundleMapper2D.cpp * mitk-all * * Created by HAL9000 on 1/17/11. * Copyright 2011 __MyCompanyName__. All rights reserved. * */ #include "mitkFiberBundleXMapper2D.h" #include #include #include #include #include //#include //#include #include #include #include #include #include #include #include #include //#include #include #include #include #include #include mitk::FiberBundleXMapper2D::FiberBundleXMapper2D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::FiberBundleXMapper2D::~FiberBundleXMapper2D() { } mitk::FiberBundleX* mitk::FiberBundleXMapper2D::GetInput() { return dynamic_cast< mitk::FiberBundleX * > ( GetDataNode()->GetData() ); } void mitk::FiberBundleXMapper2D::Update(mitk::BaseRenderer * renderer) { + bool visible = true; + GetDataNode()->GetVisibility(visible, renderer, "visible"); + if ( !visible ) + return; + + // Calculate time step of the input data for the specified renderer (integer value) + // this method is implemented in mitkMapper + this->CalculateTimeStep( renderer ); + + //check if updates occured in the node or on the display + FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); + + //set renderer independent shader properties + const DataNode::Pointer node = this->GetDataNode(); + float thickness = 2.0; + if(!this->GetDataNode()->GetPropertyValue("Fiber2DSliceThickness",thickness)) + MITK_INFO << "FIBER2D SLICE THICKNESS PROPERTY ERROR"; + + bool fiberfading = false; + if(!this->GetDataNode()->GetPropertyValue("Fiber2DfadeEFX",fiberfading)) + MITK_INFO << "FIBER2D SLICE FADE EFX PROPERTY ERROR"; + + float fiberOpacity; + this->GetDataNode()->GetOpacity(fiberOpacity, NULL); + node->SetFloatProperty("shader.mitkShaderFiberClipping.fiberThickness",thickness); + node->SetIntProperty("shader.mitkShaderFiberClipping.fiberFadingON",fiberfading); + node->SetFloatProperty("shader.mitkShaderFiberClipping.fiberOpacity",fiberOpacity); + + if ((localStorage->m_LastUpdateTime < renderer->GetDisplayGeometry()->GetMTime()) ) //was the display geometry modified? e.g. zooming, panning) + { + this->UpdateShaderParameter(renderer); + } - bool visible = true; - GetDataNode()->GetVisibility(visible, renderer, "visible"); - - if ( !visible ) return; - - - MITK_DEBUG << "MapperFBX 2D update: "; - // Calculate time step of the input data for the specified renderer (integer value) - // this method is implemented in mitkMapper - this->CalculateTimeStep( renderer ); - - //check if updates occured in the node or on the display - FBXLocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); - - //set renderer independent shader properties - const DataNode::Pointer node = this->GetDataNode(); - float thickness = 2.0; - if(!this->GetDataNode()->GetPropertyValue("Fiber2DSliceThickness",thickness)) - MITK_INFO << "FIBER2D SLICE THICKNESS PROPERTY ERROR"; - - bool fiberfading = false; - if(!this->GetDataNode()->GetPropertyValue("Fiber2DfadeEFX",fiberfading)) - MITK_INFO << "FIBER2D SLICE FADE EFX PROPERTY ERROR"; - - float fiberOpacity; - this->GetDataNode()->GetOpacity(fiberOpacity, NULL); - node->SetFloatProperty("shader.mitkShaderFiberClipping.fiberThickness",thickness); - node->SetIntProperty("shader.mitkShaderFiberClipping.fiberFadingON",fiberfading); - node->SetFloatProperty("shader.mitkShaderFiberClipping.fiberOpacity",fiberOpacity); - - if ((localStorage->m_LastUpdateTime < renderer->GetDisplayGeometry()->GetMTime()) ) //was the display geometry modified? e.g. zooming, panning) - { - - this->UpdateShaderParameter(renderer); - - } - - if ( (localStorage->m_LastUpdateTime < node->GetMTime()) - || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) //was a property modified? - || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) ) - { - // MITK_INFO << "UPDATE NEEDED FOR _ " << renderer->GetName(); - this->GenerateDataForRenderer( renderer ); - } - - + if ( (localStorage->m_LastUpdateTime < node->GetMTime()) + || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) //was a property modified? + || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) ) + { + // MITK_INFO << "UPDATE NEEDED FOR _ " << renderer->GetName(); + this->GenerateDataForRenderer( renderer ); + } } void mitk::FiberBundleXMapper2D::UpdateShaderParameter(mitk::BaseRenderer * renderer) { //get information about current position of views mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController(); mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry(); //generate according cutting planes based on the view position float sliceN[3], planeOrigin[3]; - // since shader uses camera coordinates, transform origin and normal from worldcoordinates to cameracoordinates - planeOrigin[0] = (float) planeGeo->GetOrigin()[0]; planeOrigin[1] = (float) planeGeo->GetOrigin()[1]; planeOrigin[2] = (float) planeGeo->GetOrigin()[2]; sliceN[0] = planeGeo->GetNormal()[0]; sliceN[1] = planeGeo->GetNormal()[1]; sliceN[2] = planeGeo->GetNormal()[2]; float tmp1 = planeOrigin[0] * sliceN[0]; float tmp2 = planeOrigin[1] * sliceN[1]; float tmp3 = planeOrigin[2] * sliceN[2]; float d1 = tmp1 + tmp2 + tmp3; //attention, correct normalvector float plane1[4]; plane1[0] = sliceN[0]; plane1[1] = sliceN[1]; plane1[2] = sliceN[2]; plane1[3] = d1; DataNode::Pointer node = this->GetDataNode(); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.w",plane1[3],renderer); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.x",plane1[0],renderer); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.y",plane1[1],renderer); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.z",plane1[2],renderer); - } -// ALL RAW DATA FOR VISUALIZATION IS GENERATED HERE. // vtkActors and Mappers are feeded here void mitk::FiberBundleXMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { + mitk::FiberBundleX* fiberBundle = this->GetInput(); + if (fiberBundle==NULL) + return; + //the handler of local storage gets feeded in this method with requested data for related renderwindow - FBXLocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); + FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); - //this procedure is depricated, - //not needed after initializaton anymore mitk::DataNode* node = this->GetDataNode(); if ( node == NULL ) return; - ///THIS GET INPUT - mitk::FiberBundleX* fbx = this->GetInput(); - - localStorage->m_PointMapper->ScalarVisibilityOn(); - localStorage->m_PointMapper->SetScalarModeToUsePointFieldData(); - localStorage->m_PointMapper->SetLookupTable(m_lut); //apply the properties after the slice was set + localStorage->m_FiberMapper->ScalarVisibilityOn(); + localStorage->m_FiberMapper->SetScalarModeToUsePointFieldData(); + localStorage->m_FiberMapper->SetLookupTable(m_lut); //apply the properties after the slice was set localStorage->m_PointActor->GetProperty()->SetOpacity(0.999); // set color - if (fbx->GetCurrentColorCoding() != NULL){ -// localStorage->m_PointMapper->SelectColorArray(""); - localStorage->m_PointMapper->SelectColorArray(fbx->GetCurrentColorCoding()); - MITK_DEBUG << "MapperFBX 2D: " << fbx->GetCurrentColorCoding(); + if (fiberBundle->GetCurrentColorCoding() != NULL) + { + localStorage->m_FiberMapper->SelectColorArray(fiberBundle->GetCurrentColorCoding()); - if(fbx->GetCurrentColorCoding() == fbx->COLORCODING_CUSTOM){ + if(fiberBundle->GetCurrentColorCoding() == fiberBundle->COLORCODING_CUSTOM){ float temprgb[3]; this->GetDataNode()->GetColor( temprgb, NULL ); double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; localStorage->m_PointActor->GetProperty()->SetColor(trgb); } } int lineWidth = 1; node->GetIntProperty("LineWidth",lineWidth); - localStorage->m_PointMapper->SetInputData(fbx->GetFiberPolyData()); - localStorage->m_PointActor->SetMapper(localStorage->m_PointMapper); + localStorage->m_FiberMapper->SetInputData(fiberBundle->GetFiberPolyData()); + localStorage->m_PointActor->SetMapper(localStorage->m_FiberMapper); localStorage->m_PointActor->GetProperty()->ShadingOn(); localStorage->m_PointActor->GetProperty()->SetLineWidth(lineWidth); // Applying shading properties this->ApplyShaderProperties(renderer); // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } vtkProp* mitk::FiberBundleXMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { - //MITK_INFO << "FiberBundleMapper2D GetVtkProp(renderer)"; this->Update(renderer); - return m_LSH.GetLocalStorage(renderer)->m_PointActor; + return m_LocalStorageHandler.GetLocalStorage(renderer)->m_PointActor; } void mitk::FiberBundleXMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) -{ //add shader to datano +{ node->SetProperty("shader",mitk::ShaderProperty::New("mitkShaderFiberClipping")); // Shaders IShaderRepository* shaderRepo = CoreServices::GetShaderRepository(); if (shaderRepo) { shaderRepo->AddDefaultProperties(node, renderer, overwrite); } //add other parameters to propertylist node->AddProperty( "Fiber2DSliceThickness", mitk::FloatProperty::New(2.0f), renderer, overwrite ); node->AddProperty( "Fiber2DfadeEFX", mitk::BoolProperty::New(true), renderer, overwrite ); Superclass::SetDefaultProperties(node, renderer, overwrite); } mitk::FiberBundleXMapper2D::FBXLocalStorage::FBXLocalStorage() { m_PointActor = vtkSmartPointer::New(); - m_PointMapper = vtkSmartPointer::New(); - + m_FiberMapper = vtkSmartPointer::New(); } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.h index f4cb17cbcf..6832499c4f 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.h +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.h @@ -1,109 +1,108 @@ /*=================================================================== 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 FIBERBUNDLEXMAPPER2D_H_HEADER_INCLUDED #define FIBERBUNDLEXMAPPER2D_H_HEADER_INCLUDED //MITK Rendering #include #include //#include #include #include #include class vtkActor; //class vtkPropAssembly; //lets see if we need it class mitkBaseRenderer; class vtkPolyDataMapper; class vtkCutter; class vtkPlane; class vtkPolyData; namespace mitk { - struct IShaderRepository; +struct IShaderRepository; - class FiberBundleXMapper2D : public VtkMapper - { +class FiberBundleXMapper2D : public VtkMapper +{ - public: +public: mitkClassMacro(FiberBundleXMapper2D, VtkMapper); itkFactorylessNewMacro(Self) itkCloneMacro(Self) mitk::FiberBundleX* GetInput(); - /** \brief Checks whether this mapper needs to update itself and generate - * data. */ + /** \brief Checks whether this mapper needs to update itself and generate data. */ virtual void Update(mitk::BaseRenderer * renderer); - static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = NULL, bool overwrite = false ); + static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = NULL, bool overwrite = false ); //### methods of MITK-VTK rendering pipeline virtual vtkProp* GetVtkProp(mitk::BaseRenderer* renderer); //### end of methods of MITK-VTK rendering pipeline class FBXLocalStorage : public mitk::Mapper::BaseLocalStorage { public: - /** \brief Point Actor of a 2D render window. */ - vtkSmartPointer m_PointActor; - /** \brief Point Mapper of a 2D render window. */ - vtkSmartPointer m_PointMapper; - vtkSmartPointer m_SlicingPlane; //needed later when optimized 2D mapper - vtkSmartPointer m_SlicedResult; //might be depricated in optimized 2D mapper - - /** \brief Timestamp of last update of stored data. */ - itk::TimeStamp m_LastUpdateTime; - /** \brief Constructor of the local storage. Do as much actions as possible in here to avoid double executions. */ - FBXLocalStorage(); //if u copy&paste from this 2Dmapper, be aware that the implementation of this constructor is in the cpp file - - ~FBXLocalStorage() - { - } + /** \brief Point Actor of a 2D render window. */ + vtkSmartPointer m_PointActor; + /** \brief Point Mapper of a 2D render window. */ + vtkSmartPointer m_FiberMapper; + vtkSmartPointer m_SlicingPlane; //needed later when optimized 2D mapper + vtkSmartPointer m_SlicedResult; //might be depricated in optimized 2D mapper + + /** \brief Timestamp of last update of stored data. */ + itk::TimeStamp m_LastUpdateTime; + /** \brief Constructor of the local storage. Do as much actions as possible in here to avoid double executions. */ + FBXLocalStorage(); //if u copy&paste from this 2Dmapper, be aware that the implementation of this constructor is in the cpp file + + ~FBXLocalStorage() + { + } }; /** \brief This member holds all three LocalStorages for the three 2D render windows. */ - mitk::LocalStorageHandler m_LSH; + mitk::LocalStorageHandler m_LocalStorageHandler; - protected: +protected: FiberBundleXMapper2D(); virtual ~FiberBundleXMapper2D(); /** Does the actual resampling, without rendering. */ virtual void GenerateDataForRenderer(mitk::BaseRenderer*); void UpdateShaderParameter(mitk::BaseRenderer*); - private: +private: vtkSmartPointer m_lut; - }; +}; }//end namespace #endif diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp index 2ab7ecdbf0..0437372345 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp @@ -1,186 +1,189 @@ /*=================================================================== 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 "mitkFiberBundleXMapper3D.h" #include //#include //#include #include #include #include #include //not essential for mapper // #include mitk::FiberBundleXMapper3D::FiberBundleXMapper3D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::FiberBundleXMapper3D::~FiberBundleXMapper3D() { } const mitk::FiberBundleX* mitk::FiberBundleXMapper3D::GetInput() { return static_cast ( GetDataNode()->GetData() ); } /* This method is called once the mapper gets new input, for UI rotation or changes in colorcoding this method is NOT called */ void mitk::FiberBundleXMapper3D::InternalGenerateData(mitk::BaseRenderer *renderer) { - mitk::FiberBundleX* FBX = dynamic_cast (GetDataNode()->GetData()); - if (FBX == NULL) + mitk::FiberBundleX* fiberBundle = dynamic_cast (GetDataNode()->GetData()); + if (fiberBundle == NULL) return; - vtkSmartPointer FiberData = FBX->GetFiberPolyData(); - - if (FiberData == NULL) + vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); + if (fiberPolyData == NULL) return; FBXLocalStorage3D *localStorage = m_LSH.GetLocalStorage(renderer); - localStorage->m_FiberMapper->SetInputData(FiberData); + localStorage->m_FiberMapper->SetInputData(fiberPolyData); - if ( FiberData->GetPointData()->GetNumberOfArrays() > 0 ) - localStorage->m_FiberMapper->SelectColorArray( FBX->GetCurrentColorCoding() ); + if ( fiberPolyData->GetPointData()->GetNumberOfArrays() > 0 ) + localStorage->m_FiberMapper->SelectColorArray( fiberBundle->GetCurrentColorCoding() ); localStorage->m_FiberMapper->ScalarVisibilityOn(); localStorage->m_FiberMapper->SetScalarModeToUsePointFieldData(); localStorage->m_FiberActor->SetMapper(localStorage->m_FiberMapper); localStorage->m_FiberMapper->SetLookupTable(m_lut); // set Opacity float tmpopa; this->GetDataNode()->GetOpacity(tmpopa, NULL); localStorage->m_FiberActor->GetProperty()->SetOpacity((double) tmpopa); int lineWidth = 1; this->GetDataNode()->GetIntProperty("LineWidth",lineWidth); localStorage->m_FiberActor->GetProperty()->SetLineWidth(lineWidth); // set color - if (FBX->GetCurrentColorCoding() != NULL){ -// localStorage->m_FiberMapper->SelectColorArray(""); - localStorage->m_FiberMapper->SelectColorArray(FBX->GetCurrentColorCoding()); - MITK_DEBUG << "MapperFBX: " << FBX->GetCurrentColorCoding(); + if (fiberBundle->GetCurrentColorCoding() != NULL){ + // localStorage->m_FiberMapper->SelectColorArray(""); + localStorage->m_FiberMapper->SelectColorArray(fiberBundle->GetCurrentColorCoding()); + MITK_DEBUG << "MapperFBX: " << fiberBundle->GetCurrentColorCoding(); - if(FBX->GetCurrentColorCoding() == FBX->COLORCODING_CUSTOM) { + if(fiberBundle->GetCurrentColorCoding() == fiberBundle->COLORCODING_CUSTOM) { float temprgb[3]; this->GetDataNode()->GetColor( temprgb, NULL ); double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; localStorage->m_FiberActor->GetProperty()->SetColor(trgb); } } localStorage->m_FiberAssembly->AddPart(localStorage->m_FiberActor); localStorage->m_LastUpdateTime.Modified(); //since this method is called after generating all necessary data for fiber visualization, all modifications are represented so far. } void mitk::FiberBundleXMapper3D::GenerateDataForRenderer( mitk::BaseRenderer *renderer ) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); - if ( !visible ) return; + mitk::FiberBundleX* fiberBundle = dynamic_cast (GetDataNode()->GetData()); + if (!fiberBundle->GetUpdateMapper3D()) + return; + fiberBundle->SetUpdateMapper3D(false); + // Calculate time step of the input data for the specified renderer (integer value) // this method is implemented in mitkMapper this->CalculateTimeStep( renderer ); //check if updates occured in the node or on the display FBXLocalStorage3D *localStorage = m_LSH.GetLocalStorage(renderer); const DataNode *node = this->GetDataNode(); if ( (localStorage->m_LastUpdateTime < node->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) //was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) ) { MITK_DEBUG << "UPDATE NEEDED FOR _ " << renderer->GetName(); this->InternalGenerateData(renderer); } } void mitk::FiberBundleXMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { // MITK_INFO << "FiberBundleXxXXMapper3D()SetDefaultProperties"; //MITK_INFO << "FiberBundleMapperX3D SetDefault Properties(...)"; // node->AddProperty( "DisplayChannel", mitk::IntProperty::New( true ), renderer, overwrite ); node->AddProperty( "LineWidth", mitk::IntProperty::New( true ), renderer, overwrite ); node->AddProperty( "opacity", mitk::FloatProperty::New( 1.0 ), renderer, overwrite); // node->AddProperty( "VertexOpacity_1", mitk::BoolProperty::New( false ), renderer, overwrite); // node->AddProperty( "Set_FA_VertexAlpha", mitk::BoolProperty::New( false ), renderer, overwrite); // node->AddProperty( "pointSize", mitk::FloatProperty::New(0.5), renderer, overwrite); // node->AddProperty( "setShading", mitk::IntProperty::New(1), renderer, overwrite); // node->AddProperty( "Xmove", mitk::IntProperty::New( 0 ), renderer, overwrite); // node->AddProperty( "Ymove", mitk::IntProperty::New( 0 ), renderer, overwrite); // node->AddProperty( "Zmove", mitk::IntProperty::New( 0 ), renderer, overwrite); // node->AddProperty( "RepPoints", mitk::BoolProperty::New( false ), renderer, overwrite); // node->AddProperty( "TubeSides", mitk::IntProperty::New( 8 ), renderer, overwrite); // node->AddProperty( "TubeRadius", mitk::FloatProperty::New( 0.15 ), renderer, overwrite); // node->AddProperty( "TubeOpacity", mitk::FloatProperty::New( 1.0 ), renderer, overwrite); node->AddProperty( "pickable", mitk::BoolProperty::New( true ), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } vtkProp* mitk::FiberBundleXMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { //MITK_INFO << "FiberBundleXxXXMapper3D()GetVTKProp"; //this->GenerateData(); return m_LSH.GetLocalStorage(renderer)->m_FiberAssembly; } void mitk::FiberBundleXMapper3D::UpdateVtkObjects() { } void mitk::FiberBundleXMapper3D::SetVtkMapperImmediateModeRendering(vtkMapper *) { } mitk::FiberBundleXMapper3D::FBXLocalStorage3D::FBXLocalStorage3D() { m_FiberActor = vtkSmartPointer::New(); m_FiberMapper = vtkSmartPointer::New(); m_FiberAssembly = vtkSmartPointer::New(); } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.h index d8df222d8d..554ea35f63 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.h +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.h @@ -1,103 +1,103 @@ /*=================================================================== 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 FiberBundleXMapper3D_H_HEADER_INCLUDED #define FiberBundleXMapper3D_H_HEADER_INCLUDED //#include //?? necessary #include #include #include #include #include #include class vtkPropAssembly; namespace mitk { //##Documentation //## @brief Mapper for FiberBundleX //## @ingroup Mapper class FiberBundleXMapper3D : public VtkMapper { public: - mitkClassMacro(FiberBundleXMapper3D, VtkMapper); + mitkClassMacro(FiberBundleXMapper3D, VtkMapper) itkFactorylessNewMacro(Self) itkCloneMacro(Self) //========== essential implementation for 3D mapper ======== const FiberBundleX* GetInput(); virtual vtkProp *GetVtkProp(mitk::BaseRenderer *renderer); //looks like depricated.. should be replaced bz GetViewProp() static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = NULL, bool overwrite = false ); static void SetVtkMapperImmediateModeRendering(vtkMapper *mapper); virtual void GenerateDataForRenderer(mitk::BaseRenderer* renderer); //========================================================= class FBXLocalStorage3D : public mitk::Mapper::BaseLocalStorage { public: /** \brief Point Actor of a 3D render window. */ vtkSmartPointer m_FiberActor; /** \brief Point Mapper of a 3D render window. */ vtkSmartPointer m_FiberMapper; vtkSmartPointer m_FiberAssembly; /** \brief Timestamp of last update of stored data. */ itk::TimeStamp m_LastUpdateTime; /** \brief Constructor of the local storage. Do as much actions as possible in here to avoid double executions. */ FBXLocalStorage3D(); //if u copy&paste from this 2Dmapper, be aware that the implementation of this constructor is in the cpp file ~FBXLocalStorage3D() { } }; /** \brief This member holds all three LocalStorages for the 3D render window(s). */ mitk::LocalStorageHandler m_LSH; protected: FiberBundleXMapper3D(); virtual ~FiberBundleXMapper3D(); void InternalGenerateData(mitk::BaseRenderer *renderer); void UpdateVtkObjects(); //?? private: vtkSmartPointer m_lut; }; } // end namespace mitk #endif /* FiberBundleXMapper3D_H_HEADER_INCLUDED */ diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index a04083cce4..6790c64617 100755 