diff --git a/Modules/DiffusionImaging/IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp b/Modules/DiffusionImaging/IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp index 5420bb11e3..423c93b81d 100644 --- a/Modules/DiffusionImaging/IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp +++ b/Modules/DiffusionImaging/IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp @@ -1,328 +1,324 @@ /*========================================================================= 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 __mitkNrrdDiffusionImageWriter__cpp #define __mitkNrrdDiffusionImageWriter__cpp #include "mitkNrrdDiffusionImageWriter.h" #include "itkMetaDataDictionary.h" #include "itkMetaDataObject.h" #include "itkNrrdImageIO.h" #include "itkNiftiImageIO.h" #include "itkImageFileWriter.h" #include "itksys/SystemTools.hxx" #include #include template mitk::NrrdDiffusionImageWriter::NrrdDiffusionImageWriter() : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) { this->SetNumberOfRequiredInputs( 1 ); } template mitk::NrrdDiffusionImageWriter::~NrrdDiffusionImageWriter() {} template void mitk::NrrdDiffusionImageWriter::GenerateData() { m_Success = false; InputType* input = this->GetInput(); if (input == NULL) { itkWarningMacro(<<"Sorry, input to NrrdDiffusionImageWriter is NULL!"); return; } if ( m_FileName == "" ) { itkWarningMacro( << "Sorry, filename has not been set!" ); return ; } 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; } } char keybuffer[512]; char valbuffer[512]; - std::string tmp; - - itk::VectorImage::Pointer img = input->GetVectorImage(); - img->GetMetaDataDictionary(); //itk::MetaDataDictionary dic = input->GetImage()->GetMetaDataDictionary(); vnl_matrix_fixed measurementFrame = input->GetMeasurementFrame(); if (measurementFrame(0,0) || measurementFrame(0,1) || measurementFrame(0,2) || measurementFrame(1,0) || measurementFrame(1,1) || measurementFrame(1,2) || measurementFrame(2,0) || measurementFrame(2,1) || measurementFrame(2,2)) { - sprintf( valbuffer, " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", measurementFrame(0,0), measurementFrame(0,1), measurementFrame(0,2), measurementFrame(1,0), measurementFrame(1,1), measurementFrame(1,2), measurementFrame(2,0), measurementFrame(2,1), measurementFrame(2,2)); + sprintf( valbuffer, " (%lf,%lf,%lf) (%lf,%lf,%lf) (%lf,%lf,%lf)", measurementFrame(0,0), measurementFrame(0,1), measurementFrame(0,2), measurementFrame(1,0), measurementFrame(1,1), measurementFrame(1,2), measurementFrame(2,0), measurementFrame(2,1), measurementFrame(2,2)); itk::EncapsulateMetaData(input->GetVectorImage()->GetMetaDataDictionary(),std::string("measurement frame"),std::string(valbuffer)); } sprintf( valbuffer, "DWMRI"); itk::EncapsulateMetaData(input->GetVectorImage()->GetMetaDataDictionary(),std::string("modality"),std::string(valbuffer)); if(input->GetOriginalDirections()->Size()) { sprintf( valbuffer, "%1f", input->GetB_Value() ); itk::EncapsulateMetaData(input->GetVectorImage()->GetMetaDataDictionary(),std::string("DWMRI_b-value"),std::string(valbuffer)); } for(unsigned int i=0; iGetOriginalDirections()->Size(); i++) { sprintf( keybuffer, "DWMRI_gradient_%04d", i ); /*if(itk::ExposeMetaData(input->GetMetaDataDictionary(), std::string(keybuffer),tmp)) continue;*/ sprintf( valbuffer, "%1f %1f %1f", input->GetOriginalDirections()->ElementAt(i).get(0), input->GetOriginalDirections()->ElementAt(i).get(1), input->GetOriginalDirections()->ElementAt(i).get(2)); itk::EncapsulateMetaData(input->GetVectorImage()->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer)); } typedef itk::VectorImage ImageType; std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); ext = itksys::SystemTools::LowerCase(ext); if (ext == ".hdwi" || ext == ".dwi") { itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); //io->SetNrrdVectorType( nrrdKindList ); io->SetFileType( itk::ImageIOBase::Binary ); io->UseCompressionOn(); typedef itk::ImageFileWriter WriterType; typename WriterType::Pointer nrrdWriter = WriterType::New(); nrrdWriter->UseInputMetaDataDictionaryOn(); nrrdWriter->SetInput( input->GetVectorImage() ); nrrdWriter->SetImageIO(io); nrrdWriter->SetFileName(m_FileName); nrrdWriter->UseCompressionOn(); nrrdWriter->SetImageIO(io); try { nrrdWriter->Update(); } catch (itk::ExceptionObject e) { std::cout << e << std::endl; throw; } } else if (ext == ".fsl" || ext == ".fslgz") { MITK_INFO << "Writing Nifti-Image for FSL"; typename ImageType::Pointer vecimg = input->GetVectorImage(); typedef itk::Image ImageType4D; typename ImageType4D::Pointer img4 = ImageType4D::New(); typename ImageType::SpacingType spacing = vecimg->GetSpacing(); typename ImageType4D::SpacingType spacing4; for(int i=0; i<3; i++) spacing4[i] = spacing[i]; spacing4[3] = 1; img4->SetSpacing( spacing4 ); // Set the image spacing typename ImageType::PointType origin = vecimg->GetOrigin(); typename ImageType4D::PointType origin4; for(int i=0; i<3; i++) origin4[i] = origin[i]; origin4[3] = 0; img4->SetOrigin( origin4 ); // Set the image origin typename ImageType::DirectionType direction = vecimg->GetDirection(); typename ImageType4D::DirectionType direction4; for(int i=0; i<3; i++) for(int j=0; j<3; j++) direction4[i][j] = direction[i][j]; for(int i=0; i<4; i++) direction4[i][3] = 0; for(int i=0; i<4; i++) direction4[3][i] = 0; direction4[3][3] = 1; img4->SetDirection( direction4 ); // Set the image direction typename ImageType::RegionType region = vecimg->GetLargestPossibleRegion(); typename ImageType4D::RegionType region4; typename ImageType::RegionType::SizeType size = region.GetSize(); typename ImageType4D::RegionType::SizeType size4; for(int i=0; i<3; i++) size4[i] = size[i]; size4[3] = vecimg->GetVectorLength(); typename ImageType::RegionType::IndexType index = region.GetIndex(); typename ImageType4D::RegionType::IndexType index4; for(int i=0; i<3; i++) index4[i] = index[i]; index4[3] = 0; region4.SetSize(size4); region4.SetIndex(index4); img4->SetRegions( region4 ); img4->Allocate(); itk::ImageRegionIterator it (vecimg, vecimg->GetLargestPossibleRegion() ); typedef typename ImageType::PixelType VecPixType; for (it = it.Begin(); !it.IsAtEnd(); ++it) { VecPixType vec = it.Get(); typename ImageType::IndexType currentIndex = it.GetIndex(); for(unsigned int ind=0; indSetPixel(index4, vec[ind]); } } // create copy of file with correct ending for mitk std::string fname3 = m_FileName; std::string::iterator itend = fname3.end(); if (ext == ".fsl") fname3.replace( itend-3, itend, "nii"); else fname3.replace( itend-5, itend, "nii.gz"); itk::NiftiImageIO::Pointer io4 = itk::NiftiImageIO::New(); typedef itk::VectorImage ImageType; typedef itk::ImageFileWriter WriterType4; typename WriterType4::Pointer nrrdWriter4 = WriterType4::New(); nrrdWriter4->UseInputMetaDataDictionaryOn(); nrrdWriter4->SetInput( img4 ); nrrdWriter4->SetFileName(fname3); nrrdWriter4->UseCompressionOn(); nrrdWriter4->SetImageIO(io4); try { nrrdWriter4->Update(); } catch (itk::ExceptionObject e) { std::cout << e << std::endl; throw; } itksys::SystemTools::CopyAFile(fname3.c_str(), m_FileName.c_str()); if(input->GetDirections()->Size()) { std::ofstream myfile; std::string fname = m_FileName; fname += ".bvals"; myfile.open (fname.c_str()); for(unsigned int i=0; iGetDirections()->Size(); i++) { double twonorm = input->GetDirections()->ElementAt(i).two_norm(); myfile << input->GetB_Value()*twonorm*twonorm << " "; } myfile.close(); std::ofstream myfile2; std::string fname2 = m_FileName; fname2 += ".bvecs"; myfile2.open (fname2.c_str()); for(int j=0; j<3; j++) { for(unsigned int i=0; iGetDirections()->Size(); i++) { myfile2 << input->GetDirections()->ElementAt(i).get(j) << " "; } myfile2 << std::endl; } std::ofstream myfile3; std::string fname4 = m_FileName; fname4 += ".ttk"; myfile3.open (fname4.c_str()); for(unsigned int i=0; iGetDirections()->Size(); i++) { for(int j=0; j<3; j++) { myfile3 << input->GetDirections()->ElementAt(i).get(j) << " "; } myfile3 << std::endl; } } } try { setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } m_Success = true; } template void mitk::NrrdDiffusionImageWriter::SetInput( InputType* diffVolumes ) { this->ProcessObject::SetNthInput( 0, diffVolumes ); } template mitk::DiffusionImage* mitk::NrrdDiffusionImageWriter::GetInput() { if ( this->GetNumberOfInputs() < 1 ) { return NULL; } else { return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); } } template std::vector mitk::NrrdDiffusionImageWriter::GetPossibleFileExtensions() { std::vector possibleFileExtensions; possibleFileExtensions.push_back(".dwi"); possibleFileExtensions.push_back(".hdwi"); possibleFileExtensions.push_back(".fsl"); possibleFileExtensions.push_back(".fslgz"); return possibleFileExtensions; } #endif //__mitkNrrdDiffusionImageWriter__cpp