diff --git a/Modules/DiffusionImaging/DiffusionIO/files.cmake b/Modules/DiffusionImaging/DiffusionIO/files.cmake index 8031712b17..1422e03ba4 100644 --- a/Modules/DiffusionImaging/DiffusionIO/files.cmake +++ b/Modules/DiffusionImaging/DiffusionIO/files.cmake @@ -1,40 +1,41 @@ set(CPP_FILES + mitkDiffusionModuleActivator.cpp mitkNrrdTbssImageWriterFactory.cpp - mitkFiberBundleXIOFactory.cpp + #mitkFiberBundleXIOFactory.cpp mitkConnectomicsNetworkIOFactory.cpp mitkConnectomicsNetworkReader.cpp mitkConnectomicsNetworkWriter.cpp mitkConnectomicsNetworkSerializer.cpp mitkConnectomicsNetworkDefinitions.cpp mitkNrrdTbssRoiImageIOFactory.cpp - mitkFiberBundleXWriterFactory.cpp + #mitkFiberBundleXWriterFactory.cpp mitkConnectomicsNetworkWriterFactory.cpp mitkNrrdTbssRoiImageWriterFactory.cpp mitkNrrdTensorImageReader.cpp mitkNrrdTensorImageWriter.cpp mitkNrrdTensorImageIOFactory.cpp mitkNrrdTensorImageWriterFactory.cpp mitkTensorImageSerializer.cpp mitkTensorImageSource.cpp mitkFiberTrackingObjectFactory.cpp mitkConnectomicsObjectFactory.cpp mitkQuantificationObjectFactory.cpp mitkNrrdTbssImageIOFactory.cpp mitkDiffusionCoreObjectFactory.cpp mitkNrrdDiffusionImageReader.cpp mitkNrrdDiffusionImageIOFactory.cpp mitkNrrdDiffusionImageWriterFactory.cpp mitkDiffusionImageSerializer.cpp mitkNrrdQBallImageReader.cpp mitkNrrdQBallImageWriter.cpp mitkNrrdQBallImageIOFactory.cpp mitkNrrdQBallImageWriterFactory.cpp mitkQBallImageSerializer.cpp mitkFiberBundleXMapper2D.cpp mitkFiberBundleXMapper3D.cpp mitkCompositeMapper.cpp ) diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionModuleActivator.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionModuleActivator.cpp new file mode 100644 index 0000000000..a8f3a1f1c8 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionModuleActivator.cpp @@ -0,0 +1,50 @@ +/*=================================================================== + +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 + +namespace mitk +{ + /** + \brief Registers services for segmentation module. + */ + class DiffusionModuleActivator : public us::ModuleActivator + { + public: + + void Load(us::ModuleContext* /*context*/) + { + m_FiberBundleXReader = new FiberBundleXReader(); + m_FiberBundleXWriter = new FiberBundleXWriter(); + } + + void Unload(us::ModuleContext*) + { + delete m_FiberBundleXReader; + delete m_FiberBundleXWriter; + } + + private: + + FiberBundleXReader * m_FiberBundleXReader; + FiberBundleXWriter * m_FiberBundleXWriter; + + }; +} + +US_EXPORT_MODULE_ACTIVATOR(mitk::DiffusionModuleActivator) diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXIOFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXIOFactory.cpp deleted file mode 100644 index 7ee1d84e0b..0000000000 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXIOFactory.cpp +++ /dev/null @@ -1,53 +0,0 @@ -/*=================================================================== - -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 "mitkFiberBundleXIOFactory.h" -#include "mitkIOAdapter.h" -#include "mitkFiberBundleXReader.h" - -#include "itkVersion.h" - -//NOTE>umbenennen in FBReaderType - - -namespace mitk -{ - -FiberBundleXIOFactory::FiberBundleXIOFactory() -{ - typedef FiberBundleXReader FiberBundleXReaderType; - this->RegisterOverride("mitkIOAdapter", //beibehalten - "mitkFiberBundleXReader", //umbenennen - "Fiber Bundle IO", //angezeigter name - 1, - itk::CreateObjectFunction >::New()); -} - -FiberBundleXIOFactory::~FiberBundleXIOFactory() -{ -} - -const char* FiberBundleXIOFactory::GetITKSourceVersion() const -{ - return ITK_SOURCE_VERSION; -} - -const char* FiberBundleXIOFactory::GetDescription() const -{ - return "FibreBundleIOFactory, allows the loading of FibreBundles"; -} - -} // end namespace mitk diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXIOFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXIOFactory.h deleted file mode 100644 index d8b7acff21..0000000000 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXIOFactory.h +++ /dev/null @@ -1,66 +0,0 @@ -/*=================================================================== - -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_FIBER_BUNDLEX_IO_FACTORY_H_HEADER__ -#define __MITK_FIBER_BUNDLEX_IO_FACTORY_H_HEADER__ - -#ifdef _MSC_VER -#pragma warning ( disable : 4786 ) -#endif - -#include "itkObjectFactoryBase.h" -#include "mitkBaseData.h" - -//NOTE>umbenennen in internal FiberBundleIOFactory - - -namespace mitk -{ -//##Documentation -//## @brief Create instances of NrrdQBallImageReader objects using an object factory. -//## -class FiberBundleXIOFactory : public itk::ObjectFactoryBase -{ -public: - /** Standard class typedefs. */ - typedef FiberBundleXIOFactory Self; - typedef itk::ObjectFactoryBase Superclass; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - /** Class methods used to interface with the registered factories. */ - virtual const char* GetITKSourceVersion(void) const; - virtual const char* GetDescription(void) const; - - /** Method for class instantiation. */ - itkFactorylessNewMacro(Self); - static FiberBundleXIOFactory* FactoryNew() { return new FiberBundleXIOFactory;} - /** Run-time type information (and related methods). */ - itkTypeMacro(FiberBundleXIOFactory, ObjectFactoryBase); - -protected: - FiberBundleXIOFactory(); - ~FiberBundleXIOFactory(); - -private: - FiberBundleXIOFactory(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - -}; - - -} // end namespace mitk - -#endif // __MITK_FIBER_BUNDLE_IO_FACTORY_H_HEADER__ diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriterFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriterFactory.cpp deleted file mode 100644 index 6bf582bb75..0000000000 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriterFactory.cpp +++ /dev/null @@ -1,75 +0,0 @@ -/*=================================================================== - -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 "mitkFiberBundleXWriterFactory.h" - -#include "itkCreateObjectFunction.h" -#include "itkVersion.h" - -#include "mitkFiberBundleXWriter.h" - -namespace mitk -{ - -template -class CreateFiberBundleXWriter : public itk::CreateObjectFunctionBase -{ -public: - - /** Standard class typedefs. */ - typedef CreateFiberBundleXWriter Self; - typedef itk::SmartPointer Pointer; - - /** Methods from itk:LightObject. */ - itkFactorylessNewMacro(Self); - LightObject::Pointer CreateObject() { typename T::Pointer p = T::New(); - p->Register(); - return p.GetPointer(); - } - -protected: - CreateFiberBundleXWriter() {} - ~CreateFiberBundleXWriter() {} - -private: - CreateFiberBundleXWriter(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented -}; - -FiberBundleXWriterFactory::FiberBundleXWriterFactory() -{ - this->RegisterOverride("IOWriter", - "FiberBundleXWriter", - "FiberBundleX Writer", - 1, - mitk::CreateFiberBundleXWriter< mitk::FiberBundleXWriter >::New()); -} - -FiberBundleXWriterFactory::~FiberBundleXWriterFactory() -{ -} - -const char* FiberBundleXWriterFactory::GetITKSourceVersion() const -{ - return ITK_SOURCE_VERSION; -} - -const char* FiberBundleXWriterFactory::GetDescription() const -{ - return "FiberBundleXWriterFactory"; -} - -} // end namespace mitk diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriterFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriterFactory.h deleted file mode 100644 index a6f9408af1..0000000000 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriterFactory.h +++ /dev/null @@ -1,54 +0,0 @@ -/*=================================================================== - -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 FIBERBUNDLEX_WRITERFACTORY_H_HEADER_INCLUDED -#define FIBERBUNDLEX_WRITERFACTORY_H_HEADER_INCLUDED - -#include "itkObjectFactoryBase.h" -#include "mitkBaseData.h" - -namespace mitk -{ - -class FiberBundleXWriterFactory : public itk::ObjectFactoryBase -{ -public: - - mitkClassMacro( mitk::FiberBundleXWriterFactory, itk::ObjectFactoryBase ) - - /** Class methods used to interface with the registered factories. */ - virtual const char* GetITKSourceVersion(void) const; - virtual const char* GetDescription(void) const; - - /** Method for class instantiation. */ - itkFactorylessNewMacro(Self); - -protected: - FiberBundleXWriterFactory(); - ~FiberBundleXWriterFactory(); - -private: - FiberBundleXWriterFactory(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - -}; - -} // end namespace mitk - -#endif // FiberBundleX_WRITERFACTORY_H_HEADER_INCLUDED - - - diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp index 3781e5ef5f..160e33d600 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp @@ -1,137 +1,111 @@ #include "mitkFiberTrackingObjectFactory.h" mitk::FiberTrackingObjectFactory::FiberTrackingObjectFactory() : CoreObjectFactoryBase() - , m_FiberBundleXIOFactory(mitk::FiberBundleXIOFactory::New().GetPointer()) - , m_FiberBundleXWriterFactory(mitk::FiberBundleXWriterFactory::New().GetPointer()) { - - static bool alreadyDone = false; - if (!alreadyDone) - { - MITK_DEBUG << "FiberTrackingObjectFactory c'tor" << std::endl; - - itk::ObjectFactoryBase::RegisterFactory(m_FiberBundleXIOFactory); - itk::ObjectFactoryBase::RegisterFactory(m_FiberBundleXWriterFactory); - - m_FileWriters.push_back( mitk::FiberBundleXWriter::New().GetPointer() );//modernized - - CreateFileExtensionsMap(); - - alreadyDone = true; - } - } mitk::FiberTrackingObjectFactory::~FiberTrackingObjectFactory() { - itk::ObjectFactoryBase::UnRegisterFactory(m_FiberBundleXWriterFactory); - itk::ObjectFactoryBase::UnRegisterFactory(m_FiberBundleXIOFactory); } mitk::Mapper::Pointer mitk::FiberTrackingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper=NULL; if ( id == mitk::BaseRenderer::Standard2D ) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleXMapper2D::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleXMapper3D::New(); newMapper->SetDataNode(node); } // classname = "FiberBundleXThreadMonitor"; // if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) // { // newMapper = mitk::FiberBundleXThreadMonitorMapper3D::New(); // newMapper->SetDataNode(node); // } } return newMapper; } void mitk::FiberTrackingObjectFactory::SetDefaultProperties(mitk::DataNode* node) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::FiberBundleXMapper3D::SetDefaultProperties(node); mitk::FiberBundleXMapper2D::SetDefaultProperties(node); } // classname = "FiberBundleXThreadMonitor"; // if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) // { // mitk::FiberBundleXThreadMonitorMapper3D::SetDefaultProperties(node); // } } const char* mitk::FiberTrackingObjectFactory::GetFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); return fileExtension.c_str(); } mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } const char* mitk::FiberTrackingObjectFactory::GetSaveFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); return fileExtension.c_str(); } mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } void mitk::FiberTrackingObjectFactory::CreateFileExtensionsMap() { - m_FileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); - m_FileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle")); - m_FileExtensionsMap.insert(std::pair("*.trk", "TrackVis Fiber Bundle")); - m_SaveFileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); - m_SaveFileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle")); - m_SaveFileExtensionsMap.insert(std::pair("*.trk", "TrackVis