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,1961 +1,1964 @@ /*=================================================================== 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 _USE_MATH_DEFINES #include "mitkFiberBundleX.h" #include #include #include #include "mitkImagePixelReadAccessor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient"; //const char* mitk::FiberBundleX::COLORCODING_FA_AS_OPACITY = "Color_Orient_FA_Opacity"; const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "FA_Values"; const char* mitk::FiberBundleX::COLORCODING_CUSTOM = "custom"; const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs"; using namespace std; mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData ) : m_CurrentColorCoding(NULL) , m_NumFibers(0) , m_FiberSampling(0) + , m_UpdateMapper3D(false) { m_FiberPolyData = vtkSmartPointer::New(); if (fiberPolyData != NULL) { m_FiberPolyData = fiberPolyData; //m_FiberPolyData->DeepCopy(fiberPolyData); this->DoColorCodingOrientationBased(); } this->UpdateFiberGeometry(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); this->GenerateFiberIds(); } mitk::FiberBundleX::~FiberBundleX() { } mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy() { mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(m_FiberPolyData); newFib->SetColorCoding(m_CurrentColorCoding); return newFib; } vtkSmartPointer mitk::FiberBundleX::GeneratePolyDataByIds(std::vector fiberIds) { MITK_DEBUG << "\n=====FINAL RESULT: fib_id ======\n"; MITK_DEBUG << "Number of new Fibers: " << fiberIds.size(); // iterate through the vectorcontainer hosting all desired fiber Ids vtkSmartPointer newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); // if FA array available, initialize fa double array // if color orient array is available init color array vtkSmartPointer faValueArray; vtkSmartPointer colorsT; //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = sizeof(rgba); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ MITK_DEBUG << "FA VALUES AVAILABLE, init array for new fiberbundle"; faValueArray = vtkSmartPointer::New(); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ MITK_DEBUG << "colorValues available, init array for new fiberbundle"; colorsT = vtkUnsignedCharArray::New(); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); } std::vector::iterator finIt = fiberIds.begin(); while ( finIt != fiberIds.end() ) { if (*finIt < 0 || *finIt>GetNumFibers()){ MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt; break; } vtkSmartPointer fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); vtkSmartPointer fibPoints = fiber->GetPoints(); vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); i++) { // MITK_DEBUG << "id: " << fiber->GetPointId(i); // MITK_DEBUG << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2]; newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints()); newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ // MITK_DEBUG << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i)); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ // MITK_DEBUG << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0]; } } newLineSet->InsertNextCell(newFiber); ++finIt; } newFiberPolyData->SetPoints(newPointSet); newFiberPolyData->SetLines(newLineSet); MITK_DEBUG << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints(); MITK_DEBUG << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines(); MITK_DEBUG << "=====================\n"; // mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData); return newFiberPolyData; } // merge two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::AddBundle(mitk::FiberBundleX* fib) { if (fib==NULL) { MITK_WARN << "trying to call AddBundle with NULL argument"; return NULL; } MITK_INFO << "Adding fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); return newFib; } // subtract two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::SubtractBundle(mitk::FiberBundleX* fib) { MITK_INFO << "Subtracting fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // iterate over current fibers boost::progress_display disp(m_NumFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==NULL || numPoints<=0) continue; int numFibers2 = fib->GetNumFibers(); bool contained = false; for( int i2=0; i2GetFiberPolyData()->GetCell(i2); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (points2==NULL)// || numPoints2<=0) continue; // check endpoints if (numPoints2==numPoints) { itk::Point point_start = GetItkPoint(points->GetPoint(0)); itk::Point point_end = GetItkPoint(points->GetPoint(numPoints-1)); itk::Point point2_start = GetItkPoint(points2->GetPoint(0)); itk::Point point2_end = GetItkPoint(points2->GetPoint(numPoints2-1)); if ((point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps) || (point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps)) { // further checking ??? contained = true; break; } } } // add to result because fiber is not subtracted if (!contained) { vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(points->GetPoint(j)); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } } if(vNewLines->GetNumberOfCells()==0) return NULL; // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle return mitk::FiberBundleX::New(vNewPolyData); } itk::Point mitk::FiberBundleX::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } /* * set polydata (additional flag to recompute fiber geometry, default = true) */ void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer fiberPD, bool updateGeometry) { if (fiberPD == NULL) this->m_FiberPolyData = vtkSmartPointer::New(); else { m_FiberPolyData->DeepCopy(fiberPD); DoColorCodingOrientationBased(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); SetColorCoding(COLORCODING_ORIENTATION_BASED); GenerateFiberIds(); } /* * return vtkPolyData */ vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() { return m_FiberPolyData; } void mitk::FiberBundleX::DoColorCodingOrientationBased() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also polydata needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= /* make sure that processing colorcoding is only called when necessary */ if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && m_FiberPolyData->GetNumberOfPoints() == m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) { // fiberstructure is already colorcoded MITK_DEBUG << " NO NEED TO REGENERATE COLORCODING! " ; this->ResetFiberOpacity(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); return; } /* Finally, execute color calculation */ vtkPoints* extrPoints = NULL; extrPoints = m_FiberPolyData->GetPoints(); int numOfPoints = 0; if (extrPoints!=NULL) numOfPoints = extrPoints->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; // int componentSize = sizeof(rgba); int componentSize = 4; vtkSmartPointer colorsT = vtkSmartPointer::New(); colorsT->Allocate(numOfPoints * componentSize); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); /* checkpoint: does polydata contain any fibers */ int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) { MITK_DEBUG << "\n ========= Number of Fibers is 0 and below ========= \n"; return; } /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); // MITK_DEBUG << "Fib#: " << fi << " of " << numOfFibers << " pnts in fiber: " << pointsPerFiber ; /* single fiber checkpoints: is number of points valid */ if (pointsPerFiber > 1) { /* operate on points of single fiber */ for (int i=0; i 0) { /* The color value of the current point is influenced by the previous point and next point. */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; diff.