diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.cpp b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.cpp new file mode 100644 index 0000000000..fdd6887633 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.cpp @@ -0,0 +1,119 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2008-12-10 18:05:13 +0100 (Mi, 10 Dez 2008) $ +Version: $Revision: 15922 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#ifndef __mitkNrrdTbssGradientImageWriter__cpp +#define __mitkNrrdTbssGradientImageWriter__cpp + +#include "mitkNrrdTbssGradientImageWriter.h" +#include "itkMetaDataDictionary.h" +#include "itkMetaDataObject.h" +#include "itkNrrdImageIO.h" +//#include "itkNiftiImageIO.h" +#include "itkImageFileWriter.h" +#include "itksys/SystemTools.hxx" +#include "boost/lexical_cast.hpp" + +#include +#include + + +mitk::NrrdTbssGradientImageWriter::NrrdTbssGradientImageWriter() + : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) +{ + this->SetNumberOfRequiredInputs( 1 ); +} + +mitk::NrrdTbssGradientImageWriter::~NrrdTbssGradientImageWriter() +{} + + +void mitk::NrrdTbssGradientImageWriter::GenerateData() +{ + m_Success = false; + InputType* input = this->GetInput(); + if (input == NULL) + { + itkWarningMacro(<<"Sorry, input to NrrdTbssGradientImageWriter is NULL!"); + return; + } + if ( m_FileName == "" ) + { + itkWarningMacro( << "Sorry, filename has not been set!" ); + return ; + } + + typedef itk::VectorImage ImageType; + + ImageType::Pointer img = input->GetImage(); + + itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); + io->SetFileType( itk::ImageIOBase::Binary ); + io->UseCompressionOn(); + + + typedef itk::ImageFileWriter WriterType; + WriterType::Pointer nrrdWriter = WriterType::New(); + // nrrdWriter->UseInputMetaDataDictionaryOn(); + nrrdWriter->SetInput( img ); + nrrdWriter->SetImageIO(io); + nrrdWriter->SetFileName(m_FileName); + nrrdWriter->UseCompressionOn(); + nrrdWriter->SetImageIO(io); + try + { + nrrdWriter->Update(); + } + catch (itk::ExceptionObject e) + { + std::cout << e << std::endl; + } + + m_Success = true; +} + + + + + + +void mitk::NrrdTbssGradientImageWriter::SetInput( InputType* tbssVol ) +{ + this->ProcessObject::SetNthInput( 0, tbssVol ); +} + + +mitk::TbssGradientImage* mitk::NrrdTbssGradientImageWriter::GetInput() +{ + if ( this->GetNumberOfInputs() < 1 ) + { + return NULL; + } + else + { + return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); + } +} + + +std::vector mitk::NrrdTbssGradientImageWriter::GetPossibleFileExtensions() +{ + std::vector possibleFileExtensions; + possibleFileExtensions.push_back(".tgi"); // tgi = tbss gradient image + return possibleFileExtensions; +} + +#endif //__mitkNrrdTbssImageWriter__cpp diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.h b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.h new file mode 100644 index 0000000000..270142b4f8 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.h @@ -0,0 +1,141 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2008-08-27 17:18:46 +0200 (Mi, 27 Aug 2008) $ +Version: $Revision: 15096 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#ifndef _MITK_NRRDTBSSGRADIENTVOL_WRITER__H_ +#define _MITK_NRRDTBSSGRADIENTVOL_WRITER__H_ + +#include +#include +#include +#include +#include "MitkDiffusionImagingExports.h" + +namespace mitk +{ + +/** + * Writes diffusion volumes to a file + * @ingroup Process + */ + +class MitkDiffusionImaging_EXPORT NrrdTbssGradientImageWriter : public mitk::FileWriterWithInformation +{ +public: + + mitkClassMacro( NrrdTbssGradientImageWriter, mitk::FileWriterWithInformation ) + + mitkWriterMacro + + itkNewMacro( Self ) + + typedef mitk::TbssGradientImage InputType; + + /** + * Sets the filename of the file to write. + * @param FileName the nameInputType 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 ) + + /**image + * Sets the input object for the filter. + * @param input the diffusion volumes to write to file. + */ + void SetInput( InputType* input ); + /**itk::VectorImage + * @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(); + + // FileWriterWithInformation methods + virtual const char * GetDefaultFilename() { return "TbssGradientImage.tgi"; } + virtual const char * GetFileDialogPattern() { return "Tbss Gradient Images (*.tgi)"; } + virtual const char * GetDefaultExtension() { return ".tgi"; } + virtual bool CanWriteBaseDataType(BaseData::Pointer data) + { + return (dynamic_cast(data.GetPointer()) != NULL); + } + + + virtual void DoWrite(BaseData::Pointer data) { + if (CanWriteBaseDataType(data)) { + this->SetInput(dynamic_cast(data.GetPointer())); + this->Update(); + } + } + +protected: + + NrrdTbssGradientImageWriter(); + + virtual ~NrrdTbssGradientImageWriter(); + + virtual void GenerateData(); + + std::string m_FileName; + + std::string m_FilePrefix; + + std::string m_FilePattern; + + bool m_Success; + + + //std::string RetrieveString(mitk::TbssGradientImage::MetaDataFunction meta); + +}; + + +} // end of namespace mitk + + + +#endif diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.cpp b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.cpp new file mode 100644 index 0000000000..6c0c158e85 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.cpp @@ -0,0 +1,52 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2007-12-11 14:46:19 +0100 (Di, 11 Dez 2007) $ +Version: $Revision: 11215 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#include "mitkNrrdTbssGradientImageWriterFactory.h" + +#include "itkCreateObjectFunction.h" +#include "itkVersion.h" + +#include + +namespace mitk +{ + +NrrdTbssGradientImageWriterFactory::NrrdTbssGradientImageWriterFactory() +{ + typedef int TbssGradientPixelType; + this->RegisterOverride("IOWriter", + "NrrdTbssGradientImageWriter", + "NrrdTbssGradientImage Writer", + 1, + itk::CreateObjectFunction< mitk::NrrdTbssGradientImageWriter >::New()); +} + +NrrdTbssGradientImageWriterFactory::~NrrdTbssGradientImageWriterFactory() +{ +} + +const char* NrrdTbssGradientImageWriterFactory::GetITKSourceVersion() const +{ + return ITK_SOURCE_VERSION; +} + +const char* NrrdTbssGradientImageWriterFactory::GetDescription() const +{ + return "NrrdTbssGradientImageWriterFactory"; +} + +} // end namespace mitk diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.h b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.h new file mode 100644 index 0000000000..22ff6b4bde --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.h @@ -0,0 +1,69 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-13 18:06:46 +0200 (Mi, 13 Mai 2009) $ +Version: $Revision: 11215 $ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#ifndef NRRDTBSSGRADIENTIMAGE_WRITERFACTORY_H_HEADER_INCLUDED +#define NRRDTBSSGRADIENTIMAGE_WRITERFACTORY_H_HEADER_INCLUDED + +#include "itkObjectFactoryBase.h" +#include "mitkBaseData.h" +#include "MitkDiffusionImagingExports.h" +#include "MitkDiffusionImagingExports.h" + +namespace mitk +{ + +class MitkDiffusionImaging_EXPORT NrrdTbssGradientImageWriterFactory : public itk::ObjectFactoryBase +{ +public: + + mitkClassMacro( mitk::NrrdTbssGradientImageWriterFactory, 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); + + /** Register one factory of this type */ + static void RegisterOneFactory(void) + { + static bool IsRegistered = false; + if ( !IsRegistered ) + { + mitk::NrrdTbssGradientImageWriterFactory::Pointer fac = mitk::NrrdTbssGradientImageWriterFactory::New(); + ObjectFactoryBase::RegisterFactory( fac ); + IsRegistered = true; + } + } + +protected: + NrrdTbssGradientImageWriterFactory(); + ~NrrdTbssGradientImageWriterFactory(); + +private: + NrrdTbssGradientImageWriterFactory(const Self&); //purposely not implemented + void operator=(const Self&); //purposely not implemented + +}; + +} // end namespace mitk + +#endif // NRRDTBSSGRADIENTIMAGE_WRITERFACTORY_H_HEADER_INCLUDED + + + diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.cpp b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.cpp index 3c8a68e4e8..402de5772f 100644 --- a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.cpp +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.cpp @@ -1,117 +1,117 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-02-08 11:19:03 +0100 (Fr, 08 Feb 2008) $ Version: $Revision: 11989 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __mitkTbssImage__cpp #define __mitkTbssImage__cpp #include "mitkTbssImage.h" #include "itkImageRegionIterator.h" #include "itkImageRegionConstIterator.h" #include "mitkImageCast.h" mitk::TbssImage::TbssImage() - : m_IsMeta(false) + : m_IsMeta(false), m_ContainsGradient(false) { } void mitk::TbssImage::InitializeFromVectorImage() { if(!m_Image) { MITK_INFO << "TBSS Image could not be initialized. Set all members first!" << std::endl; return; } typedef itk::Image ImgType; ImgType::Pointer img = ImgType::New(); img->SetSpacing( m_Image->GetSpacing() ); // Set the image spacing img->SetOrigin( m_Image->GetOrigin() ); // Set the image origin img->SetDirection( m_Image->GetDirection() ); // Set the image direction img->SetLargestPossibleRegion( m_Image->GetLargestPossibleRegion()); img->SetBufferedRegion( m_Image->GetLargestPossibleRegion() ); img->Allocate(); int vecLength = m_Image->GetVectorLength(); InitializeByItk( img.GetPointer(), 1, vecLength ); //for(int i=0; i itw (img, img->GetLargestPossibleRegion() ); itw = itw.Begin(); itk::ImageRegionConstIterator