diff --git a/Core/Code/IO/mitkFileWriterSelector.cpp b/Core/Code/IO/mitkFileWriterSelector.cpp index 77e59bf989..7c44d3e414 100644 --- a/Core/Code/IO/mitkFileWriterSelector.cpp +++ b/Core/Code/IO/mitkFileWriterSelector.cpp @@ -1,356 +1,368 @@ /*=================================================================== 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 "mitkFileWriterSelector.h" #include #include #include #include #include #include #include #include #include #include #include namespace mitk { struct FileWriterSelector::Item::Impl : us::SharedData { Impl() : m_FileWriter(NULL) , m_ConfidenceLevel(IFileWriter::Unsupported) , m_BaseDataIndex(0) , m_Id(-1) {} us::ServiceReference m_FileWriterRef; IFileWriter* m_FileWriter; IFileWriter::ConfidenceLevel m_ConfidenceLevel; std::size_t m_BaseDataIndex; MimeType m_MimeType; long m_Id; }; struct FileWriterSelector::Impl : us::SharedData { Impl() : m_BestId(-1) , m_SelectedId(m_BestId) {} Impl(const Impl& other) : us::SharedData(other) , m_BestId(-1) , m_SelectedId(m_BestId) {} FileWriterRegistry m_WriterRegistry; std::map m_Items; std::set m_MimeTypes; long m_BestId; long m_SelectedId; }; FileWriterSelector::FileWriterSelector(const FileWriterSelector& other) : m_Data(other.m_Data) { } FileWriterSelector::FileWriterSelector(const BaseData* baseData, const std::string& mimeType, const std::string& path) : m_Data(new Impl) { mitk::CoreServicePointer mimeTypeProvider(mitk::CoreServices::GetMimeTypeProvider()); + std::vector refs; + std::string destMimeType = mimeType; if (destMimeType.empty() && !path.empty()) { // try to derive a mime-type from the file std::vector mimeTypes = mimeTypeProvider->GetMimeTypesForFile(path); if (!mimeTypes.empty()) { - destMimeType = mimeTypes.front().GetName(); + for( unsigned int index = 0; index < mimeTypes.size(); index++) + { + std::vector tempRefs = m_Data->m_WriterRegistry.GetReferences(baseData, mimeTypes.at(index).GetName()); + for( unsigned int innerIndex = 0; innerIndex < tempRefs.size(); innerIndex++) + { + refs.push_back( tempRefs.at(innerIndex) ); + } + } } else if (!itksys::SystemTools::GetFilenameExtension(path).empty()) { // If there are no suitable mime-type for the file AND an extension // was supplied, we stop here. return; } } + else + { + refs = m_Data->m_WriterRegistry.GetReferences(baseData, destMimeType); + } std::vector classHierarchy = baseData->GetClassHierarchy(); // Get all writers and their mime types for the given base data type - std::vector refs = m_Data->m_WriterRegistry.GetReferences(baseData, destMimeType); Item bestItem; for (std::vector::const_iterator iter = refs.begin(), iterEnd = refs.end(); iter != iterEnd; ++iter) { std::string mimeTypeName = iter->GetProperty(IFileWriter::PROP_MIMETYPE()).ToString(); if (!mimeTypeName.empty()) { MimeType mimeType = mimeTypeProvider->GetMimeTypeForName(mimeTypeName); if (mimeType.IsValid()) { // There is a registered mime-type for this writer. Now get the confidence level // of this writer for writing the given base data object. IFileWriter* writer = m_Data->m_WriterRegistry.GetWriter(*iter); if (writer == NULL) continue; try { writer->SetInput(baseData); IFileWriter::ConfidenceLevel confidenceLevel = writer->GetConfidenceLevel(); if (confidenceLevel == IFileWriter::Unsupported) { continue; } std::string baseDataType = iter->GetProperty(IFileWriter::PROP_BASEDATA_TYPE()).ToString(); std::vector::iterator idxIter = std::find(classHierarchy.begin(), classHierarchy.end(), baseDataType); std::size_t baseDataIndex = std::numeric_limits::max(); if (idxIter != classHierarchy.end()) { baseDataIndex = std::distance(classHierarchy.begin(), idxIter); } Item item; item.d->m_FileWriterRef = *iter; item.d->m_FileWriter = writer; item.d->m_ConfidenceLevel = confidenceLevel; item.d->m_BaseDataIndex = baseDataIndex; item.d->m_MimeType = mimeType; item.d->m_Id = us::any_cast(iter->GetProperty(us::ServiceConstants::SERVICE_ID())); m_Data->m_Items.insert(std::make_pair(item.d->m_Id, item)); m_Data->m_MimeTypes.insert(mimeType); if (!bestItem.GetReference() || bestItem < item) { bestItem = item; } } catch (const us::BadAnyCastException& e) { MITK_WARN << "Unexpected: " << e.what(); } catch (const std::exception& e) { // Log the error but continue MITK_WARN << "IFileWriter::GetConfidenceLevel exception: " << e.what(); } } } } if (bestItem.GetReference()) { m_Data->m_BestId = bestItem.GetServiceId(); m_Data->m_SelectedId = m_Data->m_BestId; } } FileWriterSelector::~FileWriterSelector() { } FileWriterSelector& FileWriterSelector::operator=(const FileWriterSelector& other) { m_Data = other.m_Data; return *this; } bool FileWriterSelector::IsEmpty() const { return m_Data->m_Items.empty(); } std::vector FileWriterSelector::Get(const std::string& mimeType) const { std::vector result; for (std::map::const_iterator iter = m_Data->m_Items.begin(), iterEnd = m_Data->m_Items.end(); iter != iterEnd; ++iter) { if (mimeType.empty() || iter->second.GetMimeType().GetName() == mimeType) { result.push_back(iter->second); } } std::sort(result.begin(), result.end()); return result; } std::vector FileWriterSelector::Get() const { return Get(this->GetSelected().d->m_MimeType.GetName()); } FileWriterSelector::Item FileWriterSelector::Get(long id) const { std::map::const_iterator iter = m_Data->m_Items.find(id); if (iter != m_Data->m_Items.end()) { return iter->second; } return Item(); } FileWriterSelector::Item FileWriterSelector::GetDefault() const { return Get(m_Data->m_BestId); } long FileWriterSelector::GetDefaultId() const { return m_Data->m_BestId; } FileWriterSelector::Item FileWriterSelector::GetSelected() const { return Get(m_Data->m_SelectedId); } long FileWriterSelector::GetSelectedId() const { return m_Data->m_SelectedId; } bool FileWriterSelector::Select(const std::string& mimeType) { std::vector items = Get(mimeType); if (items.empty()) return false; return Select(items.back()); } bool FileWriterSelector::Select(const FileWriterSelector::Item& item) { return Select(item.d->m_Id); } bool FileWriterSelector::Select(long id) { if (id > -1) { if (m_Data->m_Items.find(id) == m_Data->m_Items.end()) { return false; } m_Data->m_SelectedId = id; return true; } return false; } std::vector FileWriterSelector::GetMimeTypes() const { std::vector result; result.reserve(m_Data->m_MimeTypes.size()); result.assign(m_Data->m_MimeTypes.begin(), m_Data->m_MimeTypes.end()); return result; } void FileWriterSelector::Swap(FileWriterSelector& fws) { m_Data.Swap(fws.m_Data); } FileWriterSelector::Item::Item(const FileWriterSelector::Item& other) : d(other.d) { } FileWriterSelector::Item::~Item() { } FileWriterSelector::Item& FileWriterSelector::Item::operator=(const FileWriterSelector::Item& other) { d = other.d; return *this; } IFileWriter* FileWriterSelector::Item::GetWriter() const { return d->m_FileWriter; } std::string FileWriterSelector::Item::GetDescription() const { us::Any descr = d->m_FileWriterRef.GetProperty(IFileWriter::PROP_DESCRIPTION()); if (descr.Empty()) return std::string(); return descr.ToString(); } IFileWriter::ConfidenceLevel FileWriterSelector::Item::GetConfidenceLevel() const { return d->m_ConfidenceLevel; } MimeType FileWriterSelector::Item::GetMimeType() const { return d->m_MimeType; } std::string FileWriterSelector::Item::GetBaseDataType() const { us::Any any = d->m_FileWriterRef.GetProperty(IFileWriter::PROP_BASEDATA_TYPE()); if (any.Empty()) return std::string(); return any.ToString(); } us::ServiceReference FileWriterSelector::Item::GetReference() const { return d->m_FileWriterRef; } long FileWriterSelector::Item::GetServiceId() const { return d->m_Id; } bool FileWriterSelector::Item::operator<(const FileWriterSelector::Item& other) const { // sort by confidence level first (ascending) if (d->m_ConfidenceLevel == other.d->m_ConfidenceLevel) { // sort by class hierarchy index (writers for more derived // based data types are considered a better match) if (d->m_BaseDataIndex == other.d->m_BaseDataIndex) { // sort by file writer service ranking return d->m_FileWriterRef < other.d->m_FileWriterRef; } return other.d->m_BaseDataIndex < d->m_BaseDataIndex; } return d->m_ConfidenceLevel < other.d->m_ConfidenceLevel; } FileWriterSelector::Item::Item() : d(new