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2])); rgba[3] = (unsigned char) (255.0); } else if (i==0) { /* First point has no previous point, therefore only diff1 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; diff1.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==pointsPerFiber-1) { /* Last point has no next point, therefore only diff2 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2])); rgba[3] = (unsigned char) (255.0); } colorsT->InsertTupleValue(idList[i], rgba); } //end for loop } else if (pointsPerFiber == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; // colorsT->InsertTupleValue(0, rgba); } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } }//end for loop m_FiberPolyData->GetPointData()->AddArray(colorsT); /*========================= - this is more relevant for renderer than for fiberbundleX datastructure - think about sourcing this to a explicit method which coordinates colorcoding */ this->SetColorCoding(COLORCODING_ORIENTATION_BASED); // =========================== //mini test, shall be ported to MITK TESTINGS! if (colorsT->GetSize() != numOfPoints*componentSize) MITK_DEBUG << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; } void mitk::FiberBundleX::DoColorCodingFaBased() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; this->SetColorCoding(COLORCODING_FA_BASED); MITK_DEBUG << "FBX: done CC FA based"; this->GenerateFiberIds(); } void mitk::FiberBundleX::DoUseFaFiberOpacity() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) != 1 ) return; vtkDoubleArray* FAValArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_FA_BASED); vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); for(long i=0; iGetNumberOfTuples(); i++) { double faValue = FAValArray->GetValue(i); faValue = faValue * 255.0; ColorArray->SetComponent(i,3, (unsigned char) faValue ); } this->SetColorCoding(COLORCODING_ORIENTATION_BASED); MITK_DEBUG << "FBX: done CC OPACITY"; this->GenerateFiberIds(); } void mitk::FiberBundleX::ResetFiberOpacity() { vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); if (ColorArray==NULL) return; for(long i=0; iGetNumberOfTuples(); i++) ColorArray->SetComponent(i,3, 255.0 ); } void mitk::FiberBundleX::SetFAMap(mitk::Image::Pointer FAimage) { mitkPixelTypeMultiplex1( SetFAMap, FAimage->GetPixelType(), FAimage ); } template void mitk::FiberBundleX::SetFAMap(const mitk::PixelType, mitk::Image::Pointer FAimage) { MITK_DEBUG << "SetFAMap"; vtkSmartPointer faValues = vtkSmartPointer::New(); faValues->SetName(COLORCODING_FA_BASED); faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); mitk::ImagePixelReadAccessor readFAimage (FAimage, FAimage->GetVolumeData(0)); vtkPoints* pointSet = m_FiberPolyData->GetPoints(); for(long i=0; iGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; double faPixelValue = 1-readFAimage.GetPixelByWorldCoordinates(px); faValues->InsertValue(i, faPixelValue); } m_FiberPolyData->GetPointData()->AddArray(faValues); this->GenerateFiberIds(); if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED)) MITK_DEBUG << "FA VALUE ARRAY SET"; } void mitk::FiberBundleX::GenerateFiberIds() { if (m_FiberPolyData == NULL) return; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInputData(m_FiberPolyData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); MITK_DEBUG << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint, bool invert) { vtkSmartPointer polyData = m_FiberPolyData; if (anyPoint) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleFibers(minSpacing/5); polyData = fibCopy->GetFiberPolyData(); } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Extracting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cellOriginal = m_FiberPolyData->GetCell(i); int numPointsOriginal = cellOriginal->GetNumberOfPoints(); vtkPoints* pointsOriginal = cellOriginal->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1 && numPointsOriginal) { if (anyPoint) { if (!invert) { for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } break; } } } else { bool includeFiber = true; for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { includeFiber = false; break; } } if (includeFiber) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } else { double* start = pointsOriginal->GetPoint(0); itk::Point itkStart; itkStart[0] = start[0]; itkStart[1] = start[1]; itkStart[2] = start[2]; itk::Index<3> idxStart; mask->TransformPhysicalPointToIndex(itkStart, idxStart); double* end = pointsOriginal->GetPoint(numPointsOriginal-1); itk::Point itkEnd; itkEnd[0] = end[0]; itkEnd[1] = end[1]; itkEnd[2] = end[2]; itk::Index<3> idxEnd; mask->TransformPhysicalPointToIndex(itkEnd, idxEnd); if ( mask->GetPixel(idxStart)>0 && mask->GetPixel(idxEnd)>0 && mask->GetLargestPossibleRegion().IsInside(idxStart) && mask->GetLargestPossibleRegion().IsInside(idxEnd) ) { for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); return mitk::FiberBundleX::New(newPolyData); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::RemoveFibersOutside(ItkUcharImgType* mask, bool invert) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleFibers(minSpacing/10); vtkSmartPointer polyData =fibCopy->GetFiberPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Cutting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1) { int newNumPoints = 0; for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) && !invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if ( (mask->GetPixel(idx)<=0 || !mask->GetLargestPossibleRegion().IsInside(idx)) && invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if (newNumPoints>0) { vtkNewCells->InsertNextCell(container); newNumPoints = 0; container = vtkSmartPointer::New(); } } if (newNumPoints>0) vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newPolyData); newFib->ResampleFibers(minSpacing/2); return newFib; } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(BaseData* roi) { if (roi==NULL || !