itr (m_Image, m_Image->GetLargestPossibleRegion() ); itr = itr.Begin(); while(!itr.IsAtEnd()) { itw.Set(itr.Get().GetElement(0)); ++itr; ++itw; } // init SetImportVolume(img->GetBufferPointer());//, 0, 0, CopyMemory); //SetVolume( img->GetBufferPointer(), i ); //}:: m_DisplayIndex = 0; MITK_INFO << "Tbss-Image successfully initialized."; } void mitk::TbssImage::SetDisplayIndexForRendering(int displayIndex) { MITK_INFO << "displayindex: " << displayIndex; int index = displayIndex; int vecLength = m_Image->GetVectorLength(); index = index > vecLength-1 ? vecLength-1 : index; if( m_DisplayIndex != index ) { typedef itk::Image ImgType; ImgType::Pointer img = ImgType::New(); CastToItkImage(this, img); itk::ImageRegionIterator itw (img, img->GetLargestPossibleRegion() ); itw = itw.Begin(); itk::ImageRegionConstIterator itr (m_Image, m_Image->GetLargestPossibleRegion() ); itr = itr.Begin(); while(!itr.IsAtEnd()) { itw.Set(itr.Get().GetElement(index)); ++itr; ++itw; } } m_DisplayIndex = index; } #endif /* __mitkTbssImage__cpp */ diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.h b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.h index 3b5e5605bb..e953386b04 100644 --- a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.h +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImage.h @@ -1,167 +1,171 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-02-07 17:17:57 +0100 (Do, 07 Feb 2008) $ Version: $Revision: 11989 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __mitkTbssImage__h #define __mitkTbssImage__h #include "mitkImage.h" #include "itkVectorImage.h" #include "mitkImageCast.h" #include "MitkDiffusionImagingExports.h" namespace mitk { /** * \brief this class encapsulates diffusion volumes (vectorimages not * yet supported by mitkImage) */ class MitkDiffusionImaging_EXPORT TbssImage : public Image { public: typedef itk::VectorImage ImageType; typedef itk::Index<3> IndexType; //typedef typename std::vector > RoiType; mitkClassMacro( TbssImage, Image ) itkNewMacro(Self) enum MetaDataFunction { MEAN_FA_SKELETON, MEAN_FA_SKELETON_MASK, + GRADIENT_X, + GRADIENT_Y, + GRADIENT_Z, MISC }; //void SetRequestedRegionToLargestPossibleReg tbssRoi->SetTbssType(mitk::TbssImage::ROI);ion(); //bool RequestedRegionIsOutsideOfTheBufferedRegion(); //virtual bool VerifyRequestedRegion(); //void SetRequestedRegion(itk::DataObject *data); ImageType::Pointer GetImage() { return m_Image; } void SetImage(ImageType::Pointer image ) { this->m_Image = image; } void InitializeFromImage() { MITK_INFO << "make an mitk image that can be shown by mitk"; this->InitializeByItk(m_Image.GetPointer(),1,1); } void SetGroupInfo( std::vector< std::pair > info) { m_GroupInfo = info; } std::vector< std::pair > GetGroupInfo() { return m_GroupInfo; } void SetMetaInfo( std::vector< std::pair > info) { m_MetaInfo = info; } std::vector< std::pair > GetMetaInfo() { return m_MetaInfo; } void SetMeasurementInfo(std::string s) { m_MeasurementInfo = s; } std::string GetMeasurementInfo() { return m_MeasurementInfo; } void InitializeFromVectorImage(); void SetDisplayIndexForRendering(int displayIndex); void SetIsMeta(bool b) { m_IsMeta = b; } bool GetIsMeta() { return m_IsMeta; } protected: TbssImage(); virtual ~TbssImage(){} ImageType::Pointer m_Image; std::vector< std::pair > m_GroupInfo; std::vector< std::pair > m_MetaInfo; int m_DisplayIndex; std::string m_MeasurementInfo; bool m_IsMeta; + bool m_ContainsGradient; }; /* // Does the same es the normal CastToMitkImage, but needed to reimplemented due to the templatet pixeltype template void CastToTbssImage(const ItkOutputImageType* itkimage, itk::SmartPointer< mitk::TbssImage >& tbssoutputimage) { if(tbssoutputimage.IsNull()) { tbssoutputimage = mitk::TbssImage::New(); } tbssoutputimage->InitializeByItk(itkimage); tbssoutputimage->SetChannel(itkimage->GetBufferPointer()); } */ } // namespace mitk //#include "mitkTbssImage.cpp" #endif /* __mitkTbssImage__h */ diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.cpp b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.cpp index 2aff58ce42..7555640c18 100644 --- a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.cpp +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.cpp @@ -1,248 +1,264 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ Version: $Revision: 18127 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __mitkTbssImporter_cpp #define __mitkTbssImporter_cpp #include "mitkTbssImporter.h" #include #include namespace mitk { mitk::TbssImporter::TbssImporter() { } mitk::TbssImporter::TbssImporter(std::string path) : m_File(path) { } mitk::TbssImage::Pointer mitk::TbssImporter::Import() { // read all