Fiber Bundle")); } void mitk::FiberTrackingObjectFactory::RegisterIOFactories() { } struct RegisterFiberTrackingObjectFactory{ RegisterFiberTrackingObjectFactory() : m_Factory( mitk::FiberTrackingObjectFactory::New() ) { mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory ); } ~RegisterFiberTrackingObjectFactory() { mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory ); } mitk::FiberTrackingObjectFactory::Pointer m_Factory; }; static RegisterFiberTrackingObjectFactory registerFiberTrackingObjectFactory; diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h index 86795426c3..f78bc04bc9 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h @@ -1,59 +1,54 @@ #ifndef MITKFIBERTRACKINGOBJECTFACTORY_H #define MITKFIBERTRACKINGOBJECTFACTORY_H #include "mitkCoreObjectFactory.h" //modernized fiberbundle datastrucutre #include "mitkFiberBundleX.h" -#include "mitkFiberBundleXIOFactory.h" -#include "mitkFiberBundleXWriterFactory.h" -#include "mitkFiberBundleXWriter.h" #include "mitkFiberBundleXMapper3D.h" #include "mitkFiberBundleXMapper2D.h" //#include "mitkFiberBundleXThreadMonitorMapper3D.h" //#include "mitkFiberBundleXThreadMonitor.h" namespace mitk { class FiberTrackingObjectFactory : public CoreObjectFactoryBase { public: mitkClassMacro(FiberTrackingObjectFactory,CoreObjectFactoryBase) itkFactorylessNewMacro(Self) itkCloneMacro(Self) ~FiberTrackingObjectFactory(); virtual Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId); virtual void SetDefaultProperties(mitk::DataNode* node); virtual const char* GetFileExtensions(); virtual mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap(); virtual const char* GetSaveFileExtensions(); virtual mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap(); void RegisterIOFactories(); protected: FiberTrackingObjectFactory(); private: void CreateFileExtensionsMap(); std::string m_ExternalFileExtensions; std::string m_InternalFileExtensions; std::string m_SaveFileExtensions; MultimapType m_FileExtensionsMap; MultimapType m_SaveFileExtensionsMap; - itk::ObjectFactoryBase::Pointer m_FiberBundleXIOFactory; - itk::ObjectFactoryBase::Pointer m_FiberBundleXWriterFactory; }; } #endif // MITKFIBERTRACKINGOBJECTFACTORY_H diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index cd192a0503..b5a612c043 100755 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,1945 +1,1945 @@ /*=================================================================== 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_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() +vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() const { 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) return; /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); /* 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; } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } }//end for loop m_FiberPolyData->GetPointData()->AddArray(colorsT); 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); // 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); // 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(false); 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_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } 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; 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 } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } 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 857e98adf5..2978be04dd 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h @@ -1,172 +1,173 @@ /*=================================================================== 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(); + vtkSmartPointer GetFiberPolyData() const; std::vector< std::string > GetAvailableColorCodings(); char* GetCurrentColorCoding(); itkGetMacro( NumFibers, int) - itkGetMacro( FiberSampling, int) + //itkGetMacro( FiberSampling, int) + int GetNumFibers() const {return m_NumFibers;} itkGetMacro( MinFiberLength, float ) itkGetMacro( MaxFiberLength, float ) itkGetMacro( MeanFiberLength, float ) itkGetMacro( MedianFiberLength, float ) itkGetMacro( LengthStDev, float ) itkGetMacro( UpdateTime2D, itk::TimeStamp ) itkGetMacro( UpdateTime3D, itk::TimeStamp ) void RequestUpdate2D(){ m_UpdateTime2D.Modified(); } void RequestUpdate3D(){ m_UpdateTime3D.Modified(); } unsigned long GetNumberOfPoints(); // copy fiber bundle mitk::FiberBundleX::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundleX* fib, double eps=0.0001); itkSetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) - itkGetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) + itkGetConstMacro( ReferenceGeometry, mitk::BaseGeometry::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; itk::TimeStamp m_UpdateTime2D; itk::TimeStamp m_UpdateTime3D; mitk::BaseGeometry::Pointer m_ReferenceGeometry; }; } // namespace mitk #endif /* _MITK_FiberBundleX_H */ diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp index 22b31f140b..cda259ab09 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp @@ -1,176 +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. ===================================================================*/ #include "mitkFiberBundleXReader.h" #include #include #include #include #include #include #include #include #include #include #include +#include -namespace mitk -{ -void FiberBundleXReader -::GenerateData() +mitk::FiberBundleXReader::FiberBundleXReader() + :mitk::AbstractFileReader() { - if ( ( ! m_OutputCache ) ) - { - Superclass::SetNumberOfRequiredOutputs(0); - this->GenerateOutputInformation(); - } - - if (!m_OutputCache) - { - itkWarningMacro("Output cache is empty!"); - } - + std::string category = "Fiber Bundle File"; + mitk::CustomMimeType customMimeType; + customMimeType.SetCategory(category); + customMimeType.AddExtension("fib"); + customMimeType.AddExtension("trk"); + customMimeType.AddExtension("vtk"); - Superclass::SetNumberOfRequiredOutputs(1); - Superclass::SetNthOutput(0, m_OutputCache.GetPointer()); -} - -void FiberBundleXReader::GenerateOutputInformation() -{ - try - { - const std::string& locale = "C"; - const std::string& currLocale = setlocale( LC_ALL, NULL ); - setlocale(LC_ALL, locale.c_str()); - - std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); - ext = itksys::SystemTools::LowerCase(ext); - - if (ext==".trk") - { - m_OutputCache = OutputType::New(); - TrackVisFiberReader reader; - reader.open(m_FileName); - reader.read(m_OutputCache); - return; - } - - vtkSmartPointer chooser=vtkSmartPointer::New(); - chooser->SetFileName(m_FileName.c_str() ); - if( chooser->IsFilePolyData()) - { - vtkSmartPointer reader = vtkSmartPointer::New(); - reader->SetFileName( m_FileName.c_str() ); - reader->Update(); - - if ( reader->GetOutput() != NULL ) - { - vtkSmartPointer fiberPolyData = reader->GetOutput(); - m_OutputCache = OutputType::New(fiberPolyData); - } - } - setlocale(LC_ALL, currLocale.c_str()); - MITK_INFO << "Fiber bundle read"; - } - catch(...) - { - throw; - } -} + this->SetDescription(category); + this->SetMimeType(customMimeType); -void FiberBundleXReader::Update() -{ - this->GenerateData(); + m_ServiceReg = this->RegisterService(); } -const char* FiberBundleXReader -::GetFileName() const +mitk::FiberBundleXReader::FiberBundleXReader(const FiberBundleXReader &other) + :mitk::AbstractFileReader(other) { - return m_FileName.c_str(); } - -void FiberBundleXReader -::SetFileName(const char* aFileName) +mitk::FiberBundleXReader * mitk::FiberBundleXReader::Clone() const { - m_FileName = aFileName; + return new FiberBundleXReader(*this); } -const char* FiberBundleXReader -::GetFilePrefix() const +std::vector > mitk::FiberBundleXReader::Read() { - return m_FilePrefix.c_str(); -} + std::vector > result; + try + { + const std::string& locale = "C"; + const std::string& currLocale = setlocale( LC_ALL, NULL ); + setlocale(LC_ALL, locale.c_str()); -void FiberBundleXReader -::SetFilePrefix(const char* aFilePrefix) -{ - m_FilePrefix = aFilePrefix; -} + std::string filename = this->GetInputLocation(); - -const char* FiberBundleXReader -::GetFilePattern() const -{ - return m_FilePattern.c_str(); -} - - -void FiberBundleXReader -::SetFilePattern(const char* aFilePattern) -{ - m_FilePattern = aFilePattern; -} - - -bool FiberBundleXReader -::CanReadFile(const std::string filename, const std::string /*filePrefix*/, const std::string /*filePattern*/) -{ - // First check the extension - if( filename == "" ) - { - return false; - } std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); ext = itksys::SystemTools::LowerCase(ext); - if (ext == ".fib" || ext == ".trk") + if (ext==".trk") { - return true; + FiberBundleX::Pointer image = FiberBundleX::New(); + TrackVisFiberReader reader; + reader.open(this->GetInputLocation().c_str()); + reader.read(image.GetPointer()); + result.push_back(image.GetPointer()); + return result; } - return false; -} - -BaseDataSource::DataObjectPointer FiberBundleXReader::MakeOutput(const DataObjectIdentifierType &name) -{ - itkDebugMacro("MakeOutput(" << name << ")"); - if( this->IsIndexedOutputName(name) ) + vtkSmartPointer chooser=vtkSmartPointer::New(); + chooser->SetFileName( this->GetInputLocation().c_str() ); + if( chooser->IsFilePolyData()) { - return this->MakeOutput( this->MakeIndexFromOutputName(name) ); + vtkSmartPointer reader = vtkSmartPointer::New(); + reader->SetFileName( this->GetInputLocation().c_str() ); + reader->Update(); + + if ( reader->GetOutput() != NULL ) + { + vtkSmartPointer fiberPolyData = reader->GetOutput(); + FiberBundleX::Pointer image = FiberBundleX::New(fiberPolyData); + result.push_back(image.GetPointer()); + return result; + } } - return static_cast(OutputType::New().GetPointer()); + setlocale(LC_ALL, currLocale.c_str()); + MITK_INFO << "Fiber bundle read"; + } + catch(...) + { + throw; + } + return result; } - -BaseDataSource::DataObjectPointer FiberBundleXReader::MakeOutput(DataObjectPointerArraySizeType /*idx*/) -{ - return OutputType::New().GetPointer(); -} - -} //namespace MITK diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h index e05e54afe2..386fdad556 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h @@ -1,77 +1,52 @@ /*=================================================================== 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 __mitkFiberBundleXReader_h #define __mitkFiberBundleXReader_h #include #include #include #include -#include + +#include namespace mitk { /** \brief */ - class MitkFiberTracking_EXPORT FiberBundleXReader : public FileReader, public BaseDataSource + class FiberBundleXReader : public AbstractFileReader { public: - /** Types for the standardized TractContainer **/ - /* direct linked includes of mitkFiberBundleX DataStructure */ - - typedef mitk::FiberBundleX OutputType; - - mitkClassMacro( FiberBundleXReader, BaseDataSource ) - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - const char* GetFileName() const; - void SetFileName(const char* aFileName); - const char* GetFilePrefix() const; - void SetFilePrefix(const char* aFilePrefix); - const char* GetFilePattern() const; - void SetFilePattern(const char* aFilePattern); - - static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern); - - virtual void