(dynamic_cast(roi) || dynamic_cast(roi)) ) return NULL; std::vector tmp = ExtractFiberIdSubset(roi); if (tmp.size()<=0) return mitk::FiberBundleX::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp); return mitk::FiberBundleX::New(pTmp); } std::vector mitk::FiberBundleX::ExtractFiberIdSubset(BaseData* roi) { std::vector result; if (roi==NULL) return result; mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast(roi); if (!pfc.IsNull()) // handle composite { switch (pfc->getOperationType()) { case 0: // AND { result = this->ExtractFiberIdSubset(pfc->getChildAt(0)); std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { std::vector inRoi = this->ExtractFiberIdSubset(pfc->getChildAt(i)); std::vector rest(std::min(result.size(),inRoi.size())); it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } case 1: // OR { result = ExtractFiberIdSubset(pfc->getChildAt(0)); std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { it = result.end(); std::vector inRoi = ExtractFiberIdSubset(pfc->getChildAt(i)); result.insert(it, inRoi.begin(), inRoi.end()); } // remove duplicates sort(result.begin(), result.end()); it = unique(result.begin(), result.end()); result.resize( it - result.begin() ); break; } case 2: // NOT { for(long i=0; iGetNumFibers(); i++) result.push_back(i); std::vector::iterator it; for (long i=0; igetNumberOfChildren(); ++i) { std::vector inRoi = ExtractFiberIdSubset(pfc->getChildAt(i)); std::vector rest(result.size()-inRoi.size()); it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } } } else if ( dynamic_cast(roi) ) // actual extraction { mitk::PlanarFigure::Pointer planarFigure = dynamic_cast(roi); Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal(); planeNormal.Normalize(); Point3D planeOrigin = planarFigure->GetPlaneGeometry()->GetOrigin(); // define cutting plane by ROI geometry (PlanarFigure) vtkSmartPointer plane = vtkSmartPointer::New(); plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]); plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]); // get all fiber/plane intersection points vtkSmartPointer clipper = vtkSmartPointer::New(); clipper->SetInputData(m_FiberIdDataSet); clipper->SetClipFunction(plane); clipper->GenerateClipScalarsOn(); clipper->GenerateClippedOutputOn(); clipper->Update(); vtkSmartPointer clipperout = clipper->GetClippedOutput(); if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY)) return result; vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); vtkIdType numPoints = distanceList->GetNumberOfTuples(); std::vector pointsOnPlane; pointsOnPlane.reserve(numPoints); for (int i=0; iGetTuple(i)[0]; // check if point is on plane if (distance >= -0.01 && distance <= 0.01) pointsOnPlane.push_back(i); } if (pointsOnPlane.empty()) return result; // get all point IDs inside the ROI std::vector pointsInROI; pointsInROI.reserve(pointsOnPlane.size()); mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if ( planarFigure->GetNameOfClass() == circleName->GetNameOfClass() ) { //calculate circle radius mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = planarFigure->GetWorldControlPoint(1); //radiusPoint double radius = V1w.EuclideanDistanceTo(V2w); radius *= radius; for (unsigned int i=0; iGetPoint(pointsOnPlane[i], p); double dist = (p[0]-V1w[0])*(p[0]-V1w[0])+(p[1]-V1w[1])*(p[1]-V1w[1])+(p[2]-V1w[2])*(p[2]-V1w[2]); if( dist <= radius) pointsInROI.push_back(pointsOnPlane[i]); } } else if ( planarFigure->GetNameOfClass() == polyName->GetNameOfClass() ) { //create vtkPolygon using controlpoints from planarFigure polygon vtkSmartPointer polygonVtk = vtkSmartPointer::New(); for (unsigned int i=0; iGetNumberOfControlPoints(); ++i) { itk::Point p = planarFigure->GetWorldControlPoint(i); polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[2] ); } //prepare everything for using pointInPolygon function double n[3]; polygonVtk->ComputeNormal(polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n); double bounds[6]; polygonVtk->GetPoints()->GetBounds(bounds); for (unsigned int i=0; iGetPoint(pointsOnPlane[i], p); int isInPolygon = polygonVtk->PointInPolygon(p, polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n); if( isInPolygon ) pointsInROI.push_back(pointsOnPlane[i]); } } if (pointsInROI.empty()) return result; // get the fiber IDs corresponding to all clipped points std::vector< long > pointToFiberMap; // pointToFiberMap[PointID] = FiberIndex pointToFiberMap.resize(clipperout->GetNumberOfPoints()); vtkCellArray* clipperlines = clipperout->GetLines(); clipperlines->InitTraversal(); for (int i=0, ic=0 ; iGetNumberOfCells(); i++, ic+=3) { // ic is the index counter for the cells hosting the desired information. each cell consits of 3 items. long fiberID = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0]; vtkIdType numPoints; vtkIdType* pointIDs; clipperlines->GetCell(ic, numPoints, pointIDs); for (long j=0; j=0) result.push_back( pointToFiberMap[pointsInROI[k]] ); else MITK_INFO << "ERROR in ExtractFiberIdSubset; impossible fiber id detected"; } // remove duplicates std::vector::iterator it; sort(result.begin(), result.end()); it = unique (result.begin(), result.end()); result.resize( it - result.begin() ); } return result; } void mitk::FiberBundleX::UpdateFiberGeometry() { vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInputData(m_FiberPolyData); cleaner->PointMergingOff(); cleaner->Update(); m_FiberPolyData = cleaner->GetOutput(); m_FiberLengths.clear(); m_MeanFiberLength = 0; m_MedianFiberLength = 0; m_LengthStDev = 0; m_NumFibers = m_FiberPolyData->GetNumberOfCells(); if (m_NumFibers<=0) // no fibers present; apply default geometry { m_MinFiberLength = 0; m_MaxFiberLength = 0; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetImageGeometry(true); float b[] = {0, 1, 0, 1, 0, 1}; geometry->SetFloatBounds(b); SetGeometry(geometry); return; } double b[6]; m_FiberPolyData->GetBounds(b); // calculate statistics for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float length = 0; for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); float dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); length += dist; } m_FiberLengths.push_back(length); m_MeanFiberLength += length; if (i==0) { m_MinFiberLength = length; m_MaxFiberLength = length; } else { if (lengthm_MaxFiberLength) m_MaxFiberLength = length; } } m_MeanFiberLength /= m_NumFibers; std::vector< float > sortedLengths = m_FiberLengths; std::sort(sortedLengths.begin(), sortedLengths.end()); for (int i=0; i1) m_LengthStDev /= (m_NumFibers-1); else m_LengthStDev = 0; m_LengthStDev = std::sqrt(m_LengthStDev); m_MedianFiberLength = sortedLengths.at(m_NumFibers/2); mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetFloatBounds(b); this->SetGeometry(geometry); + + m_UpdateMapper3D = true; } std::vector mitk::FiberBundleX::GetAvailableColorCodings() { std::vector availableColorCodings; int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); for(int i=0; iGetPointData()->GetArrayName(i)); } //this controlstructure shall be implemented by the calling method if (availableColorCodings.empty()) MITK_DEBUG << "no colorcodings available in fiberbundleX"; return availableColorCodings; } char* mitk::FiberBundleX::GetCurrentColorCoding() { return m_CurrentColorCoding; } void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding) { if (requestedColorCoding==NULL) return; MITK_DEBUG << "SetColorCoding:" << requestedColorCoding; if( strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_ORIENTATION_BASED; } else if( strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_FA_BASED; } else if( strcmp (COLORCODING_CUSTOM,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; } else { MITK_DEBUG << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure"; this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; //will cause blank colorcoding of fibers } } itk::Matrix< double, 3, 3 > mitk::FiberBundleX::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; m = rot*m; return m; } itk::Point mitk::FiberBundleX::TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); point[0] -= center[0]; point[1] -= center[1]; point[2] -= center[2]; point = rot*point; point[0] += center[0]+tx; point[1] += center[1]+ty; point[2] += center[2]+tz; itk::Point