images with all_*.nii.gz mitk::TbssImage::Pointer tbssImg = mitk::TbssImage::New(); FileReaderType4D::Pointer reader = FileReaderType4D::New(); reader->SetFileName(m_File); reader->Update(); FloatImage4DType::Pointer img = FloatImage4DType::New(); img = reader->GetOutput(); m_Data = DataImageType::New(); FloatImage4DType::SizeType size = img->GetLargestPossibleRegion().GetSize(); FloatImage4DType::SpacingType spacing = img->GetSpacing(); DataImageType::SizeType dataSize; dataSize[0] = size[0]; dataSize[1] = size[1]; dataSize[2] = size[2]; m_Data->SetRegions(dataSize); DataImageType::SpacingType dataSpacing; dataSpacing[0] = spacing[0]; dataSpacing[1] = spacing[1]; dataSpacing[2] = spacing[2]; m_Data->SetSpacing(dataSpacing); FloatImage4DType::PointType origin = img->GetOrigin(); DataImageType::PointType dataOrigin; dataOrigin[0] = origin[0]; dataOrigin[1] = origin[1]; dataOrigin[2] = origin[2]; m_Data->SetOrigin(dataOrigin); FloatImage4DType::DirectionType dir = img->GetDirection(); DataImageType::DirectionType dataDir; for(int i=0; i<=2; i++) { for(int j=0; j<=2; j++) { dataDir[i][j] = dir[i][j]; } } m_Data->SetDirection(dataDir); // Set the length to one because otherwise allocate fails. Should be changed when groups/measurements are added m_Data->SetVectorLength(size[3]); m_Data->Allocate(); for(int i=0; i ix; ix[0] = i; ix[1] = j; ix[2] = k; itk::VariableLengthVector pixel = m_Data->GetPixel(ix); int vecSize = pixel.Size(); for(int z=0; z ix4; ix4[0] = i; ix4[1] = j; ix4[2] = k; ix4[3] = z; float value = img->GetPixel(ix4); pixel.SetElement(z, value); } m_Data->SetPixel(ix, pixel); } } } // mitk::CastToTbssImage(m_Data.GetPointer(), tbssImg); tbssImg->SetGroupInfo(m_Groups); tbssImg->SetMeasurementInfo(m_MeasurementInfo); tbssImg->SetImage(m_Data); tbssImg->InitializeFromVectorImage(); return tbssImg; } mitk::TbssImage::Pointer mitk::TbssImporter::ImportMeta() { mitk::TbssImage::Pointer tbssImg = mitk::TbssImage::New(); m_Data = DataImageType::New(); std::vector< std::pair > metaInfo; - for(int i=0; i p = m_MetaFiles.at(i); std::string function = p.first; std::string file = p.second; // Add to metainfo to give the tbss image a function-index pair std::pair pair; pair.first = RetrieveTbssFunction(function); pair.second = i; metaInfo.push_back(pair); - FileReaderType3D::Pointer fileReader = FileReaderType3D::New(); - fileReader->SetFileName(file); - fileReader->Update(); - - FloatImage3DType::Pointer img = fileReader->GetOutput(); - FloatImage3DType::SizeType size = img->GetLargestPossibleRegion().GetSize(); - - if(i==0) + if(pair.first == mitk::TbssImage::GRADIENT_X) { - // First image in serie. Properties should be used to initialize m_Data - m_Data->SetRegions(img->GetLargestPossibleRegion().GetSize()); - m_Data->SetSpacing(img->GetSpacing()); - m_Data->SetOrigin(img->GetOrigin()); - m_Data->SetDirection(img->GetDirection()); - m_Data->SetVectorLength(m_MetaFiles.size()); - m_Data->Allocate(); + extradims +=3; + + // Read vector image and add to m_Data } - for(int x=0; x ix; - ix[0] = x; - ix[1] = y; - ix[2] = z; + else { + FileReaderType3D::Pointer fileReader = FileReaderType3D::New(); + fileReader->SetFileName(file); + fileReader->Update(); + + FloatImage3DType::Pointer img = fileReader->GetOutput(); - float f = img->GetPixel(ix); - itk::VariableLengthVector pixel = m_Data->GetPixel(ix); - pixel.SetElement(i, f); - m_Data->SetPixel(ix, pixel); + FloatImage3DType::SizeType size = img->GetLargestPossibleRegion().GetSize(); + if(i==0) + { + // First image in serie. Properties should be used to initialize m_Data + m_Data->SetRegions(img->GetLargestPossibleRegion().GetSize()); + m_Data->SetSpacing(img->GetSpacing()); + m_Data->SetOrigin(img->GetOrigin()); + m_Data->SetDirection(img->GetDirection()); + m_Data->SetVectorLength(m_MetaFiles.size()); + m_Data->Allocate(); + } + + for(int x=0; x ix; + ix[0] = x; + ix[1] = y; + ix[2] = z; + + float f = img->GetPixel(ix); + itk::VariableLengthVector pixel = m_Data->GetPixel(ix); + pixel.SetElement(i, f); + m_Data->SetPixel(ix, pixel); + + } } } } - } tbssImg->SetIsMeta(true); tbssImg->SetImage(m_Data); tbssImg->SetMetaInfo(metaInfo); tbssImg->InitializeFromVectorImage(); return tbssImg; } mitk::TbssImage::MetaDataFunction mitk::TbssImporter::RetrieveTbssFunction(std::string s) { if(s == "skeleton mask") { return mitk::TbssImage::MEAN_FA_SKELETON_MASK; } else if(s == "mean fa skeleton") { return mitk::TbssImage::MEAN_FA_SKELETON; } + else if(s == "gradient image") + { + return mitk::TbssImage::GRADIENT_X; + } return mitk::TbssImage::MISC; } } #endif // __mitkTbssImporter_cpp diff --git a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.h