Impl()) {} void swap(FileWriterSelector& fws1, FileWriterSelector& fws2) { fws1.Swap(fws2); } } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp index 53c649bd9d..20ac728707 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp @@ -1,235 +1,233 @@ /*=================================================================== 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 "mitkDiffusionIOMimeTypes.h" #include "mitkIOMimeTypes.h" #include #include #include #include #include namespace mitk { std::vector DiffusionIOMimeTypes::Get() { std::vector mimeTypes; // order matters here (descending rank for mime types) mimeTypes.push_back(DWI_MIMETYPE().Clone()); mimeTypes.push_back(DTI_MIMETYPE().Clone()); mimeTypes.push_back(QBI_MIMETYPE().Clone()); mimeTypes.push_back(FIBERBUNDLE_MIMETYPE().Clone()); mimeTypes.push_back(CONNECTOMICS_MIMETYPE().Clone()); return mimeTypes; } // Mime Types CustomMimeType DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE() { CustomMimeType mimeType(FIBERBUNDLE_MIMETYPE_NAME()); std::string category = "Fiber Bundle File"; mimeType.SetComment("Fiber Bundles"); mimeType.SetCategory(category); mimeType.AddExtension("fib"); mimeType.AddExtension("trk"); //mimeType.AddExtension("vtk"); return mimeType; } DiffusionIOMimeTypes::DwiMimeType::DwiMimeType() : CustomMimeType(DWI_MIMETYPE_NAME()) { std::string category = "Diffusion Weighted Image"; this->SetCategory(category); this->SetComment("Diffusion Weighted Images"); this->AddExtension("dwi"); this->AddExtension("hdwi"); this->AddExtension("fsl"); this->AddExtension("fslgz"); - // this is commented out to fix the dashboard, should be enabled again - // once mime types have a way to check the base data for properties - //this->AddExtension("nrrd"); + this->AddExtension("nrrd"); } bool DiffusionIOMimeTypes::DwiMimeType::AppliesTo(const std::string &path) const { bool canRead( CustomMimeType::AppliesTo(path) ); // fix for bug 18572 // Currently this function is called for writing as well as reading, in that case // the image information can of course not be read // This is a bug, this function should only be called for reading. if( ! itksys::SystemTools::FileExists( path.c_str() ) ) { return canRead; } //end fix for bug 18572 std::string ext = itksys::SystemTools::GetFilenameLastExtension( path ); ext = itksys::SystemTools::LowerCase( ext ); // Simple NRRD files should only be considered for this mime type if they contain // corresponding tags if( ext == ".nrrd" ) { itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); io->SetFileName(path); try { io->ReadImageInformation(); itk::MetaDataDictionary imgMetaDictionary = io->GetMetaDataDictionary(); std::vector imgMetaKeys = imgMetaDictionary.GetKeys(); std::vector::const_iterator itKey = imgMetaKeys.begin(); std::string metaString; for (; itKey != imgMetaKeys.end(); itKey ++) { itk::ExposeMetaData (imgMetaDictionary, *itKey, metaString); if (itKey->find("modality") != std::string::npos) { if (metaString.find("DWMRI") != std::string::npos) { return canRead; } } } } catch( const itk::ExceptionObject &e ) { MITK_ERROR << "ITK Exception: " << e.what(); } canRead = false; } return canRead; } DiffusionIOMimeTypes::DwiMimeType* DiffusionIOMimeTypes::DwiMimeType::Clone() const { return new DwiMimeType(*this); } DiffusionIOMimeTypes::DwiMimeType DiffusionIOMimeTypes::DWI_MIMETYPE() { return DwiMimeType(); } CustomMimeType DiffusionIOMimeTypes::DTI_MIMETYPE() { CustomMimeType mimeType(DTI_MIMETYPE_NAME()); std::string category = "Tensor Images"; mimeType.SetComment("Diffusion Tensor Images"); mimeType.SetCategory(category); mimeType.AddExtension("dti"); mimeType.AddExtension("hdti"); return mimeType; } CustomMimeType DiffusionIOMimeTypes::QBI_MIMETYPE() { CustomMimeType mimeType(QBI_MIMETYPE_NAME()); std::string category = "Q-Ball Images"; mimeType.SetComment("Diffusion Q-Ball Images"); mimeType.SetCategory(category); mimeType.AddExtension("qbi"); mimeType.AddExtension("hqbi"); return mimeType; } CustomMimeType DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE() { CustomMimeType