out; out[0] = point[0]; out[1] = point[1]; out[2] = point[2]; return out; } void mitk::FiberBundleX::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rot*dir; dir[0] += center[0]+tx; dir[1] += center[1]+ty; dir[2] += center[2]+tz; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::RotateAroundAxis(double x, double y, double z) { x = x*M_PI/180; y = y*M_PI/180; z = z*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rotZ*rotY*rotX*dir; dir[0] += center[0]; dir[1] += center[1]; dir[2] += center[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::ScaleFibers(double x, double y, double z) { MITK_INFO << "Scaling fibers"; boost::progress_display disp(m_NumFibers); mitk::BaseGeometry* geom = this->GetGeometry(); mitk::Point3D c = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2]; p[0] *= x; p[1] *= y; p[2] *= z; p[0] += c[0]; p[1] += c[1]; p[2] += c[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::TranslateFibers(double x, double y, double z) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] += x; p[1] += y; p[2] += z; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::MirrorFibers(unsigned int axis) { if (axis>2) return; MITK_INFO << "Mirroring fibers"; boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[axis] = -p[axis]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } bool mitk::FiberBundleX::ApplyCurvatureThreshold(float minRadius, bool deleteFibers) { if (minRadius<0) return true; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Applying curvature threshold"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); double p3[3]; points->GetPoint(j+2, p3); vnl_vector_fixed< float, 3 > v1, v2, v3; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; v2[0] = p3[0]-p2[0]; v2[1] = p3[1]-p2[1]; v2[2] = p3[2]-p2[2]; v3[0] = p1[0]-p3[0]; v3[1] = p1[1]-p3[1]; v3[2] = p1[2]-p3[2]; float a = v1.magnitude(); float b = v2.magnitude(); float c = v3.magnitude(); float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); if (deleteFibers && rInsertNextCell(container); container = vtkSmartPointer::New(); } else if (j==numPoints-3) { id = vtkNewPoints->InsertNextPoint(p2); container->GetPointIds()->InsertNextId(id); id = vtkNewPoints->InsertNextPoint(p3); container->GetPointIds()->InsertNextId(id); vtkNewCells->InsertNextCell(container); } } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } bool mitk::FiberBundleX::RemoveShortFibers(float lengthInMM) { MITK_INFO << "Removing short fibers"; if (lengthInMM<=0 || lengthInMMm_MaxFiberLength) // can't remove all fibers { MITK_WARN << "Process aborted. No fibers would be left!"; return false; } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); float min = m_MaxFiberLength; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)>=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); if (m_FiberLengths.at(i)GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } bool mitk::FiberBundleX::RemoveLongFibers(float lengthInMM) { if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength) return true; if (lengthInMM vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Removing long fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)<=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias ) { if (pointDistance<=0) return; vtkSmartPointer vtkSmoothPoints = vtkSmartPointer::New(); //in smoothpoints the interpolated points representing a fiber are stored. //in vtkcells all polylines are stored, actually all id's of them are stored vtkSmartPointer vtkSmoothCells = vtkSmartPointer::New(); //cellcontainer for smoothed lines vtkIdType pointHelperCnt = 0; MITK_INFO << "Smoothing fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer newPoints = vtkSmartPointer::New(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); float length = m_FiberLengths.at(i); int sampling = std::ceil(length/pointDistance); vtkSmartPointer xSpline = vtkSmartPointer::New(); vtkSmartPointer ySpline = vtkSmartPointer::New(); vtkSmartPointer zSpline = vtkSmartPointer::New(); xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity); ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity); zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity); vtkSmartPointer spline = vtkSmartPointer::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(newPoints); vtkSmartPointer functionSource = vtkSmartPointer::New(); functionSource->SetParametricFunction(spline); functionSource->SetUResolution(sampling); functionSource->SetVResolution(sampling); functionSource->SetWResolution(sampling); functionSource->Update(); vtkPolyData* outputFunction = functionSource->GetOutput(); vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber vtkSmartPointer smoothLine = vtkSmartPointer::New(); smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); for (int j=0; jGetNumberOfPoints(); j++) { smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt); vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); } vtkSmoothCells->InsertNextCell(smoothLine); pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints(); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkSmoothPoints); m_FiberPolyData->SetLines(vtkSmoothCells); UpdateColorCoding(); UpdateFiberGeometry(); m_FiberSampling = 10/pointDistance; } void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance) { DoFiberSmoothing(pointDistance, 0, 0, 0 ); } unsigned long mitk::FiberBundleX::GetNumberOfPoints() { unsigned long points = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); points += cell->GetNumberOfPoints(); } return points; } void mitk::FiberBundleX::CompressFibers(float error) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Compressing fibers"; unsigned long numRemovedPoints = 0; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures std::vector< int > removedPoints; removedPoints.resize(numPoints, 0); removedPoints[0]=-1; removedPoints[numPoints-1]=-1; vtkSmartPointer container = vtkSmartPointer::New(); bool pointFound = true; while (pointFound) { pointFound = false; double minError = error; int removeIndex = -1; for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< double, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; int validP = -1; vnl_vector_fixed< double, 3 > pred; for (int k=j-1; k>=0; k--) if (removedPoints[k]<=0) { double ref[3]; points->GetPoint(k, ref); pred[0]=ref[0]; pred[1]=ref[1]; pred[2]=ref[2]; validP = k; break; } int validS = -1; vnl_vector_fixed< double, 3 > succ; for (int k=j+1; kGetPoint(k, ref); succ[0]=ref[0]; succ[1]=ref[1]; succ[2]=ref[2]; validS = k; break; } if (validP>=0 && validS>=0) { double a = (candV-pred).magnitude(); double b = (candV-succ).magnitude(); double c = (pred-succ).magnitude(); double s=0.5*(a+b+c); double hc=(2.0/c)*sqrt(fabs(s*(s-a)*(s-b)*(s-c))); if (hcGetPoint(j, cand); vtkIdType id = vtkNewPoints->InsertNextPoint(cand); container->GetPointIds()->InsertNextId(id); } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()>0) { MITK_INFO << "Removed points: " << numRemovedPoints; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } } // Resample fiber to get equidistant points void mitk::FiberBundleX::ResampleFibers(float pointDistance) { if (pointDistance<=0.00001) return; vtkSmartPointer