b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.h index 7a84f42829..febd596039 100644 --- a/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.h +++ b/Modules/DiffusionImaging/IODataStructures/TbssImages/mitkTbssImporter.h @@ -1,113 +1,114 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ Version: $Revision: 18127 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __mitkTbssImporter_h #define __mitkTbssImporter_h #include "mitkCommon.h" #include "mitkFileReader.h" #include "itkImage.h" #include "itkVectorImage.h" #include "itkImageFileReader.h" #include "mitkTbssImage.h" namespace mitk { //template class TbssImporter : public itk::Object { public: // typedef TPixelType PixelType; typedef itk::VectorImage DataImageType; // type of the 3d vector image containing the skeletonized images + typedef itk::VectorImage VectorImageType; // Datatype of the tbss gradient images typedef itk::Image FloatImage4DType; typedef itk::ImageFileReader FileReaderType4D; typedef itk::Image FloatImage3DType; typedef itk::ImageFileReader FileReaderType3D; TbssImporter(); mitkClassMacro( TbssImporter, Object ) itkNewMacro(Self) TbssImporter(std::string path); void SetInputFile(std::string f) { m_File = f; } mitk::TbssImage::Pointer Import(); mitk::TbssImage::Pointer ImportMeta(); void SetGroupInfo(std::vector< std::pair > groups) { m_Groups = groups; } std::vector< std::pair > GetGroupInfo() { return m_Groups; } void SetTbssDatasets(std::vector< std::pair > files) { m_MetaFiles = files; } void SetMeasurementInfo(std::string s) { m_MeasurementInfo = s; } std::string GetMeasurementInfo() { return m_MeasurementInfo; } protected: virtual ~TbssImporter(){} std::string m_File; DataImageType::Pointer m_Data; std::vector< std::pair > m_Groups; std::vector< std::pair > m_MetaFiles; std::string m_MeasurementInfo; mitk::TbssImage::MetaDataFunction RetrieveTbssFunction(std::string s); }; } #include "mitkTbssImporter.cpp" #endif // __mitkTbssImporter_h diff --git a/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp b/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp index c82d5715d3..1cb9568fdf 100644 --- a/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp +++ b/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp @@ -1,394 +1,401 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-06-18 15:59:04 +0200 (Do, 18 Jun 2009) $ Version: $Revision: 16916 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkDiffusionImagingObjectFactory.h" #include "mitkProperties.h" #include "mitkBaseRenderer.h" #include "mitkDataNode.h" #include "mitkNrrdDiffusionImageIOFactory.h" #include "mitkNrrdDiffusionImageWriterFactory.h" #include "mitkNrrdDiffusionImageWriter.h" #include "mitkDiffusionImage.h" #include "mitkNrrdQBallImageIOFactory.h" #include "mitkNrrdQBallImageWriterFactory.h" #include "mitkNrrdQBallImageWriter.h" #include "mitkNrrdTensorImageIOFactory.h" #include "mitkNrrdTensorImageWriterFactory.h" #include "mitkNrrdTensorImageWriter.h" #include "mitkCompositeMapper.h" #include "mitkDiffusionImageMapper.h" #include "mitkGPUVolumeMapper3D.h" #include "mitkVolumeDataVtkMapper3D.h" #include "mitkTbssImageMapper.h" #include "mitkTbssGradientImageMapper.h" //====depricated fiberstructure===== #include "mitkFiberBundle.h" #include "mitkFiberBundleMapper2D.h" #include "mitkFiberBundleMapper3D.h" #include "mitkFiberBundleIOFactory.h" #include "mitkFiberBundleWriterFactory.h" #include "mitkFiberBundleWriter.h" //================================== //modernized fiberbundle datastrucutre #include "mitkFiberBundleX.h" #include "mitkFiberBundleXIOFactory.h" #include "mitkFiberBundleXWriterFactory.h" #include "mitkFiberBundleXWriter.h" #include "mitkFiberBundleXMapper3D.h" #include "mitkFiberBundleXThreadMonitorMapper3D.h" #include "mitkFiberBundleXThreadMonitor.h" #include "mitkNrrdTbssImageIOFactory.h" #include "mitkNrrdTbssImageWriterFactory.h" #include "mitkNrrdTbssImageWriter.h" #include "mitkNrrdTbssRoiImageIOFactory.h" #include "mitkNrrdTbssRoiImageWriterFactory.h" #include "mitkNrrdTbssRoiImageWriter.h" +#include "mitkNrrdTbssGradientImageWriterFactory.h" +#include "mitkNrrdTbssGradientImageWriter.h" + typedef short DiffusionPixelType; typedef char TbssRoiPixelType; typedef float TbssPixelType; - +typedef int TbssGradientPixelType; typedef mitk::DiffusionImage DiffusionImageShort; typedef std::multimap MultimapType; mitk::DiffusionImagingObjectFactory::DiffusionImagingObjectFactory(bool /*registerSelf*/) :CoreObjectFactoryBase() { static bool alreadyDone = false; if (!alreadyDone) { MITK_DEBUG << "DiffusionImagingObjectFactory