Update(); + FiberBundleXReader(); + virtual ~FiberBundleXReader(){} + FiberBundleXReader(const FiberBundleXReader& other); + virtual FiberBundleXReader * Clone() const; - BaseDataSource::DataObjectPointer MakeOutput(const DataObjectIdentifierType &name); - BaseDataSource::DataObjectPointer MakeOutput( DataObjectPointerArraySizeType idx); - - protected: - - /** Does the real work. */ - virtual void GenerateData(); - virtual void GenerateOutputInformation(); - - OutputType::Pointer m_OutputCache; - - std::string m_FileName; - std::string m_FilePrefix; - std::string m_FilePattern; + using mitk::AbstractFileReader::Read; + virtual std::vector > Read(); private: - void operator=(const Self&); //purposely not implemented + + us::ServiceRegistration m_ServiceReg; }; } //namespace MITK #endif // __mitkFiberBundleXReader_h diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp index 629ff43cd3..cd9b2a3725 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp @@ -1,74 +1,72 @@ /*=================================================================== 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 "mitkFiberBundleXSerializer.h" #include "mitkFiberBundleX.h" #include "mitkFiberBundleXWriter.h" #include +#include MITK_REGISTER_SERIALIZER(FiberBundleXSerializer) mitk::FiberBundleXSerializer::FiberBundleXSerializer() { } mitk::FiberBundleXSerializer::~FiberBundleXSerializer() { } std::string mitk::FiberBundleXSerializer::Serialize() { const FiberBundleX* fb = dynamic_cast( m_Data.GetPointer() ); if (fb == NULL) { MITK_ERROR << " Object at " << (const void*) this->m_Data << " is not an mitk::FiberBundleX. Cannot serialize as FiberBundleX."; return ""; } std::string filename( this->GetUniqueFilenameInWorkingDirectory() ); filename += "_"; filename += m_FilenameHint; filename += ".fib"; std::string fullname(m_WorkingDirectory); fullname += "/"; fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str()); try { - FiberBundleXWriter::Pointer writer = FiberBundleXWriter::New(); - writer->SetFileName(fullname); - writer->SetInputFiberBundleX(const_cast(fb)); - writer->Write(); + mitk::IOUtil::Save(const_cast(fb),fullname); } catch (std::exception& e) { MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data << " to " << fullname << ": " << e.what(); return ""; } return filename; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp index 757e6d1c1c..5c8eef50de 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp @@ -1,140 +1,137 @@ /*=================================================================== 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 "mitkFiberBundleXWriter.h" #include #include #include #include #include +#include +#include + mitk::FiberBundleXWriter::FiberBundleXWriter() - : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) + : mitk::AbstractFileWriter(mitk::FiberBundleX::GetStaticNameOfClass()) { - this->SetNumberOfRequiredInputs( 1 ); + std::string category = "Fiber Bundle File"; + mitk::CustomMimeType customMimeType; + customMimeType.SetCategory(category); + customMimeType.AddExtension("fib"); + customMimeType.AddExtension("afib"); + customMimeType.AddExtension("vtk"); + customMimeType.AddExtension("avtk"); + customMimeType.AddExtension("trk"); + + this->SetDescription(category); + this->SetMimeType(customMimeType); + + RegisterService(); } +mitk::FiberBundleXWriter::FiberBundleXWriter(const mitk::FiberBundleXWriter & other) + :mitk::AbstractFileWriter(other) +{} mitk::FiberBundleXWriter::~FiberBundleXWriter() {} +mitk::FiberBundleXWriter * mitk::FiberBundleXWriter::Clone() const +{ + return new mitk::FiberBundleXWriter(*this); +} -void mitk::FiberBundleXWriter::GenerateData() +void mitk::FiberBundleXWriter::Write() { + + std::ostream* out; + std::ofstream outStream; + + if( this->GetOutputStream() ) + { + out = this->GetOutputStream(); + }else{ + outStream.open( this->GetOutputLocation().c_str() ); + out = &outStream; + } + + if ( !out->good() ) + { + mitkThrow() << "Stream not good."; + } + try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); setlocale(LC_ALL, locale.c_str()); - m_Success = false; - InputType* input = this->GetInput(); - if (input == NULL) - { - itkWarningMacro(<<"Sorry, input to FiberBundleXWriter is NULL!"); - return; - } - else if ( m_FileName == "" ) - { - itkWarningMacro( << "Sorry, filename has not been set!" ); - return ; - } - std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); + std::locale previousLocale(out->getloc()); + std::locale I("C"); + out->imbue(I); + + std::string filename = this->GetOutputLocation().c_str(); + + mitk::FiberBundleX::ConstPointer input = dynamic_cast(this->GetInput()); + std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation().c_str()); if (ext==".fib" || ext==".vtk") { MITK_INFO << "Writing fiber bundle as binary VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); writer->SetInputData(input->GetFiberPolyData()); - writer->SetFileName(m_FileName.c_str()); + writer->SetFileName(this->GetOutputLocation().c_str()); writer->SetFileTypeToBinary(); writer->Write(); } else if (ext==".afib") { - itksys::SystemTools::ReplaceString(m_FileName,".afib",".fib"); + itksys::SystemTools::ReplaceString(filename,".afib",".fib"); MITK_INFO << "Writing fiber bundle as ascii VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); writer->SetInputData(input->GetFiberPolyData()); - writer->SetFileName(m_FileName.c_str()); + writer->SetFileName(this->GetOutputLocation().c_str()); writer->SetFileTypeToASCII(); writer->Write(); } else if (ext==".avtk") { - itksys::SystemTools::ReplaceString(m_FileName,".avtk",".vtk"); + itksys::SystemTools::ReplaceString(filename,".avtk",".vtk"); MITK_INFO << "Writing fiber bundle as ascii VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); writer->SetInputData(input->GetFiberPolyData()); - writer->SetFileName(m_FileName.c_str()); + writer->SetFileName(this->GetOutputLocation().c_str()); writer->SetFileTypeToASCII(); writer->Write(); } else if (ext==".trk") { MITK_INFO << "Writing fiber bundle as TRK"; TrackVisFiberReader trk; - trk.create(m_FileName, input); + trk.create(filename, input.GetPointer()); trk.writeHdr(); - trk.append(input); + trk.append(input.GetPointer()); } setlocale(LC_ALL, currLocale.c_str()); - m_Success = true; MITK_INFO << "Fiber bundle written"; } catch(...) { throw; } } - - -void mitk::FiberBundleXWriter::SetInputFiberBundleX( InputType* diffVolumes ) -{ - this->ProcessObject::SetNthInput( 0, diffVolumes ); -} - - -mitk::FiberBundleX* mitk::FiberBundleXWriter::GetInput() -{ - if ( this->GetNumberOfInputs() < 1 ) - { - return NULL; - } - else - { - return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); - } -} - - -std::vector mitk::FiberBundleXWriter::GetPossibleFileExtensions() -{ - std::vector possibleFileExtensions; - possibleFileExtensions.push_back(".fib"); - possibleFileExtensions.push_back(".afib"); - possibleFileExtensions.push_back(".vtk"); - possibleFileExtensions.push_back(".avtk"); - possibleFileExtensions.push_back(".trk"); - return possibleFileExtensions; -} - -string mitk::FiberBundleXWriter::GetSupportedBaseData() const -{ - return FiberBundleX::GetStaticNameOfClass(); -} diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h index 94f25579a2..e7c7194e03 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h @@ -1,219 +1,118 @@ /*=================================================================== 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 __mitkFiberBundleXWriter_h #define __mitkFiberBundleXWriter_h -#include -#include +#include + #include "mitkFiberBundleX.h" #include -#include + namespace mitk { /** * Writes fiber bundles to a file * @ingroup Process */ -class MitkFiberTracking_EXPORT FiberBundleXWriter : public mitk::FileWriterWithInformation +class FiberBundleXWriter : public mitk::AbstractFileWriter { public: - mitkClassMacro( FiberBundleXWriter, mitk::FileWriterWithInformation ); - - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - //mitkWriterMacro; - - virtual void Write() - { - if ( this->GetInput() == NULL ) - { - itkExceptionMacro(<<"Write:Please specify an input!"); - return; - } - /* Fill in image information.*/ - this->UpdateOutputInformation(); - (*(this->GetInputs().begin()))->SetRequestedRegionToLargestPossibleRegion(); - this->PropagateRequestedRegion(NULL); - this->UpdateOutputData(NULL); - } - - virtual void Update() - { - Write(); - } - - typedef mitk::FiberBundleX InputType; - - /** - * Sets the filename of the file to write. - * @param FileName the name of the file to write. - */ - itkSetStringMacro( FileName ); - - /** - * @returns the name of the file to be written to disk. - */ - itkGetStringMacro( FileName ); - - /** - * @warning multiple write not (yet) supported - */ - itkSetStringMacro( FilePrefix ); - - /** - * @warning multiple write not (yet) supported - */ - itkGetStringMacro( FilePrefix ); - - /** - * @warning multiple write not (yet) supported - */ - itkSetStringMacro( FilePattern ); - - /** - * @warning multiple write not (yet) supported - */ - itkGetStringMacro( FilePattern ); - - /** - * Sets the input object for the filter. - * @param input the diffusion volumes to write to file. - */ - void SetInputFiberBundleX( InputType* input ); - - /** - * @returns the 0'th input object of the filter. - */ - InputType* GetInput(); - - /** - * Returns false if an error happened during writing - */ - itkGetMacro( Success, bool ); - - /** - * @return possible file extensions for the data type associated with the writer - */ - virtual std::vector GetPossibleFileExtensions(); - - std::string GetSupportedBaseData() const; - - // FileWriterWithInformation methods - virtual const char * GetDefaultFilename() { return "FiberBundle.fib"; } - virtual const char * GetFileDialogPattern() { return "Fiber Bundle (*.fib *.vtk *.trk *.afib *.avtk)"; } - virtual const char * GetDefaultExtension() { return ".fib"; } - virtual bool CanWriteBaseDataType(BaseData::Pointer data) { return (dynamic_cast(data.GetPointer()) != NULL); }; - virtual void DoWrite(BaseData::Pointer data) { - if (CanWriteBaseDataType(data)) { - this->SetInputFiberBundleX(dynamic_cast(data.GetPointer())); - this->Update(); - } - }; + + FiberBundleXWriter(); + FiberBundleXWriter(const FiberBundleXWriter & other); + virtual FiberBundleXWriter * Clone() const; + virtual ~FiberBundleXWriter(); + + using mitk::AbstractFileWriter::Write; + virtual void Write(); static const char* XML_GEOMETRY; static const char* XML_MATRIX_XX; static const char* XML_MATRIX_XY; static const char* XML_MATRIX_XZ; static const char* XML_MATRIX_YX; static const char* XML_MATRIX_YY; static const char* XML_MATRIX_YZ; static const char* XML_MATRIX_ZX; static const char* XML_MATRIX_ZY; static const char* XML_MATRIX_ZZ; static const char* XML_ORIGIN_X; static const char* XML_ORIGIN_Y; static const char* XML_ORIGIN_Z; static const char* XML_SPACING_X; static const char* XML_SPACING_Y; static const char* XML_SPACING_Z; static const char* XML_SIZE_X; static const char* XML_SIZE_Y; static const char* XML_SIZE_Z; static const char* XML_FIBER_BUNDLE; static const char* XML_FIBER; static const char* XML_PARTICLE; static const char* XML_ID; static const char* XML_POS_X; static const char* XML_POS_Y; static const char* XML_POS_Z; static const char* VERSION_STRING; static const char* XML_FIBER_BUNDLE_FILE; static