newPoly = vtkSmartPointer::New(); vtkSmartPointer newCellArray = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); int numberOfLines = m_NumFibers; MITK_INFO << "Resampling fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); double* point = points->GetPoint(0); vtkIdType pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); float dtau = 0; int cur_p = 1; itk::Vector dR; float normdR = 0; for (;;) { while (dtau <= pointDistance && cur_p < numPoints) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2; point = points->GetPoint(cur_p); v2[0] = point[0]; v2[1] = point[1]; v2[2] = point[2]; dR = v2 - v1; normdR = std::sqrt(dR.GetSquaredNorm()); dtau += normdR; cur_p++; } if (dtau >= pointDistance) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2 = v1 - dR*( (dtau-pointDistance)/normdR ); pointId = newPoints->InsertNextPoint(v2.GetDataPointer()); container->GetPointIds()->InsertNextId(pointId); } else { point = points->GetPoint(numPoints-1); pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); break; } dtau = dtau-pointDistance; } newCellArray->InsertNextCell(container); } newPoly->SetPoints(newPoints); newPoly->SetLines(newCellArray); m_FiberPolyData = newPoly; UpdateFiberGeometry(); UpdateColorCoding(); m_FiberSampling = 10/pointDistance; } // reapply selected colorcoding in case polydata structure has changed void mitk::FiberBundleX::UpdateColorCoding() { char* cc = GetCurrentColorCoding(); if( strcmp (COLORCODING_ORIENTATION_BASED,cc) == 0 ) DoColorCodingOrientationBased(); else if( strcmp (COLORCODING_FA_BASED,cc) == 0 ) DoColorCodingFaBased(); } // reapply selected colorcoding in case polydata structure has changed bool mitk::FiberBundleX::Equals(mitk::FiberBundleX* fib, double eps) { if (fib==NULL) { MITK_INFO << "Reference bundle is NULL!"; return false; } if (m_NumFibers!=fib->GetNumFibers()) { MITK_INFO << "Unequal number of fibers!"; MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers(); return false; } for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (numPoints2!=numPoints) { MITK_INFO << "Unequal number of points in fiber " << i << "!"; MITK_INFO << numPoints2 << " vs. " << numPoints; return false; } for (int j=0; jGetPoint(j); double* p2 = points2->GetPoint(j); if (fabs(p1[0]-p2[0])>eps || fabs(p1[1]-p2[1])>eps || fabs(p1[2]-p2[2])>eps) { MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!"; MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2]; MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2]; return false; } } } return true; } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundleX::UpdateOutputInformation() { } void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundleX::VerifyRequestedRegion() { return true; } void mitk::FiberBundleX::SetRequestedRegion(const itk::DataObject* ) { } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h index e6db6c0863..03ebdc4498 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h @@ -1,167 +1,170 @@ /*=================================================================== 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 _MITK_FiberBundleX_H #define _MITK_FiberBundleX_H //includes for MITK datastructure #include #include #include //includes storing fiberdata #include #include #include #include #include //#include #include #include #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class MitkFiberTracking_EXPORT FiberBundleX : public BaseData { public: typedef itk::Image ItkUcharImgType; // fiber colorcodings static const char* COLORCODING_ORIENTATION_BASED; static const char* COLORCODING_FA_BASED; static const char* COLORCODING_CUSTOM; static const char* FIBER_ID_ARRAY; virtual void UpdateOutputInformation(); virtual void SetRequestedRegionToLargestPossibleRegion(); virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); virtual bool VerifyRequestedRegion(); virtual void SetRequestedRegion(const itk::DataObject*); mitkClassMacro( FiberBundleX, BaseData ) itkFactorylessNewMacro(Self) itkCloneMacro(Self) mitkNewMacro1Param(Self, vtkSmartPointer) // custom constructor // colorcoding related methods void SetColorCoding(const char*); void SetFAMap(mitk::Image::Pointer); template void SetFAMap(const mitk::PixelType pixelType, mitk::Image::Pointer); void DoColorCodingOrientationBased(); void DoColorCodingFaBased(); void DoUseFaFiberOpacity(); void ResetFiberOpacity(); // fiber smoothing/resampling void CompressFibers(float error = 0.0); void ResampleFibers(float pointDistance = 1); void DoFiberSmoothing(float pointDistance); void DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias ); bool RemoveShortFibers(float lengthInMM); bool RemoveLongFibers(float lengthInMM); bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers); void MirrorFibers(unsigned int axis); void RotateAroundAxis(double x, double y, double z); void TranslateFibers(double x, double y, double z); void ScaleFibers(double x, double y, double z); void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz); itk::Point TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz); itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz); // add/subtract fibers FiberBundleX::Pointer AddBundle(FiberBundleX* fib); FiberBundleX::Pointer SubtractBundle(FiberBundleX* fib); // fiber subset extraction FiberBundleX::Pointer ExtractFiberSubset(BaseData* roi); std::vector ExtractFiberIdSubset(BaseData* roi); FiberBundleX::Pointer ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint, bool invert=false); FiberBundleX::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false); vtkSmartPointer GeneratePolyDataByIds( std::vector ); // TODO: make protected void GenerateFiberIds(); // TODO: make protected // get/set data void SetFiberPolyData(vtkSmartPointer, bool updateGeometry = true); vtkSmartPointer GetFiberPolyData(); std::vector< std::string > GetAvailableColorCodings(); char* GetCurrentColorCoding(); itkGetMacro( NumFibers, int) itkGetMacro( FiberSampling, int) itkGetMacro( MinFiberLength, float ) itkGetMacro( MaxFiberLength, float ) itkGetMacro( MeanFiberLength, float ) itkGetMacro( MedianFiberLength, float ) itkGetMacro( LengthStDev, float ) + itkSetMacro( UpdateMapper3D, bool ) + itkGetMacro( UpdateMapper3D, bool ) unsigned long GetNumberOfPoints(); // copy fiber bundle mitk::FiberBundleX::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundleX* fib, double eps=0.0001); itkSetMacro( ReferenceImage, mitk::Image::Pointer ) itkGetMacro( ReferenceImage, mitk::Image::Pointer ) protected: FiberBundleX( vtkPolyData* fiberPolyData = NULL ); virtual ~FiberBundleX(); itk::Point GetItkPoint(double point[3]); // calculate geometry from fiber extent void UpdateFiberGeometry(); // calculate colorcoding values according to m_CurrentColorCoding void UpdateColorCoding(); private: // actual fiber container vtkSmartPointer m_FiberPolyData; // contains fiber ids vtkSmartPointer m_FiberIdDataSet; char* m_CurrentColorCoding; int m_NumFibers; std::vector< float > m_FiberLengths; float m_MinFiberLength; float m_MaxFiberLength; float m_MeanFiberLength; float m_MedianFiberLength; float m_LengthStDev; int m_FiberSampling; + bool m_UpdateMapper3D; mitk::Image::Pointer m_ReferenceImage; }; } // namespace mitk #endif /* _MITK_FiberBundleX_H */