mimeType(CONNECTOMICS_MIMETYPE_NAME()); std::string category = "Connectomics Networks"; mimeType.SetComment("Connectomics Networks"); mimeType.SetCategory(category); mimeType.AddExtension("cnf"); return mimeType; } // Names std::string DiffusionIOMimeTypes::DWI_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".dwi"; return name; } std::string DiffusionIOMimeTypes::DTI_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".dti"; return name; } std::string DiffusionIOMimeTypes::QBI_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".qbi"; return name; } std::string DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".fib"; return name; } std::string DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".cnf"; return name; } // Descriptions std::string DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_DESCRIPTION() { static std::string description = "Fiberbundles"; return description; } std::string DiffusionIOMimeTypes::DWI_MIMETYPE_DESCRIPTION() { static std::string description = "Diffusion Weighted Images"; return description; } std::string DiffusionIOMimeTypes::DTI_MIMETYPE_DESCRIPTION() { static std::string description = "Diffusion Tensor Images"; return description; } std::string DiffusionIOMimeTypes::QBI_MIMETYPE_DESCRIPTION() { static std::string description = "Q-Ball Images"; return description; } std::string DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE_DESCRIPTION() { static std::string description = "Connectomics Networks"; return description; } } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdDiffusionImageWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdDiffusionImageWriter.cpp index 94f152f17f..95f42b98e3 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdDiffusionImageWriter.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdDiffusionImageWriter.cpp @@ -1,332 +1,332 @@ /*=================================================================== 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 __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 "mitkDiffusionIOMimeTypes.h" #include "mitkImageCast.h" #include #include mitk::NrrdDiffusionImageWriter::NrrdDiffusionImageWriter() : AbstractFileWriter(mitk::Image::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionIOMimeTypes::DWI_MIMETYPE_NAME() ), mitk::DiffusionIOMimeTypes::DWI_MIMETYPE_DESCRIPTION()) { RegisterService(); } mitk::NrrdDiffusionImageWriter::NrrdDiffusionImageWriter(const mitk::NrrdDiffusionImageWriter& other) : AbstractFileWriter(other) { } mitk::NrrdDiffusionImageWriter::~NrrdDiffusionImageWriter() {} void mitk::NrrdDiffusionImageWriter::Write() { mitk::Image::ConstPointer input = dynamic_cast(this->GetInput()); VectorImageType::Pointer itkImg; mitk::CastToItkImage(input,itkImg); if (input.IsNull()) { MITK_ERROR <<"Sorry, input to NrrdDiffusionImageWriter is NULL!"; return; } if ( this->GetOutputLocation().empty() ) { MITK_ERROR << "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]; //itk::MetaDataDictionary dic = input->GetImage()->GetMetaDataDictionary(); vnl_matrix_fixed measurementFrame = mitk::DiffusionPropertyHelper::GetMeasurementFrame(input); 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)", 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(itkImg->GetMetaDataDictionary(),std::string("measurement frame"),std::string(valbuffer)); } sprintf( valbuffer, "DWMRI"); itk::EncapsulateMetaData(itkImg->GetMetaDataDictionary(),std::string("modality"),std::string(valbuffer)); if(mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size()) { sprintf( valbuffer, "%1f", mitk::DiffusionPropertyHelper::GetReferenceBValue(input) ); itk::EncapsulateMetaData(itkImg->GetMetaDataDictionary(),std::string("DWMRI_b-value"),std::string(valbuffer)); } for(unsigned int i=0; iSize(); i++) { sprintf( keybuffer, "DWMRI_gradient_%04d", i ); /*if(itk::ExposeMetaData(input->GetMetaDataDictionary(), std::string(keybuffer),tmp)) continue;*/ sprintf( valbuffer, "%1f %1f %1f", mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(0), mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(1), mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(2)); itk::EncapsulateMetaData(itkImg->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer)); } typedef