const char* XML_FILE_VERSION; static const char* XML_NUM_FIBERS; static const char* XML_NUM_PARTICLES; static const char* ASCII_FILE; static const char* FILE_NAME; -protected: - - FiberBundleXWriter(); - - virtual ~FiberBundleXWriter(); - - virtual void GenerateData(); - - std::string m_FileName; - - std::string m_FilePrefix; - - std::string m_FilePattern; - - bool m_Success; - }; } // end of namespace mitk #endif //__mitkFiberBundleXWriter_h diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp index e34d192642..e63fdb8603 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp @@ -1,237 +1,237 @@ #include #include TrackVisFiberReader::TrackVisFiberReader() { m_Filename = ""; m_FilePointer = NULL; } TrackVisFiberReader::~TrackVisFiberReader() { if (m_FilePointer) fclose( m_FilePointer ); } // Create a TrackVis file and store standard metadata. The file is ready to append fibers. // --------------------------------------------------------------------------------------- -short TrackVisFiberReader::create(string filename , mitk::FiberBundleX *fib) +short TrackVisFiberReader::create(string filename , const mitk::FiberBundleX *fib) { // prepare the header for(int i=0; i<3 ;i++) { if (fib->GetReferenceGeometry().IsNotNull()) { m_Header.dim[i] = fib->GetReferenceGeometry()->GetExtent(i); m_Header.voxel_size[i] = fib->GetReferenceGeometry()->GetSpacing()[i]; m_Header.origin[i] = fib->GetReferenceGeometry()->GetOrigin()[i]; } else { m_Header.dim[i] = fib->GetGeometry()->GetExtent(i); m_Header.voxel_size[i] = fib->GetGeometry()->GetSpacing()[i]; m_Header.origin[i] = fib->GetGeometry()->GetOrigin()[i]; } } m_Header.n_scalars = 0; m_Header.n_properties = 0; sprintf(m_Header.voxel_order,"LPS"); m_Header.image_orientation_patient[0] = 1.0; m_Header.image_orientation_patient[1] = 0.0; m_Header.image_orientation_patient[2] = 0.0; m_Header.image_orientation_patient[3] = 0.0; m_Header.image_orientation_patient[4] = 1.0; m_Header.image_orientation_patient[5] = 0.0; m_Header.pad1[0] = 0; m_Header.pad1[1] = 0; m_Header.pad2[0] = 0; m_Header.pad2[1] = 0; m_Header.invert_x = 0; m_Header.invert_y = 0; m_Header.invert_z = 0; m_Header.swap_xy = 0; m_Header.swap_yz = 0; m_Header.swap_zx = 0; m_Header.n_count = 0; m_Header.version = 1; m_Header.hdr_size = 1000; // write the header to the file m_FilePointer = fopen(filename.c_str(),"w+b"); if (m_FilePointer == NULL) { printf("[ERROR] Unable to create file '%s'\n",filename.c_str()); return 0; } sprintf(m_Header.id_string,"TRACK"); if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000) MITK_ERROR << "TrackVis::create : Error occurding during writing fiber."; this->m_Filename = filename; return 1; } // Open an existing TrackVis file and read metadata information. // The file pointer is positiond at the beginning of fibers data // ------------------------------------------------------------- short TrackVisFiberReader::open( string filename ) { m_FilePointer = fopen(filename.c_str(),"r+b"); if (m_FilePointer == NULL) { printf("[ERROR] Unable to open file '%s'\n",filename.c_str()); return 0; } this->m_Filename = filename; return fread((char*)(&m_Header), 1, 1000, m_FilePointer); } // Append a fiber to the file // -------------------------- -short TrackVisFiberReader::append(mitk::FiberBundleX *fib) +short TrackVisFiberReader::append(const mitk::FiberBundleX *fib) { vtkPolyData* poly = fib->GetFiberPolyData(); for (int i=0; iGetNumFibers(); i++) { vtkCell* cell = poly->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); unsigned int numSaved, pos = 0; //float* tmp = new float[3*maxSteps]; std::vector< float > tmp; tmp.reserve(3*numPoints); numSaved = numPoints; for(unsigned int i=0; iGetPoint(i); tmp[pos++] = p[0]; tmp[pos++] = p[1]; tmp[pos++] = p[2]; } // write the coordinates to the file if ( fwrite((char*)&numSaved, 1, 4, m_FilePointer) != 4 ) { printf( "[ERROR] Problems saving the fiber!\n" ); return 1; } if ( fwrite((char*)&(tmp.front()), 1, 4*pos, m_FilePointer) != 4*pos ) { printf( "[ERROR] Problems saving the fiber!\n" ); return 1; } } return 0; } //// Read one fiber from the file //// ---------------------------- short TrackVisFiberReader::read( mitk::FiberBundleX* fib ) { int numPoints; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); while (fread((char*)&numPoints, 1, 4, m_FilePointer)==4) { if ( numPoints <= 0 ) { printf( "[ERROR] Trying to read a fiber with %d points!\n", numPoints ); return -1; } vtkSmartPointer container = vtkSmartPointer::New(); float tmp[3]; for(int i=0; iInsertNextPoint(tmp); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(vtkNewPoints); fiberPolyData->SetLines(vtkNewCells); MITK_INFO << "Coordinate convention: " << m_Header.voxel_order; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->Identity(); if (m_Header.voxel_order[0]=='R') matrix->SetElement(0,0,-matrix->GetElement(0,0)); if (m_Header.voxel_order[1]=='A') matrix->SetElement(1,1,-matrix->GetElement(1,1)); if (m_Header.voxel_order[2]=='I') matrix->SetElement(2,2,-matrix->GetElement(2,2)); geometry->SetIndexToWorldTransformByVtkMatrix(matrix); vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInputData(fiberPolyData); transformFilter->SetTransform(geometry->GetVtkTransform()); transformFilter->Update(); fib->SetFiberPolyData(transformFilter->GetOutput()); mitk::Point3D origin; origin[0]=m_Header.origin[0]; origin[1]=m_Header.origin[1]; origin[2]=m_Header.origin[2]; geometry->SetOrigin(origin); mitk::Vector3D spacing; spacing[0]=m_Header.voxel_size[0]; spacing[1]=m_Header.voxel_size[1]; spacing[2]=m_Header.voxel_size[2]; geometry->SetSpacing(spacing); geometry->SetExtentInMM(0, m_Header.voxel_size[0]*m_Header.dim[0]); geometry->SetExtentInMM(1, m_Header.voxel_size[1]*m_Header.dim[1]); geometry->SetExtentInMM(2, m_Header.voxel_size[2]*m_Header.dim[2]); fib->SetReferenceGeometry(dynamic_cast(geometry.GetPointer())); return numPoints; } // Update the field in the header to the new FIBER TOTAL. // ------------------------------------------------------ void TrackVisFiberReader::updateTotal( int totFibers ) { fseek(m_FilePointer, 1000-12, SEEK_SET); if (fwrite((char*)&totFibers, 1, 4, m_FilePointer) != 4) MITK_ERROR << "[ERROR] Problems saving the fiber!"; } void TrackVisFiberReader::writeHdr() { fseek(m_FilePointer, 0, SEEK_SET); if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000) MITK_ERROR << "[ERROR] Problems saving the fiber!"; } // Close the TrackVis file, but keep the metadata in the header. // ------------------------------------------------------------- void TrackVisFiberReader::close() { fclose(m_FilePointer); m_FilePointer = NULL; } bool TrackVisFiberReader::IsTransformValid() { if (fabs(m_Header.image_orientation_patient[0])<=0.001 || fabs(m_Header.image_orientation_patient[3])<=0.001 || fabs(m_Header.image_orientation_patient[5])<=0.001) return false; return true; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h index 8d9ad1a8d9..ab48c25597 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h @@ -1,82 +1,82 @@ /*=================================================================== 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 _TRACKVIS #define _TRACKVIS #include #include #include #include #include #include #include #include using namespace std; // Structure to hold metadata of a TrackVis file // --------------------------------------------- struct TrackVis_header { char id_string[6]; short int dim[3]; float voxel_size[3]; float origin[3]; short int n_scalars; char scalar_name[10][20]; short int n_properties; char property_name[10][20]; char reserved[508]; char voxel_order[4]; char pad2[4]; float image_orientation_patient[6]; char pad1[2]; unsigned char invert_x; unsigned char invert_y; unsigned char invert_z; unsigned char swap_xy; unsigned char swap_yz; unsigned char swap_zx; int n_count; int version; int hdr_size; }; // Class to handle TrackVis files. // ------------------------------- class MitkFiberTracking_EXPORT TrackVisFiberReader { private: string m_Filename; FILE* m_FilePointer; public: TrackVis_header m_Header; - short create(string m_Filename, mitk::FiberBundleX* fib); + short create(string m_Filename, const mitk::FiberBundleX* fib); short open( string m_Filename ); short read( mitk::FiberBundleX* fib ); - short append( mitk::FiberBundleX* fib ); + short append(const mitk::FiberBundleX* fib ); void writeHdr(); void updateTotal( int totFibers ); void close(); bool IsTransformValid(); TrackVisFiberReader(); ~TrackVisFiberReader(); }; #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt index f2ad9da614..3b03f3f67d 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt @@ -1,14 +1,14 @@ MITK_CREATE_MODULE_TESTS() if("${CMAKE_SIZEOF_VOID_P}" EQUAL "8") -mitkAddCustomModuleTest(mitkFiberBundleXReaderWriterTest mitkFiberBundleXReaderWriterTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib) +mitkAddCustomModuleTest(mitkFiberBundleXReaderWriterTest mitkFiberBundleXReaderWriterTest) mitkAddCustomModuleTest(mitkGibbsTrackingTest mitkGibbsTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage.qbi ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/gibbsTrackingParameters.gtp ${MITK_DATA_DIR}/DiffusionImaging/gibbsTractogram.fib) mitkAddCustomModuleTest(mitkStreamlineTrackingTest mitkStreamlineTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/tensorImage.dti ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogramInterpolated.fib) #mitkAddCustomModuleTest(mitkPeakExtractionTest mitkPeakExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_SHCoeffs.nrrd ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_VectorField.fib) mitkAddCustomModuleTest(mitkLocalFiberPlausibilityTest mitkLocalFiberPlausibilityTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_NUM_DIRECTIONS.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_VECTOR_FIELD.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE_IGNORE.nrrd) mitkAddCustomModuleTest(mitkFiberTransformationTest mitkFiberTransformationTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_transformed.fib) mitkAddCustomModuleTest(mitkFiberExtractionTest mitkFiberExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_extracted.fib ${MITK_DATA_DIR}/DiffusionImaging/ROI1.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI2.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI3.pf ${MITK_DATA_DIR}/DiffusionImaging/ROIIMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_inside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_outside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_passing-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_ending-in-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_subtracted.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_added.fib) mitkAddCustomModuleTest(mitkFiberGenerationTest mitkFiberGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_0.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_1.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_2.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/uniform.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib) mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationTest mitkFiberfoxSignalGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickAstrosticks_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickDot_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/TensorBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickTensorBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickTensorBallAstrosticks_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gibbsringing.