diff --git a/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp b/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp index f0c563025a..d35b55ce8b 100644 --- a/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp +++ b/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp @@ -1,212 +1,304 @@ /*========================================================================= 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. =========================================================================*/ #include "mitkNrrdTensorImageReader.h" #include "itkImageFileReader.h" #include "itkImageRegionIterator.h" #include "itkMetaDataObject.h" #include "itkNrrdImageIO.h" #include "itkDiffusionTensor3D.h" #include "mitkITKImageImport.h" #include "mitkImageDataItem.h" namespace mitk { void NrrdTensorImageReader ::GenerateData() { if ( m_FileName == "") { throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!"); } else { try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } typedef itk::VectorImage ImageType; itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); typedef itk::ImageFileReader FileReaderType; FileReaderType::Pointer reader = FileReaderType::New(); reader->SetImageIO(io); reader->SetFileName(this->m_FileName); reader->Update(); ImageType::Pointer img = reader->GetOutput(); typedef itk::Image,3> VecImgType; VecImgType::Pointer vecImg = VecImgType::New(); vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin vecImg->SetDirection( img->GetDirection() ); // Set the image direction vecImg->SetRegions( img->GetLargestPossibleRegion()); vecImg->Allocate(); itk::ImageRegionIterator ot (vecImg, vecImg->GetLargestPossibleRegion() ); ot = ot.Begin(); itk::ImageRegionIterator it (img, img->GetLargestPossibleRegion() ); it = it.Begin(); typedef ImageType::PixelType VarPixType; typedef VecImgType::PixelType FixPixType; int numComponents = img->GetNumberOfComponentsPerPixel(); + const std::string& locale = "C"; + const std::string& currLocale = setlocale( LC_ALL, NULL ); + + if ( locale.compare(currLocale)!=0 ) + { + try + { + MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, NULL) << " to '" << locale << "'"; + setlocale(LC_ALL, locale.c_str()); + } + catch(...) + { + MITK_INFO << "Could not set locale " << locale; + } + } + + itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary(); + std::vector imgMetaKeys = imgMetaDictionary.GetKeys(); + std::vector::const_iterator itKey = imgMetaKeys.begin(); + std::string metaString; + + bool readFrame = false; + double xx, xy, xz, yx, yy, yz, zx, zy, zz; + MeasurementFrameType measFrame; + measFrame.SetIdentity(); + MeasurementFrameType measFrameTransp; + measFrameTransp.SetIdentity(); + + for (; itKey != imgMetaKeys.end(); itKey ++) + { + itk::ExposeMetaData (imgMetaDictionary, *itKey, metaString); + if (itKey->find("measurement frame") != std::string::npos) + { + MITK_INFO << *itKey << " ---> " << metaString.c_str(); + sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz); + + if (xx>10e-10 || xy>10e-10 || xz>10e-10 || + yx>10e-10 || yy>10e-10 || yz>10e-10 || + zx>10e-10 || zy>10e-10 || zz>10e-10 ) + { + readFrame = true; + + measFrame(0,0) = xx; + measFrame(0,1) = xy; + measFrame(0,2) = xz; + measFrame(1,0) = yx; + measFrame(1,1) = yy; + measFrame(1,2) = yz; + measFrame(2,0) = zx; + measFrame(2,1) = zy; + measFrame(2,2) = zz; + + measFrameTransp = measFrame.GetTranspose(); + + MITK_INFO << "Will apply following measurement frame: \n" << measFrame; + } + } + } + + try + { + MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, NULL) << " to '" << currLocale << "'"; + setlocale(LC_ALL, currLocale.c_str()); + } + catch(...) + { + MITK_INFO << "Could not reset locale " << currLocale; + } + if (numComponents==6) { while (!it.IsAtEnd()) { + // T'=RTR' VarPixType vec = it.Get(); FixPixType fixVec(vec.GetDataPointer()); + + if(readFrame) + { + itk::DiffusionTensor3D tensor; + tensor.SetElement(0, vec.GetElement(0)); + tensor.SetElement(1, vec.GetElement(1)); + tensor.SetElement(2, vec.GetElement(2)); + tensor.SetElement(3, vec.GetElement(3)); + tensor.SetElement(4, vec.GetElement(4)); + tensor.SetElement(5, vec.GetElement(5)); + + tensor = tensor.PreMultiply(measFrame); + tensor = tensor.PostMultiply(measFrameTransp); + fixVec = tensor; + } + ot.Set(fixVec); ++ot; ++it; } } else if(numComponents==9) { while (!it.IsAtEnd()) { VarPixType vec = it.Get(); itk::DiffusionTensor3D tensor; tensor.SetElement(0, vec.GetElement(0)); tensor.SetElement(1, vec.GetElement(1)); tensor.SetElement(2, vec.GetElement(2)); tensor.SetElement(3, vec.GetElement(4)); tensor.SetElement(4, vec.GetElement(5)); tensor.SetElement(5, vec.GetElement(8)); + if(readFrame) + { + tensor = tensor.PreMultiply(measFrame); + tensor = tensor.PostMultiply(measFrameTransp); + } + FixPixType fixVec(tensor); ot.Set(fixVec); ++ot; ++it; } } else { throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!"); } this->GetOutput()->InitializeByItk(vecImg.GetPointer()); this->GetOutput()->SetVolume(vecImg->GetBufferPointer()); try { setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } } catch(std::exception& e) { throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what()); } catch(...) { throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!"); } } } void NrrdTensorImageReader::GenerateOutputInformation() { } const char* NrrdTensorImageReader ::GetFileName() const { return m_FileName.c_str(); } void NrrdTensorImageReader ::SetFileName(const char* aFileName) { m_FileName = aFileName; } const char* NrrdTensorImageReader ::GetFilePrefix() const { return m_FilePrefix.c_str(); } void NrrdTensorImageReader ::SetFilePrefix(const char* aFilePrefix) { m_FilePrefix = aFilePrefix; } const char* NrrdTensorImageReader ::GetFilePattern() const { return m_FilePattern.c_str(); } void NrrdTensorImageReader ::SetFilePattern(const char* aFilePattern) { m_FilePattern = aFilePattern; } bool NrrdTensorImageReader ::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 == ".hdti" || ext == ".dti") { return true; } return false; } } //namespace MITK diff --git a/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.h b/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.h index e706eff361..16d9e13a18 100644 --- a/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.h +++ b/Modules/DiffusionImaging/IODataStructures/TensorImages/mitkNrrdTensorImageReader.h @@ -1,70 +1,71 @@ /*========================================================================= 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 __mitkNrrdTensorImageReader_h #define __mitkNrrdTensorImageReader_h #include "mitkCommon.h" #include "itkVectorContainer.h" #include "mitkFileReader.h" #include "vnl/vnl_vector_fixed.h" #include "mitkTensorImage.h" #include "mitkTensorImageSource.h" #include "itkVectorImage.h" namespace mitk { /** \brief */ class NrrdTensorImageReader : public mitk::TensorImageSource, public FileReader { public: typedef mitk::TensorImage OutputType; typedef mitk::TensorImageSource DTImgSourceType; - + typedef itk::Matrix< float, 3, 3 > MeasurementFrameType; + mitkClassMacro( NrrdTensorImageReader, DTImgSourceType ); itkNewMacro(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); protected: /** Does the real work. */ virtual void GenerateData(); virtual void GenerateOutputInformation(); std::string m_FileName; std::string m_FilePrefix; std::string m_FilePattern; private: void operator=(const Self&); //purposely not implemented }; } //namespace MITK #endif // __mitkNrrdTensorImageReader_h