c'tor" << std::endl; RegisterIOFactories(); mitk::NrrdDiffusionImageIOFactory::RegisterOneFactory(); mitk::NrrdQBallImageIOFactory::RegisterOneFactory(); mitk::NrrdTensorImageIOFactory::RegisterOneFactory(); mitk::FiberBundleIOFactory::RegisterOneFactory(); mitk::NrrdTbssImageIOFactory::RegisterOneFactory(); mitk::NrrdTbssRoiImageIOFactory::RegisterOneFactory(); mitk::FiberBundleXIOFactory::RegisterOneFactory(); //modernized mitk::NrrdDiffusionImageWriterFactory::RegisterOneFactory(); mitk::NrrdQBallImageWriterFactory::RegisterOneFactory(); mitk::NrrdTensorImageWriterFactory::RegisterOneFactory(); mitk::FiberBundleWriterFactory::RegisterOneFactory(); mitk::NrrdTbssImageWriterFactory::RegisterOneFactory(); mitk::NrrdTbssRoiImageWriterFactory::RegisterOneFactory(); mitk::FiberBundleXWriterFactory::RegisterOneFactory();//modernized + mitk::NrrdTbssGradientImageWriterFactory::RegisterOneFactory(); m_FileWriters.push_back( NrrdDiffusionImageWriter::New().GetPointer() ); m_FileWriters.push_back( NrrdQBallImageWriter::New().GetPointer() ); m_FileWriters.push_back( NrrdTensorImageWriter::New().GetPointer() ); m_FileWriters.push_back( mitk::FiberBundleWriter::New().GetPointer() ); m_FileWriters.push_back( NrrdTbssImageWriter::New().GetPointer() ); m_FileWriters.push_back( NrrdTbssRoiImageWriter::New().GetPointer() ); m_FileWriters.push_back( mitk::FiberBundleXWriter::New().GetPointer() );//modernized + m_FileWriters.push_back( mitk::NrrdTbssGradientImageWriter::New().GetPointer() ); mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(this); CreateFileExtensionsMap(); alreadyDone = true; } } mitk::Mapper::Pointer mitk::DiffusionImagingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper=NULL; if ( id == mitk::BaseRenderer::Standard2D ) { std::string classname("QBallImage"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::CompositeMapper::New(); newMapper->SetDataNode(node); node->SetMapper(3, ((CompositeMapper*)newMapper.GetPointer())->GetImageMapper()); } classname = "TensorImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::CompositeMapper::New(); newMapper->SetDataNode(node); node->SetMapper(3, ((CompositeMapper*)newMapper.GetPointer())->GetImageMapper()); } classname = "DiffusionImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::DiffusionImageMapper::New(); newMapper->SetDataNode(node); } classname = "TbssRoiImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::ImageVtkMapper2D::New(); newMapper->SetDataNode(node); } classname = "FiberBundle"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { // newMapper = mitk::FiberBundleMapper2D::New(); // newMapper->SetDataNode(node); } classname = "FiberBundleX"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleMapper2D::New(); newMapper->SetDataNode(node); } classname = "TbssImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::TbssImageMapper::New(); newMapper->SetDataNode(node); } classname = "TbssGradientImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::TbssGradientImageMapper::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { std::string classname("QBallImage"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } classname = "TensorImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } classname = "DiffusionImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } classname = "FiberBundle"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleMapper3D::New(); newMapper->SetDataNode(node); } 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); } classname = "TbssRoiImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::VolumeDataVtkMapper3D::New(); newMapper->SetDataNode(node); } classname = "TbssImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::TbssImageMapper::New(); newMapper->SetDataNode(node); } classname = "TbssGradientImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::TbssGradientImageMapper::New(); newMapper->SetDataNode(node); } } return newMapper; } void mitk::DiffusionImagingObjectFactory::SetDefaultProperties(mitk::DataNode* node) { std::string classname = "QBallImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::CompositeMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "TensorImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::CompositeMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "DiffusionImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::DiffusionImageMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "FiberBundle"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::FiberBundleMapper3D::SetDefaultProperties(node); mitk::FiberBundleMapper2D::SetDefaultProperties(node); } 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); } classname = "TbssRoiImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::ImageVtkMapper2D::SetDefaultProperties(node); mitk::VolumeDataVtkMapper3D::SetDefaultProperties(node); } classname = "TbssImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::TbssImageMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "TbssGradientImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::TbssGradientImageMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } } const char* mitk::DiffusionImagingObjectFactory::GetFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); return fileExtension.c_str(); }; mitk::CoreObjectFactoryBase::MultimapType mitk::DiffusionImagingObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } const char* mitk::DiffusionImagingObjectFactory::GetSaveFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); return fileExtension.c_str(); }; mitk::CoreObjectFactoryBase::MultimapType mitk::DiffusionImagingObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } void mitk::DiffusionImagingObjectFactory::CreateFileExtensionsMap() { m_FileExtensionsMap.insert(std::pair("*.dwi", "Diffusion Weighted Images")); m_FileExtensionsMap.insert(std::pair("*.hdwi", "Diffusion Weighted Images")); m_FileExtensionsMap.insert(std::pair("*.nii", "Diffusion Weighted Images for FSL")); m_FileExtensionsMap.insert(std::pair("*.fsl", "Diffusion Weighted Images for FSL")); m_FileExtensionsMap.insert(std::pair("*.fslgz", "Diffusion Weighted Images for FSL")); m_FileExtensionsMap.insert(std::pair("*.qbi", "Q-Ball Images")); m_FileExtensionsMap.insert(std::pair("*.hqbi", "Q-Ball Images")); m_FileExtensionsMap.insert(std::pair("*.dti", "Tensor Images")); m_FileExtensionsMap.insert(std::pair("*.hdti", "Tensor Images")); m_FileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); m_FileExtensionsMap.insert(std::pair("*.vfib", "Fiber Bundle Polydata")); m_FileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle Polydata")); m_FileExtensionsMap.insert(std::pair("*.tbss", "TBSS data")); m_FileExtensionsMap.insert(std::pair("*.pf", "Planar Figure File")); m_FileExtensionsMap.insert(std::pair("*.roi", "TBSS ROI data")); + m_FileExtensionsMap.insert(std::pair("*.tgi", "TBSS gradient image")); m_SaveFileExtensionsMap.insert(std::pair("*.dwi", "Diffusion Weighted Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hdwi", "Diffusion Weighted Images")); m_SaveFileExtensionsMap.insert(std::pair("*.nii", "Diffusion Weighted Images for FSL")); m_SaveFileExtensionsMap.insert(std::pair("*.fsl", "Diffusion Weighted Images for FSL")); m_SaveFileExtensionsMap.insert(std::pair("*.fslgz", "Diffusion Weighted Images for FSL")); m_SaveFileExtensionsMap.insert(std::pair("*.qbi", "Q-Ball Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hqbi", "Q-Ball Images")); m_SaveFileExtensionsMap.insert(std::pair("*.dti", "Tensor Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hdti", "Tensor Images")); m_SaveFileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); m_SaveFileExtensionsMap.insert(std::pair("*.vfib", "Fiber Bundle Polydata")); m_SaveFileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle Polydata")); m_SaveFileExtensionsMap.insert(std::pair("*.tbss", "TBSS data")); m_SaveFileExtensionsMap.insert(std::pair("*.pf", "Planar Figure File")); m_SaveFileExtensionsMap.insert(std::pair("*.roi", "TBSS ROI data")); + m_SaveFileExtensionsMap.insert(std::pair("*.tgi", "TBSS gradient image")); } void mitk::DiffusionImagingObjectFactory::RegisterIOFactories() { } void RegisterDiffusionImagingObjectFactory() { static bool oneDiffusionImagingObjectFactoryRegistered = false; if ( ! oneDiffusionImagingObjectFactoryRegistered ) { MITK_DEBUG << "Registering DiffusionImagingObjectFactory..." << std::endl; mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(mitk::DiffusionImagingObjectFactory::New()); oneDiffusionImagingObjectFactoryRegistered = true; } } diff --git a/Modules/DiffusionImaging/files.cmake b/Modules/DiffusionImaging/files.cmake index c9f698c18d..e21a1ac38e 100644 --- a/Modules/DiffusionImaging/files.cmake +++ b/Modules/DiffusionImaging/files.cmake @@ -1,174 +1,176 @@ SET(CPP_FILES # DicomImport DicomImport/mitkDicomDiffusionImageReader.cpp DicomImport/mitkGroupDiffusionHeadersFilter.cpp DicomImport/mitkDicomDiffusionImageHeaderReader.cpp DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp # DataStructures IODataStructures/mitkDiffusionImagingObjectFactory.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageReader.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageIOFactory.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriterFactory.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSerializer.cpp # DataStructures -> QBall IODataStructures/QBallImages/mitkQBallImageSource.cpp IODataStructures/QBallImages/mitkNrrdQBallImageReader.