itk::VectorImage ImageType; std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation()); ext = itksys::SystemTools::LowerCase(ext); // default extension is .dwi if( ext == "") { ext = ".nrrd"; this->SetOutputLocation(this->GetOutputLocation() + ext); } if (ext == ".hdwi" || ext == ".nrrd" || ext == ".dwi") { MITK_INFO << "Extension " << ext; itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); //io->SetNrrdVectorType( nrrdKindList ); io->SetFileType( itk::ImageIOBase::Binary ); io->UseCompressionOn(); typedef itk::ImageFileWriter WriterType; WriterType::Pointer nrrdWriter = WriterType::New(); nrrdWriter->UseInputMetaDataDictionaryOn(); nrrdWriter->SetInput( itkImg ); nrrdWriter->SetImageIO(io); nrrdWriter->SetFileName(this->GetOutputLocation()); 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"; typedef itk::Image ImageType4D; ImageType4D::Pointer img4 = ImageType4D::New(); ImageType::SpacingType spacing = itkImg->GetSpacing(); ImageType4D::SpacingType spacing4; for(int i=0; i<3; i++) spacing4[i] = spacing[i]; spacing4[3] = 1; img4->SetSpacing( spacing4 ); // Set the image spacing ImageType::PointType origin = itkImg->GetOrigin(); ImageType4D::PointType origin4; for(int i=0; i<3; i++) origin4[i] = origin[i]; origin4[3] = 0; img4->SetOrigin( origin4 ); // Set the image origin ImageType::DirectionType direction = itkImg->GetDirection(); 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 ImageType::RegionType region = itkImg->GetLargestPossibleRegion(); ImageType4D::RegionType region4; ImageType::RegionType::SizeType size = region.GetSize(); ImageType4D::RegionType::SizeType size4; for(int i=0; i<3; i++) size4[i] = size[i]; size4[3] = itkImg->GetVectorLength(); ImageType::RegionType::IndexType index = region.GetIndex(); 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 (itkImg, itkImg->GetLargestPossibleRegion() ); typedef ImageType::PixelType VecPixType; for (it.GoToBegin(); !it.IsAtEnd(); ++it) { VecPixType vec = it.Get(); 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 = this->GetOutputLocation(); 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; 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(), this->GetOutputLocation().c_str()); if(mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size()) { std::ofstream myfile; std::string fname = this->GetOutputLocation(); fname += ".bvals"; myfile.open (fname.c_str()); for(unsigned int i=0; iSize(); i++) { double twonorm = mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).two_norm(); myfile << mitk::DiffusionPropertyHelper::GetReferenceBValue(input)*twonorm*twonorm << " "; } myfile.close(); std::ofstream myfile2; std::string fname2 = this->GetOutputLocation(); fname2 += ".bvecs"; myfile2.open (fname2.c_str()); for(int j=0; j<3; j++) { for(unsigned int i=0; iSize(); i++) { //need to modify the length GradientDirectionContainerType::Pointer grads = mitk::DiffusionPropertyHelper::GetGradientContainer(input); GradientDirectionType direction = grads->ElementAt(i); direction.normalize(); myfile2 << direction.get(j) << " "; //myfile2 << input->GetDirections()->ElementAt(i).get(j) << " "; } myfile2 << std::endl; } std::ofstream myfile3; std::string fname4 = this->GetOutputLocation(); fname4 += ".ttk"; myfile3.open (fname4.c_str()); for(unsigned int i=0; iSize(); i++) { for(int j=0; j<3; j++) { myfile3 << mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(j) << " "; } myfile3 << std::endl; } } } try { setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } } mitk::NrrdDiffusionImageWriter* mitk::NrrdDiffusionImageWriter::Clone() const { return new NrrdDiffusionImageWriter(*this); } mitk::IFileWriter::ConfidenceLevel mitk::NrrdDiffusionImageWriter::GetConfidenceLevel() const { mitk::Image::ConstPointer input = dynamic_cast(this->GetInput()); - if (input.IsNull() ) + if (input.IsNull() || !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( input ) ) { return Unsupported; } else { return Supported; } } #endif //__mitkNrrdDiffusionImageWriter__cpp