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/ghost.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/aliasing.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/eddy.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/linearmotion.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/randommotion.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/spikes.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/riciannoise.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/chisquarenoise.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/distortions.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fieldmap.nrrd) mitkAddCustomModuleTest(mitkFiberfoxAddArtifactsToDwiTest mitkFiberfoxAddArtifactsToDwiTest) ENDIF() diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXReaderWriterTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXReaderWriterTest.cpp index 71f9ed28b4..8e36f84548 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXReaderWriterTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleXReaderWriterTest.cpp @@ -1,75 +1,75 @@ /*=================================================================== 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 "mitkTestingMacros.h" #include #include -#include #include #include #include #include +#include -/**Documentation - * Test for fiber bundle reader and writer - */ -int mitkFiberBundleXReaderWriterTest(int argc, char* argv[]) +#include "mitkTestFixture.h" + +class mitkFiberBundleXReaderWriterTestSuite : public mitk::TestFixture { - MITK_TEST_BEGIN("mitkFiberBundleXReaderWriterTest"); - std::cout << argv[1]<1,"check for filename") +private: - mitk::FiberBundleXWriter::Pointer writer = mitk::FiberBundleXWriter::New(); + /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/ mitk::FiberBundleX::Pointer fib1; mitk::FiberBundleX::Pointer fib2; - // first test: did this work? - // using MITK_TEST_CONDITION_REQUIRED makes the test stop after failure, since - // it makes no sense to continue without an object. - MITK_TEST_CONDITION_REQUIRED(writer.IsNotNull(),"writer instantiation") +public: + + void setUp() + { + fib1 = NULL; + fib2 = NULL; - try{ - // test if fib1 can be read const std::string s1="", s2=""; + std::string filename = GetTestDataFilePath("DiffusionImaging/fiberBundleX.fib"); - std::vector fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false ); + std::vector fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); mitk::BaseData::Pointer baseData = fibInfile.at(0); fib1 = dynamic_cast(baseData.GetPointer()); - MITK_TEST_CONDITION_REQUIRED(fib1.IsNotNull(),"check if reader returned null") + } - // test if fib1 can be written - MITK_TEST_CONDITION_REQUIRED( writer->CanWriteBaseDataType(fib1.GetPointer()),"writer can write data") - writer->SetFileName( std::string(MITK_TEST_OUTPUT_DIR)+"/writerTest.fib" ); - writer->DoWrite( fib1.GetPointer() ); + void tearDown() + { + fib1 = NULL; + fib2 = NULL; + } - // test if fib1 can be read again as fib2 - fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( std::string(MITK_TEST_OUTPUT_DIR)+"/writerTest.fib", s1, s2, false ); - baseData = fibInfile.at(0); + void Equal_SaveLoad_ReturnsTrue() + { + const std::string s1="", s2=""; + mitk::IOUtil::Save(fib1.GetPointer(), std::string(MITK_TEST_OUTPUT_DIR)+"/writerTest.fib"); + std::vector fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( std::string(MITK_TEST_OUTPUT_DIR)+"/writerTest.fib", s1, s2, false ); + mitk::BaseData::Pointer baseData = fibInfile.at(0); fib2 = dynamic_cast(baseData.GetPointer()); - MITK_TEST_CONDITION_REQUIRED(fib2.IsNotNull(),"reader can read file written before") - - // test if fib1 equals fib2 - MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2),"fiber bundles are not changed during reading/writing") - } - catch(...) { - return EXIT_FAILURE; + CPPUNIT_ASSERT_MESSAGE("Should be equal", fib1->Equals(fib2)); + //MITK_ASSERT_EQUAL(fib1, fib2, "A saved and re-loaded file should be equal"); } - // always end with this! - MITK_TEST_END(); -} +}; + +MITK_TEST_SUITE_REGISTRATION(mitkFiberBundleXReaderWriter) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp index 1f28408a0a..15ba467847 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp @@ -1,276 +1,274 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #include #include #include #include +#include /**Documentation * Test the Fiberfox simulation functions (fiberBundle -> diffusion weighted image) */ bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(FiberfoxParameters parameters, FiberBundleX::Pointer fiberBundle, mitk::DiffusionImage::Pointer refImage, string message) { itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetUseConstantRandSeed(true); tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( tractsToDwiFilter->GetOutput() ); testImage->SetReferenceBValue(parameters.m_SignalGen.m_Bvalue); testImage->SetDirections(parameters.m_SignalGen.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { bool cond = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); if (!cond) { MITK_INFO << "Saving test and rference image to " << mitk::IOUtil::GetTempPath(); mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi"); mitk::IOUtil::SaveBaseData(refImage, mitk::IOUtil::GetTempPath()+"refImage.dwi"); } MITK_TEST_CONDITION_REQUIRED(cond, message); } } int mitkFiberfoxSignalGenerationTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkFiberfoxSignalGenerationTest"); MITK_TEST_CONDITION_REQUIRED(argc>=19,"check for input data"); // input fiber bundle - FiberBundleXReader::Pointer fibReader = FiberBundleXReader::New(); - fibReader->SetFileName(argv[1]); - fibReader->Update(); - FiberBundleX::Pointer fiberBundle = dynamic_cast(fibReader->GetOutput()); + FiberBundleX::Pointer fiberBundle = dynamic_cast(mitk::IOUtil::Load(argv[1])[0].GetPointer()); // reference diffusion weighted images mitk::DiffusionImage::Pointer stickBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); mitk::DiffusionImage::Pointer stickAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); mitk::DiffusionImage::Pointer stickDot = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); mitk::DiffusionImage::Pointer tensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); mitk::DiffusionImage::Pointer stickTensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData()); mitk::DiffusionImage::Pointer stickTensorBallAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData()); mitk::DiffusionImage::Pointer gibbsringing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[8])->GetData()); mitk::DiffusionImage::Pointer ghost = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[9])->GetData()); mitk::DiffusionImage::Pointer aliasing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData()); mitk::DiffusionImage::Pointer eddy = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[11])->GetData()); mitk::DiffusionImage::Pointer linearmotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[12])->GetData()); mitk::DiffusionImage::Pointer randommotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[13])->GetData()); mitk::DiffusionImage::Pointer spikes = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[14])->GetData()); mitk::DiffusionImage::Pointer riciannoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[15])->GetData()); mitk::DiffusionImage::Pointer chisquarenoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[16])->GetData()); mitk::DiffusionImage::Pointer distortions = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[17])->GetData()); mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[18])->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); FiberfoxParameters parameters; parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_SignalGen.m_SignalScale = 10000; parameters.m_SignalGen.m_ImageRegion = stickBall->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = stickBall->GetVectorImage()->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = stickBall->GetVectorImage()->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = stickBall->GetVectorImage()->GetDirection(); parameters.m_SignalGen.m_Bvalue = stickBall->GetReferenceBValue(); parameters.m_SignalGen.SetGradienDirections(stickBall->GetDirections()); // intra and inter axonal compartments mitk::StickModel stickModel; stickModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); stickModel.SetT2(110); stickModel.SetDiffusivity(0.001); stickModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::TensorModel tensorModel; tensorModel.SetT2(110); stickModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); tensorModel.SetDiffusivity1(0.001); tensorModel.SetDiffusivity2(0.00025); tensorModel.SetDiffusivity3(0.00025); tensorModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); // extra axonal compartment models mitk::BallModel ballModel; ballModel.SetT2(80); ballModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); ballModel.SetDiffusivity(0.001); ballModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::AstroStickModel astrosticksModel; astrosticksModel.SetT2(80); astrosticksModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); astrosticksModel.SetDiffusivity(0.001); astrosticksModel.SetRandomizeSticks(true); astrosticksModel.SetSeed(0); astrosticksModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::DotModel dotModel; dotModel.SetT2(80); dotModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); // noise models mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); // Rician noise mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); try{ // Stick-Ball parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickBall, argv[2]); // Srick-Astrosticks parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickAstrosticks, argv[3]); // Stick-Dot parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&dotModel); StartSimulation(parameters, fiberBundle, stickDot, argv[4]); // Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, tensorBall, argv[5]); // Stick-Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickTensorBall, argv[6]); // Stick-Tensor-Ball-Astrosticks parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickTensorBallAstrosticks, argv[7]); // Gibbs ringing parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); parameters.m_SignalGen.m_DoAddGibbsRinging = true; StartSimulation(parameters, fiberBundle, gibbsringing, argv[8]); // Ghost parameters.m_SignalGen.m_DoAddGibbsRinging = false; parameters.m_SignalGen.m_KspaceLineOffset = 0.25; StartSimulation(parameters, fiberBundle, ghost, argv[9]); // Aliasing parameters.m_SignalGen.m_KspaceLineOffset = 0; parameters.m_SignalGen.m_CroppingFactor = 0.4; parameters.m_SignalGen.m_SignalScale = 1000; StartSimulation(parameters, fiberBundle, aliasing, argv[10]); // Eddy currents parameters.m_SignalGen.m_CroppingFactor = 1; parameters.m_SignalGen.m_SignalScale = 10000; parameters.m_SignalGen.m_EddyStrength = 0.05; StartSimulation(parameters, fiberBundle, eddy, argv[11]); // Motion (linear) parameters.m_SignalGen.m_EddyStrength = 0.0; parameters.m_SignalGen.m_DoAddMotion = true; parameters.m_SignalGen.m_DoRandomizeMotion = false; parameters.m_SignalGen.m_Translation[1] = 10; parameters.m_SignalGen.m_Rotation[2] = 90; StartSimulation(parameters, fiberBundle, linearmotion, argv[12]); // Motion (random) parameters.m_SignalGen.m_DoRandomizeMotion = true; parameters.m_SignalGen.m_Translation[1] = 5; parameters.m_SignalGen.m_Rotation[2] = 45; StartSimulation(parameters, fiberBundle, randommotion, argv[13]); // Spikes parameters.m_SignalGen.m_DoAddMotion = false; parameters.m_SignalGen.m_Spikes = 5; parameters.m_SignalGen.m_SpikeAmplitude = 1; StartSimulation(parameters, fiberBundle, spikes, argv[14]); // Rician noise parameters.m_SignalGen.m_Spikes = 0; parameters.m_NoiseModel = ricianNoiseModel; StartSimulation(parameters, fiberBundle, riciannoise, argv[15]); delete parameters.m_NoiseModel; // Chi-square noise parameters.m_NoiseModel = chiSquareNoiseModel; StartSimulation(parameters, fiberBundle, chisquarenoise, argv[16]); delete parameters.m_NoiseModel; // Distortions parameters.m_NoiseModel = NULL; parameters.m_SignalGen.m_FrequencyMap = fMap; StartSimulation(parameters, fiberBundle, distortions, argv[17]); } catch (std::exception &e) { MITK_TEST_CONDITION_REQUIRED(false, e.what()); } // always end with this! MITK_TEST_END(); } diff --git a/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp b/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp index 896b1456de..3035f187bf 100755 --- a/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp +++ b/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp @@ -1,96 +1,93 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include "ctkCommandLineParser.cpp" using namespace mitk; int FileFormatConverter(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Format Converter"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input file", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast(parsedArgs["in"]); string outName = us::any_cast(parsedArgs["out"]); try { const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); if ( dynamic_cast*>(baseData.GetPointer()) ) { DiffusionImage::Pointer dwi = dynamic_cast*>(baseData.GetPointer()); NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(outName); writer->SetInput(dwi); writer->Update(); } else if ( dynamic_cast(baseData.GetPointer()) ) { - Image::Pointer image = dynamic_cast(baseData.GetPointer()); - mitk::IOUtil::SaveImage(image, outName); + mitk::IOUtil::Save(dynamic_cast(baseData.GetPointer()), outName.c_str()); } else if ( dynamic_cast(baseData.GetPointer()) ) { - FiberBundleXWriter::Pointer fibWriter = FiberBundleXWriter::New(); - fibWriter->SetFileName(outName.c_str()); - fibWriter->DoWrite( dynamic_cast(baseData.GetPointer()) ); + mitk::IOUtil::Save(dynamic_cast(baseData.GetPointer()) ,outName.c_str()); } else MITK_INFO << "File type currently not supported!"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(FileFormatConverter); diff --git a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp index 6104af810f..188b247c06 100755 --- a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp @@ -1,380 +1,379 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include +#include + mitk::Image::Pointer LoadData(std::string filename) { if( filename.empty() ) return NULL; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( infile.empty() ) { MITK_INFO << "File " << filename << " could not be read!"; return NULL; } mitk::BaseData::Pointer baseData = infile.at(0); return dynamic_cast(baseData.GetPointer()); } template int StartPeakExtraction(int argc, char* argv[]) { MITK_INFO << "StartPeakExtraction"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("image", "i", ctkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); parser.addArgument("outroot", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true); parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true); parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true); parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peak Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string imageName = us::any_cast(parsedArgs["image"]); string outRoot = us::any_cast(parsedArgs["outroot"]); // optional arguments string maskImageName(""); if (parsedArgs.count("mask")) maskImageName = us::any_cast(parsedArgs["mask"]); int normalization = 1; if (parsedArgs.count("normalization")) normalization = us::any_cast(parsedArgs["normalization"]); int numPeaks = 2; if (parsedArgs.count("numpeaks")) numPeaks = us::any_cast(parsedArgs["numpeaks"]); float peakThres = 0.4; if (parsedArgs.count("peakthres")) peakThres = us::any_cast(parsedArgs["peakthres"]); float absPeakThres = 0.06; if (parsedArgs.count("abspeakthres")) absPeakThres = us::any_cast(parsedArgs["abspeakthres"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast(parsedArgs["noFlip"]); MITK_INFO << "image: " << imageName; MITK_INFO << "outroot: " << outRoot; if (!maskImageName.empty()) MITK_INFO << "mask: " << maskImageName; else MITK_INFO << "no mask image selected"; MITK_INFO << "numpeaks: " << numPeaks; MITK_INFO << "peakthres: " << peakThres; MITK_INFO << "abspeakthres: " << absPeakThres; MITK_INFO << "shOrder: " << shOrder; try { mitk::Image::Pointer image = LoadData(imageName); mitk::Image::Pointer mask = LoadData(maskImageName); typedef itk::Image ItkUcharImgType; typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType; typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New(); int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "FSL") ) { toolkitConvention = 1; MITK_INFO << "Using FSL SH-basis"; } else if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 2; MITK_INFO << "Using MRtrix SH-basis"; } else MITK_INFO << "Using MITK SH-basis"; } else MITK_INFO << "Using MITK SH-basis"; ItkUcharImgType::Pointer itkMaskImage = NULL; if (mask.IsNotNull()) { try{ itkMaskImage = ItkUcharImgType::New(); mitk::CastToItkImage(mask, itkMaskImage); filter->SetMaskImage(itkMaskImage); } catch(...) { } } if (toolkitConvention>0) { MITK_INFO << "Converting coefficient image to MITK format"; typedef itk::ShCoefficientImageImporter< float, shOrder > ConverterType; typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput(); typename ConverterType::Pointer converter = ConverterType::New(); if (noFlip) { converter->SetInputImage(itkImage); } else { MITK_INFO << "Flipping image"; itk::FixedArray flipAxes; flipAxes[0] = true; flipAxes[1] = true; flipAxes[2] = false; flipAxes[3] = false; itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput(); itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1; flipped->SetDirection(m); itk::Point< float, 4 > o = itkImage->GetOrigin(); o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1); o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1); flipped->SetOrigin(o); converter->SetInputImage(flipped); } MITK_INFO << "Starting conversion"; switch (toolkitConvention) { case 1: converter->SetToolkit(ConverterType::FSL); filter->SetToolkit(MaximaExtractionFilterType::FSL); break; case 2: converter->SetToolkit(ConverterType::MRTRIX); filter->SetToolkit(MaximaExtractionFilterType::MRTRIX); break; default: converter->SetToolkit(ConverterType::FSL); filter->SetToolkit(MaximaExtractionFilterType::FSL); break; } converter->GenerateData(); filter->SetInput(converter->GetCoefficientImage()); } else { try{ typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType; typename CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); filter->SetInput(caster->GetOutput()); } catch(...) { MITK_INFO << "wrong image type"; return EXIT_FAILURE; } } filter->SetMaxNumPeaks(numPeaks); filter->SetPeakThreshold(peakThres); filter->SetAbsolutePeakThreshold(absPeakThres); filter->SetAngularThreshold(1); switch (normalization) { case 0: filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM); break; case 1: filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM); break; case 2: filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM); break; } MITK_INFO << "Starting extraction"; filter->Update(); // write direction images { typedef typename MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer; typename ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer(); for (unsigned int i=0; iSize(); i++) { typename MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i); if (itkMaskImage.IsNotNull()) { itkImg->SetDirection(itkMaskImage->GetDirection()); itkImg->SetOrigin(itkMaskImage->GetOrigin()); } string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); typedef itk::ImageFileWriter< typename MaximaExtractionFilterType::ItkDirectionImage > WriterType; typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outfilename); writer->SetInput(itkImg); writer->Update(); } } // write num directions image { ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage(); if (itkMaskImage.IsNotNull()) { numDirImage->SetDirection(itkMaskImage->GetDirection()); numDirImage->SetOrigin(itkMaskImage->GetOrigin()); } string outfilename = outRoot.c_str(); outfilename.append("_NUM_DIRECTIONS.nrrd"); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outfilename); writer->SetInput(numDirImage); writer->Update(); } // write vector field { mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle(); string outfilename = outRoot.c_str(); outfilename.append("_VECTOR_FIELD.fib"); - - mitk::FiberBundleXWriter::Pointer fibWriter = mitk::FiberBundleXWriter::New(); - fibWriter->SetFileName(outfilename.c_str()); - fibWriter->DoWrite(directions.GetPointer()); + mitk::IOUtil::Save(directions.GetPointer(),outfilename.c_str()); } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } int PeakExtraction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("image", "i", ctkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order"); parser.addArgument("outroot", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true); parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true); parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true); parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peak Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; int shOrder = -1; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); switch (shOrder) { case 4: return StartPeakExtraction<4>(argc, argv); case 6: return StartPeakExtraction<6>(argc, argv); case 8: return StartPeakExtraction<8>(argc, argv); case 10: return StartPeakExtraction<10>(argc, argv); case 12: return StartPeakExtraction<12>(argc, argv); } return EXIT_FAILURE; } RegisterDiffusionMiniApp(PeakExtraction); diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp index 2eca4ddbd1..364a5dc516 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp @@ -1,758 +1,756 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkGibbsTrackingView.h" #include // Qt #include #include #include // MITK #include #include #include #include -#include +#include // ITK #include #include #include // MISC #include + + QmitkTrackingWorker::QmitkTrackingWorker(QmitkGibbsTrackingView* view) : m_View(view) { } void QmitkTrackingWorker::run() { m_View->m_GlobalTracker = QmitkGibbsTrackingView::GibbsTrackingFilterType::New(); m_View->m_GlobalTracker->SetQBallImage(m_View->m_ItkQBallImage); m_View->m_GlobalTracker->SetTensorImage(m_View->m_ItkTensorImage); m_View->m_GlobalTracker->SetMaskImage(m_View->m_MaskImage); m_View->m_GlobalTracker->SetStartTemperature((float)m_View->m_Controls->m_StartTempSlider->value()/100); m_View->m_GlobalTracker->SetEndTemperature((float)m_View->m_Controls->m_EndTempSlider->value()/10000); m_View->m_GlobalTracker->SetIterations(m_View->m_Iterations); m_View->m_GlobalTracker->SetParticleWeight((float)m_View->m_Controls->m_ParticleWeightSlider->value()/10000); m_View->m_GlobalTracker->SetParticleWidth((float)(m_View->m_Controls->m_ParticleWidthSlider->value())/10); m_View->m_GlobalTracker->SetParticleLength((float)(m_View->m_Controls->m_ParticleLengthSlider->value())/10); m_View->m_GlobalTracker->SetInexBalance((float)m_View->m_Controls->m_InExBalanceSlider->value()/10); m_View->m_GlobalTracker->SetMinFiberLength(m_View->m_Controls->m_FiberLengthSlider->value()); m_View->m_GlobalTracker->SetCurvatureThreshold(cos((float)m_View->m_Controls->m_CurvatureThresholdSlider->value()*M_PI/180)); m_View->m_GlobalTracker->SetRandomSeed(m_View->m_Controls->m_RandomSeedSlider->value()); try{ m_View->m_GlobalTracker->Update(); } catch( mitk::Exception e ) { MITK_ERROR << "Internal error occured: " << e.what() << "\nAborting"; } m_View->m_TrackingThread.quit(); } const std::string QmitkGibbsTrackingView::VIEW_ID = "org.mitk.views.gibbstracking"; QmitkGibbsTrackingView::QmitkGibbsTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget(NULL) , m_FiberBundle(NULL) , m_MaskImage(NULL) , m_TensorImage(NULL) , m_QBallImage(NULL) , m_ItkQBallImage(NULL) , m_ItkTensorImage(NULL) , m_ImageNode(NULL) , m_MaskImageNode(NULL) , m_FiberBundleNode(NULL) , m_ThreadIsRunning(false) , m_ElapsedTime(0) , m_Iterations(10000000) , m_LastStep(0) , m_GlobalTracker(NULL) , m_TrackingWorker(this) { m_TrackingWorker.moveToThread(&m_TrackingThread); connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run())); connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_TrackingThread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_TrackingTimer = new QTimer(this); } QmitkGibbsTrackingView::~QmitkGibbsTrackingView() { if (m_GlobalTracker.IsNull()) return; m_GlobalTracker->SetAbortTracking(true); m_TrackingThread.wait(); } // update tracking status and generate fiber bundle void QmitkGibbsTrackingView::TimerUpdate() { int currentStep = m_GlobalTracker->GetCurrentStep(); mitk::ProgressBar::GetInstance()->Progress(currentStep-m_LastStep); UpdateTrackingStatus(); GenerateFiberBundle(); m_LastStep = currentStep; } // tell global tractography filter to stop after current step void QmitkGibbsTrackingView::StopGibbsTracking() { if (m_GlobalTracker.IsNull()) return; //mitk::ProgressBar::GetInstance()->Progress(m_GlobalTracker->GetSteps()-m_LastStep+1); m_GlobalTracker->SetAbortTracking(true); m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStop->setText("Stopping Tractography ..."); } // update gui elements and generate fiber bundle after tracking is finished void QmitkGibbsTrackingView::AfterThread() { m_ThreadIsRunning = false; m_TrackingTimer->stop(); mitk::ProgressBar::GetInstance()->Progress(m_GlobalTracker->GetSteps()-m_LastStep+1); UpdateGUI(); if( !m_GlobalTracker->GetIsInValidState() ) { QMessageBox::critical( NULL, "Gibbs Tracking", "An internal error occured. Tracking aborted.\n Please check the log for details." ); m_FiberBundleNode = NULL; return; } UpdateTrackingStatus(); if(m_Controls->m_ParticleWeightSlider->value()==0) { m_Controls->m_ParticleWeightLabel->setText(QString::number(m_GlobalTracker->GetParticleWeight())); m_Controls->m_ParticleWeightSlider->setValue(m_GlobalTracker->GetParticleWeight()*10000); } if(m_Controls->m_ParticleWidthSlider->value()==0) { m_Controls->m_ParticleWidthLabel->setText(QString::number(m_GlobalTracker->GetParticleWidth())); m_Controls->m_ParticleWidthSlider->setValue(m_GlobalTracker->GetParticleWidth()*10); } if(m_Controls->m_ParticleLengthSlider->value()==0) { m_Controls->m_ParticleLengthLabel->setText(QString::number(m_GlobalTracker->GetParticleLength())); m_Controls->m_ParticleLengthSlider->setValue(m_GlobalTracker->GetParticleLength()*10); } GenerateFiberBundle(); m_FiberBundleNode = 0; m_GlobalTracker = 0; // images not needed anymore ( relevant only for computation ) // we need to release them to remove the memory access block created through CastToItk<> calls this->m_ItkQBallImage = 0; this->m_ItkTensorImage = 0; } // start tracking timer and update gui elements before tracking is started void QmitkGibbsTrackingView::BeforeThread() { m_ThreadIsRunning = true; m_TrackingTime = QTime::currentTime(); m_ElapsedTime = 0; m_TrackingTimer->start(1000); m_LastStep = 0; UpdateGUI(); } // setup gui elements and signal/slot connections void QmitkGibbsTrackingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkGibbsTrackingViewControls; m_Controls->setupUi( parent ); AdvancedSettings(); connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) ); connect( m_Controls->m_TrackingStop, SIGNAL(clicked()), this, SLOT(StopGibbsTracking()) ); connect( m_Controls->m_TrackingStart, SIGNAL(clicked()), this, SLOT(StartGibbsTracking()) ); connect( m_Controls->m_AdvancedSettingsCheckbox, SIGNAL(clicked()), this, SLOT(AdvancedSettings()) ); connect( m_Controls->m_SaveTrackingParameters, SIGNAL(clicked()), this, SLOT(SaveTrackingParameters()) ); connect( m_Controls->m_LoadTrackingParameters, SIGNAL(clicked()), this, SLOT(LoadTrackingParameters()) ); connect( m_Controls->m_IterationsSlider, SIGNAL(valueChanged(int)), this, SLOT(SetIterations(int)) ); connect( m_Controls->m_ParticleWidthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWidth(int)) ); connect( m_Controls->m_ParticleLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleLength(int)) ); connect( m_Controls->m_InExBalanceSlider, SIGNAL(valueChanged(int)), this, SLOT(SetInExBalance(int)) ); connect( m_Controls->m_FiberLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetFiberLength(int)) ); connect( m_Controls->m_ParticleWeightSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWeight(int)) ); connect( m_Controls->m_StartTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetStartTemp(int)) ); connect( m_Controls->m_EndTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetEndTemp(int)) ); connect( m_Controls->m_CurvatureThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(SetCurvatureThreshold(int)) ); connect( m_Controls->m_RandomSeedSlider, SIGNAL(valueChanged(int)), this, SLOT(SetRandomSeed(int)) ); connect( m_Controls->m_OutputFileButton, SIGNAL(clicked()), this, SLOT(SetOutputFile()) ); } } void QmitkGibbsTrackingView::SetInExBalance(int value) { m_Controls->m_InExBalanceLabel->setText(QString::number((float)value/10)); } void QmitkGibbsTrackingView::SetFiberLength(int value) { m_Controls->m_FiberLengthLabel->setText(QString::number(value)+"mm"); } void QmitkGibbsTrackingView::SetRandomSeed(int value) { if (value>=0) m_Controls->m_RandomSeedLabel->setText(QString::number(value)); else m_Controls->m_RandomSeedLabel->setText("auto"); } void QmitkGibbsTrackingView::SetParticleWeight(int value) { if (value>0) m_Controls->m_ParticleWeightLabel->setText(QString::number((float)value/10000)); else m_Controls->m_ParticleWeightLabel->setText("auto"); } void QmitkGibbsTrackingView::SetStartTemp(int value) { m_Controls->m_StartTempLabel->setText(QString::number((float)value/100)); } void QmitkGibbsTrackingView::SetEndTemp(int value) { m_Controls->m_EndTempLabel->setText(QString::number((float)value/10000)); } void QmitkGibbsTrackingView::SetParticleWidth(int value) { if (value>0) m_Controls->m_ParticleWidthLabel->setText(QString::number((float)value/10)+" mm"); else m_Controls->m_ParticleWidthLabel->setText("auto"); } void QmitkGibbsTrackingView::SetParticleLength(int value) { if (value>0) m_Controls->m_ParticleLengthLabel->setText(QString::number((float)value/10)+" mm"); else m_Controls->m_ParticleLengthLabel->setText("auto"); } void QmitkGibbsTrackingView::SetCurvatureThreshold(int value) { m_Controls->m_CurvatureThresholdLabel->setText(QString::number(value)+"°"); } void QmitkGibbsTrackingView::SetIterations(int value) { switch(value) { case 0: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^4"); m_Iterations = 10000; break; case 1: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^4"); m_Iterations = 50000; break; case 2: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^5"); m_Iterations = 100000; break; case 3: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^5"); m_Iterations = 500000; break; case 4: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^6"); m_Iterations = 1000000; break; case 5: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^6"); m_Iterations = 5000000; break; case 6: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^7"); m_Iterations = 10000000; break; case 7: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^7"); m_Iterations = 50000000; break; case 8: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^8"); m_Iterations = 100000000; break; case 9: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^8"); m_Iterations = 500000000; break; } } void QmitkGibbsTrackingView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkGibbsTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } // called if datamanager selection changes void QmitkGibbsTrackingView::OnSelectionChanged( std::vector nodes ) { if (m_ThreadIsRunning) return; m_ImageNode = NULL; m_MaskImageNode = NULL; // iterate all selected objects for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) m_ImageNode = node; else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) m_ImageNode = node; else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(node->GetData()); if (img->GetPixelType().GetPixelType()==itk::ImageIOBase::SCALAR) m_MaskImageNode = node; } } UpdateGUI(); } // update gui elements displaying trackings status void QmitkGibbsTrackingView::UpdateTrackingStatus() { if (m_GlobalTracker.IsNull()) return; m_ElapsedTime += m_TrackingTime.elapsed()/1000; m_TrackingTime.restart(); unsigned long hours = m_ElapsedTime/3600; unsigned long minutes = (m_ElapsedTime%3600)/60; unsigned long seconds = m_ElapsedTime%60; m_Controls->m_ProposalAcceptance->setText(QString::number(m_GlobalTracker->GetProposalAcceptance()*100)+"%"); m_Controls->m_TrackingTimeLabel->setText( QString::number(hours)+QString("h ")+QString::number(minutes)+QString("m ")+QString::number(seconds)+QString("s") ); m_Controls->m_NumConnectionsLabel->setText( QString::number(m_GlobalTracker->GetNumConnections()) ); m_Controls->m_NumParticlesLabel->setText( QString::number(m_GlobalTracker->GetNumParticles()) ); m_Controls->m_CurrentStepLabel->setText( QString::number(100*(float)(m_GlobalTracker->GetCurrentStep()-1)/m_GlobalTracker->GetSteps())+"%" ); m_Controls->m_AcceptedFibersLabel->setText( QString::number(m_GlobalTracker->GetNumAcceptedFibers()) ); } // update gui elements (enable/disable elements and set tooltips) void QmitkGibbsTrackingView::UpdateGUI() { if (m_ImageNode.IsNotNull()) { m_Controls->m_QballImageLabel->setText(m_ImageNode->GetName().c_str()); m_Controls->m_DataFrame->setTitle("Input Data"); } else { m_Controls->m_QballImageLabel->setText("mandatory"); m_Controls->m_DataFrame->setTitle("Please Select Input Data"); } if (m_MaskImageNode.IsNotNull()) m_Controls->m_MaskImageLabel->setText(m_MaskImageNode->GetName().c_str()); else m_Controls->m_MaskImageLabel->setText("optional"); if (!m_ThreadIsRunning && m_ImageNode.IsNotNull()) { m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStart->setEnabled(true); m_Controls->m_LoadTrackingParameters->setEnabled(true); m_Controls->m_IterationsSlider->setEnabled(true); m_Controls->m_AdvancedFrame->setEnabled(true); m_Controls->m_TrackingStop->setText("Stop Tractography"); m_Controls->m_TrackingStart->setToolTip("Start tractography. No further change of parameters possible."); m_Controls->m_TrackingStop->setToolTip(""); } else if (!m_ThreadIsRunning) { m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStart->setEnabled(false); m_Controls->m_LoadTrackingParameters->setEnabled(true); m_Controls->m_IterationsSlider->setEnabled(true); m_Controls->m_AdvancedFrame->setEnabled(true); m_Controls->m_TrackingStop->setText("Stop Tractography"); m_Controls->m_TrackingStart->setToolTip("No Q-Ball image selected."); m_Controls->m_TrackingStop->setToolTip(""); } else { m_Controls->m_TrackingStop->setEnabled(true); m_Controls->m_TrackingStart->setEnabled(false); m_Controls->m_LoadTrackingParameters->setEnabled(false); m_Controls->m_IterationsSlider->setEnabled(false); m_Controls->m_AdvancedFrame->setEnabled(false); m_Controls->m_AdvancedFrame->setVisible(false); m_Controls->m_AdvancedSettingsCheckbox->setChecked(false); m_Controls->m_TrackingStart->setToolTip("Tracking in progress."); m_Controls->m_TrackingStop->setToolTip("Stop tracking and display results."); } } // show/hide advanced settings frame void QmitkGibbsTrackingView::AdvancedSettings() { m_Controls->m_AdvancedFrame->setVisible(m_Controls->m_AdvancedSettingsCheckbox->isChecked()); } // set mask image data node void QmitkGibbsTrackingView::SetMask() { std::vector nodes = GetDataManagerSelection(); if (nodes.empty()) { m_MaskImageNode = NULL; m_Controls->m_MaskImageLabel->setText("-"); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_MaskImageNode = node; m_Controls->m_MaskImageLabel->setText(node->GetName().c_str()); return; } } } // check for mask and qbi and start tracking thread void QmitkGibbsTrackingView::StartGibbsTracking() { if(m_ThreadIsRunning) { MITK_WARN("QmitkGibbsTrackingView")<<"Thread already running!"; return; } m_GlobalTracker = NULL; if (m_ImageNode.IsNull()) { QMessageBox::information( NULL, "Warning", "Please load and select a qball image before starting image processing."); return; } if (dynamic_cast(m_ImageNode->GetData())) m_QBallImage = dynamic_cast(m_ImageNode->GetData()); else if (dynamic_cast(m_ImageNode->GetData())) m_TensorImage = dynamic_cast(m_ImageNode->GetData()); if (m_QBallImage.IsNull() && m_TensorImage.IsNull()) return; // cast qbi to itk m_ItkTensorImage = NULL; m_ItkQBallImage = NULL; m_MaskImage = NULL; if (m_QBallImage.IsNotNull()) { m_ItkQBallImage = ItkQBallImgType::New(); mitk::CastToItkImage(m_QBallImage, m_ItkQBallImage); } else { m_ItkTensorImage = ItkTensorImage::New(); mitk::CastToItkImage(m_TensorImage, m_ItkTensorImage); } // mask image found? // catch exceptions thrown by the itkAccess macros try{ if(m_MaskImageNode.IsNotNull()) { if (dynamic_cast(m_MaskImageNode->GetData())) mitk::CastToItkImage(dynamic_cast(m_MaskImageNode->GetData()), m_MaskImage); } } catch(...){}; unsigned int steps = m_Iterations/10000; if (steps<10) steps = 10; m_LastStep = 1; mitk::ProgressBar::GetInstance()->AddStepsToDo(steps); // start worker thread m_TrackingThread.start(QThread::LowestPriority); } // generate mitkFiberBundle from tracking filter output void QmitkGibbsTrackingView::GenerateFiberBundle() { if (m_GlobalTracker.IsNull() || (!(m_Controls->m_VisualizationCheckbox->isChecked() || m_Controls->m_VisualizeOnceButton->isChecked()) && m_ThreadIsRunning)) return; if (m_Controls->m_VisualizeOnceButton->isChecked()) m_Controls->m_VisualizeOnceButton->setChecked(false); vtkSmartPointer fiberBundle = m_GlobalTracker->GetFiberBundle(); if ( m_GlobalTracker->GetNumAcceptedFibers()==0 ) return; m_FiberBundle = mitk::FiberBundleX::New(fiberBundle); m_FiberBundle->SetReferenceGeometry(dynamic_cast(m_ImageNode->GetData())->GetGeometry()); if (m_FiberBundleNode.IsNotNull()){ GetDefaultDataStorage()->Remove(m_FiberBundleNode); m_FiberBundleNode = 0; } m_FiberBundleNode = mitk::DataNode::New(); m_FiberBundleNode->SetData(m_FiberBundle); QString name("FiberBundle_"); name += m_ImageNode->GetName().c_str(); name += "_Gibbs"; m_FiberBundleNode->SetName(name.toStdString()); m_FiberBundleNode->SetVisibility(true); if (!m_OutputFileName.isEmpty() && !m_ThreadIsRunning) { - QString filename = m_OutputFileName; - mitk::FiberBundleXWriter::Pointer writer = mitk::FiberBundleXWriter::New(); - writer->SetFileName(filename.toStdString()); - writer->SetInputFiberBundleX(m_FiberBundle.GetPointer()); try { - writer->Update(); - QMessageBox::information(NULL, "Fiber bundle saved to", filename); + mitk::IOUtil::Save(m_FiberBundle.GetPointer(),m_OutputFileName.toStdString()); + QMessageBox::information(NULL, "Fiber bundle saved to", m_OutputFileName); } catch (itk::ExceptionObject &ex) { QMessageBox::information(NULL, "Fiber bundle could not be saved", QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); } } if(m_ImageNode.IsNull()) GetDataStorage()->Add(m_FiberBundleNode); else GetDataStorage()->Add(m_FiberBundleNode, m_ImageNode); } void QmitkGibbsTrackingView::SetOutputFile() { // SELECT FOLDER DIALOG m_OutputFileName = QFileDialog::getSaveFileName(0, tr("Set file name"), QDir::currentPath()+"/FiberBundle.fib", tr("Fiber Bundle (*.fib)") ); if (m_OutputFileName.isEmpty()) m_Controls->m_OutputFileLabel->setText("N/A"); else m_Controls->m_OutputFileLabel->setText(m_OutputFileName); } // save current tracking paramters as xml file (.gtp) void QmitkGibbsTrackingView::SaveTrackingParameters() { TiXmlDocument documentXML; TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); documentXML.LinkEndChild( declXML ); TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file"); mainXML->SetAttribute("file_version", "0.1"); documentXML.LinkEndChild(mainXML); TiXmlElement* paramXML = new TiXmlElement("parameter_set"); paramXML->SetAttribute("iterations", QString::number(m_Iterations).toStdString()); paramXML->SetAttribute("particle_length", QString::number((float)m_Controls->m_ParticleLengthSlider->value()/10).toStdString()); paramXML->SetAttribute("particle_width", QString::number((float)m_Controls->m_ParticleWidthSlider->value()/10).toStdString()); paramXML->SetAttribute("particle_weight", QString::number((float)m_Controls->m_ParticleWeightSlider->value()/10000).toStdString()); paramXML->SetAttribute("temp_start", QString::number((float)m_Controls->m_StartTempSlider->value()/100).toStdString()); paramXML->SetAttribute("temp_end", QString::number((float)m_Controls->m_EndTempSlider->value()/10000).toStdString()); paramXML->SetAttribute("inexbalance", QString::number((float)m_Controls->m_InExBalanceSlider->value()/10).toStdString()); paramXML->SetAttribute("fiber_length", QString::number(m_Controls->m_FiberLengthSlider->value()).toStdString()); paramXML->SetAttribute("curvature_threshold", QString::number(m_Controls->m_CurvatureThresholdSlider->value()).toStdString()); mainXML->LinkEndChild(paramXML); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), QDir::currentPath()+"/param.gtp", tr("Global Tracking Parameters (*.gtp)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".gtp")) filename += ".gtp"; documentXML.SaveFile( filename.toStdString() ); } void QmitkGibbsTrackingView::UpdateIteraionsGUI(unsigned long iterations) { switch(iterations) { case 10000: m_Controls->m_IterationsSlider->setValue(0); m_Controls->m_IterationsLabel->setText("Iterations: 10^4"); break; case 50000: m_Controls->m_IterationsSlider->setValue(1); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^4"); break; case 100000: m_Controls->m_IterationsSlider->setValue(2); m_Controls->m_IterationsLabel->setText("Iterations: 10^5"); break; case 500000: m_Controls->m_IterationsSlider->setValue(3); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^5"); break; case 1000000: m_Controls->m_IterationsSlider->setValue(4); m_Controls->m_IterationsLabel->setText("Iterations: 10^6"); break; case 5000000: m_Controls->m_IterationsSlider->setValue(5); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^6"); break; case 10000000: m_Controls->m_IterationsSlider->setValue(6); m_Controls->m_IterationsLabel->setText("Iterations: 10^7"); break; case 50000000: m_Controls->m_IterationsSlider->setValue(7); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^7"); break; case 100000000: m_Controls->m_IterationsSlider->setValue(8); m_Controls->m_IterationsLabel->setText("Iterations: 10^8"); break; case 500000000: m_Controls->m_IterationsSlider->setValue(9); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^8"); break; case 1000000000: m_Controls->m_IterationsSlider->setValue(10); m_Controls->m_IterationsLabel->setText("Iterations: 10^9"); break; case 5000000000: m_Controls->m_IterationsSlider->setValue(11); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^9"); break; } } // load current tracking paramters from xml file (.gtp) void QmitkGibbsTrackingView::LoadTrackingParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QDir::currentPath(), tr("Global Tracking Parameters (*.gtp)") ); if(filename.isEmpty() || filename.isNull()) return; TiXmlDocument doc( filename.toStdString() ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement("parameter_set").Element(); QString iterations(pElem->Attribute("iterations")); m_Iterations = iterations.toULong(); UpdateIteraionsGUI(m_Iterations); QString particleLength(pElem->Attribute("particle_length")); float pLength = particleLength.toFloat(); QString particleWidth(pElem->Attribute("particle_width")); float pWidth = particleWidth.toFloat(); if (pLength==0) m_Controls->m_ParticleLengthLabel->setText("auto"); else m_Controls->m_ParticleLengthLabel->setText(particleLength+" mm"); if (pWidth==0) m_Controls->m_ParticleWidthLabel->setText("auto"); else m_Controls->m_ParticleWidthLabel->setText(particleWidth+" mm"); m_Controls->m_ParticleWidthSlider->setValue(pWidth*10); m_Controls->m_ParticleLengthSlider->setValue(pLength*10); QString partWeight(pElem->Attribute("particle_weight")); m_Controls->m_ParticleWeightSlider->setValue(partWeight.toFloat()*10000); m_Controls->m_ParticleWeightLabel->setText(partWeight); QString startTemp(pElem->Attribute("temp_start")); m_Controls->m_StartTempSlider->setValue(startTemp.toFloat()*100); m_Controls->m_StartTempLabel->setText(startTemp); QString endTemp(pElem->Attribute("temp_end")); m_Controls->m_EndTempSlider->setValue(endTemp.toFloat()*10000); m_Controls->m_EndTempLabel->setText(endTemp); QString inExBalance(pElem->Attribute("inexbalance")); m_Controls->m_InExBalanceSlider->setValue(inExBalance.toFloat()*10); m_Controls->m_InExBalanceLabel->setText(inExBalance); QString fiberLength(pElem->Attribute("fiber_length")); m_Controls->m_FiberLengthSlider->setValue(fiberLength.toInt()); m_Controls->m_FiberLengthLabel->setText(fiberLength+"mm"); QString curvThres(pElem->Attribute("curvature_threshold")); m_Controls->m_CurvatureThresholdSlider->setValue(curvThres.toInt()); m_Controls->m_CurvatureThresholdLabel->setText(curvThres+"°"); }