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriter.cpp IODataStructures/QBallImages/mitkNrrdQBallImageIOFactory.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriterFactory.cpp IODataStructures/QBallImages/mitkQBallImage.cpp IODataStructures/QBallImages/mitkQBallImageSerializer.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImageSource.cpp IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriter.cpp IODataStructures/TensorImages/mitkNrrdTensorImageIOFactory.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriterFactory.cpp IODataStructures/TensorImages/mitkTensorImage.cpp IODataStructures/TensorImages/mitkTensorImageSerializer.cpp # DataStructures -> FiberBundle IODataStructures/FiberBundle/mitkFiberBundle.cpp IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp IODataStructures/FiberBundle/mitkFiberBundleReader.cpp IODataStructures/FiberBundle/mitkFiberBundleIOFactory.cpp IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.cpp IODataStructures/FiberBundle/mitkFiberBundleSerializer.cpp IODataStructures/FiberBundle/mitkParticle.cpp IODataStructures/FiberBundle/mitkParticleGrid.cpp # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp # DataStructures -> PlanarFigureComposite IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp # DataStructures -> Tbss IODataStructures/TbssImages/mitkTbssImageSource.cpp IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp IODataStructures/TbssImages/mitkNrrdTbssImageIOFactory.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageIOFactory.cpp IODataStructures/TbssImages/mitkTbssImage.cpp IODataStructures/TbssImages/mitkTbssRoiImage.cpp IODataStructures/TbssImages/mitkTbssGradientImage.cpp IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp IODataStructures/TbssImages/mitkNrrdTbssImageWriterFactory.cpp + IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriter.cpp + IODataStructures/TbssImages/mitkNrrdTbssGradientImageWriterFactory.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriterFactory.cpp IODataStructures/TbssImages/mitkTbssImporter.cpp # Rendering Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkCompositeMapper.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp Rendering/mitkFiberBundleMapper2D.cpp Rendering/mitkFiberBundleMapper3D.cpp Rendering/mitkFiberBundleXMapper3D.cpp Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp Rendering/mitkTbssImageMapper.cpp Rendering/mitkTbssGradientImageMapper.cpp # Interactions Interactions/mitkFiberBundleInteractor.cpp # Algorithms Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp # Tractography Tractography/itkStochasticTractographyFilter.h ) SET(H_FILES # Rendering Rendering/mitkDiffusionImageMapper.h Rendering/mitkTbssImageMapper.h Rendering/mitkTbssGradientImageMapper.h Rendering/mitkOdfVtkMapper2D.h Rendering/mitkFiberBundleMapper2D.h Rendering/mitkFiberBundleMapper3D.h Rendering/mitkFiberBundleXMapper3D.h Rendering/mitkFiberBundleXThreadMonitorMapper3D.h # Reconstruction Reconstruction/itkDiffusionQballReconstructionImageFilter.h Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h Reconstruction/itkPointShell.h Reconstruction/itkOrientationDistributionFunction.h Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h Reconstruction/itkRegularizedIVIMLocalVariationImageFilter.h Reconstruction/itkRegularizedIVIMReconstructionFilter.h Reconstruction/itkRegularizedIVIMReconstructionSingleIteration.h # IO Datastructures IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.h # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.h IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h IODataStructures/FiberBundleX/mitkFiberBundleXReader.h IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.h IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h # Tractography Tractography/itkGibbsTrackingFilter.h Tractography/itkStochasticTractographyFilter.h # Algorithms Algorithms/itkDiffusionQballGeneralizedFaImageFilter.h Algorithms/itkDiffusionQballPrepareVisualizationImageFilter.h Algorithms/itkTensorDerivedMeasurementsFilter.h Algorithms/itkBrainMaskExtractionImageFilter.h Algorithms/itkB0ImageExtractionImageFilter.h Algorithms/itkTensorImageToDiffusionImageFilter.h Algorithms/itkTensorToL2NormImageFilter.h Algorithms/itkTractsToProbabilityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h Algorithms/itkGaussianInterpolateImageFunction.h Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h Algorithms/itkDiffusionTensorPrincipleDirectionImageFilter.h Algorithms/itkCartesianToPolarVectorImageFilter.h Algorithms/itkPolarToCartesianVectorImageFilter.h ) SET( TOOL_FILES ) IF(WIN32) ENDIF(WIN32) #MITK_MULTIPLEX_PICTYPE( Algorithms/mitkImageRegistrationMethod-TYPE.cpp )