Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
#ifndef clitkWriteDicomSeriesGenericFilter_txx
#define clitkWriteDicomSeriesGenericFilter_txx
*
===================================================*/
+// clitk
+#include "clitkResampleImageWithOptionsFilter.h"
+#if GDCM_MAJOR_VERSION >= 2
+#include "gdcmUIDGenerator.h"
+#else
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
+#endif
+
namespace clitk
{
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
UpdateWithDimAndPixelType<Dimension, signed short>();
}
- // else if(PixelType == "unsigned_short"){
- // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- // UpdateWithDimAndPixelType<Dimension, unsigned short>();
- // }
+ else if(PixelType == "unsigned_short"){
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned short>();
+ }
else if (PixelType == "unsigned_char") {
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
// if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
// UpdateWithDimAndPixelType<Dimension, signed char>();
// }
+ else if (PixelType == "double") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, double>();
+ }
else {
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
UpdateWithDimAndPixelType<Dimension, float>();
}
}
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype read from
+// the dicom files. The MHD files may be resampled to match the
+// dicom spacing (and number of slices). Rounding errors in resampling
+// are handled by removing files when generating the output dicom
+// series.
+//-------------------------------------------------------------------
+template<class args_info_type>
+template <unsigned int Dimension, class PixelType>
+void
+WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+{
+
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, 2> OutputImageType;
+
+ // Read the dicom directory
+ typedef itk::ImageSeriesReader< InputImageType > ReaderType;
+ typedef itk::GDCMImageIO ImageIOType;
+ typedef itk::GDCMSeriesFileNames NamesGeneratorType;
+
+ ImageIOType::Pointer gdcmIO = ImageIOType::New();
+ NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
+ namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
+ namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
+ typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
+ typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
+
+ // Output the dicom files
+ unsigned int numberOfFilenames = filenames_in.size();
+ if (m_Verbose) {
+ std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
+ for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
+ std::cout << "filename # " << fni << " = ";
+ std::cout << filenames_in[fni] << std::endl;
+ }
+ }
+
+ // Read the series
+ typename ReaderType::Pointer reader = ReaderType::New();
+ if (m_ArgsInfo.preserve_flag) {
+#if GDCM_MAJOR_VERSION >= 2
+ gdcmIO->LoadPrivateTagsOn();
+ gdcmIO->KeepOriginalUIDOn();
+#endif
+ }
+ reader->SetImageIO( gdcmIO );
+ reader->SetFileNames( filenames_in );
+ try {
+ reader->Update();
+ } catch (itk::ExceptionObject &excp) {
+ std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
+ std::cerr << excp << std::endl;
+ }
+
+ // Read the input (MHD file)
+ typedef typename InputImageType::RegionType RegionType;
+ typedef typename RegionType::SizeType SizeType;
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer volumeReader = InputReaderType::New();
+ volumeReader->SetFileName( m_InputFileName);
+ volumeReader->Update();
+
+ typename InputImageType::Pointer input = volumeReader->GetOutput();
+ if ((!m_ArgsInfo.useSizeAsReference_flag && (input->GetSpacing() != reader->GetOutput()->GetSpacing())) ||
+ (m_ArgsInfo.useSizeAsReference_flag && (input->GetLargestPossibleRegion().GetSize() != reader->GetOutput()->GetLargestPossibleRegion().GetSize()))) {
+
+ // resampling is carried out on the fly if resolution or size between
+ // the input mhd and input dicom series is different
+
+ // Filter
+ typedef clitk::ResampleImageWithOptionsFilter<InputImageType, InputImageType> ResampleImageFilterType;
+ typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
+ filter->SetInput(input);
+ filter->SetVerboseOptions(m_Verbose);
+ filter->SetGaussianFilteringEnabled(false);
+ filter->SetDefaultPixelValue(0);
+
+ if (!m_ArgsInfo.useSizeAsReference_flag) {
+ filter->SetOutputSpacing(reader->GetOutput()->GetSpacing());
+ if (m_Verbose) {
+ std::cout << "Warning: The image spacing differs between the MHD file and the input dicom series. Performing resampling with default options using spacing as reference (for advanced options, use clitkResampleImage)." << std::endl;
+ std::cout << "MHD -> " << input->GetSpacing() << std::endl;
+ std::cout << "dicom -> " << reader->GetOutput()->GetSpacing() << std::endl;
+ }
+ }
+ else {
+ const SizeType& dicom_size = reader->GetOutput()->GetLargestPossibleRegion().GetSize();
+ SizeType output_size;
+ for (unsigned int i = 0; i < Dimension; i++)
+ output_size[i] = dicom_size[i];
+ filter->SetOutputSize(output_size);
+ if (m_Verbose) {
+ std::cout << "Warning: The image size differs between the MHD file and the input dicom series. Performing resampling with default options using size as reference (for advanced options, use clitkResampleImage)." << std::endl;
+ std::cout << "MHD -> " << input->GetLargestPossibleRegion().GetSize() << std::endl;
+ std::cout << "dicom -> " << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;
+ }
+ }
+
+ try {
+ filter->Update();
+ input = filter->GetOutput();
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Error: Exception thrown while resampling!!" << std::endl;
+ std::cerr << excp << std::endl;
+ }
+ }
+
+ // In some cases, due to resampling approximation issues,
+ // the number of slices in the MHD file may be different (smaller)
+ // from the number of files in the template dicom directory.
+ // To avoid ITK generating an exception, we reduce the number
+ // of DCM files to be considered, and a warning is printed
+ // in verbose mode
+ const RegionType volumeRegion = input->GetLargestPossibleRegion();
+ const SizeType& volumeSize = volumeRegion.GetSize();
+ if (m_Verbose) {
+ std::cout << volumeRegion << volumeSize << std::endl;
+ }
+ if (Dimension == 3 && volumeSize[2] < numberOfFilenames) {
+ if (m_Verbose)
+ std::cout << "Warning: The number of files in " << m_ArgsInfo.inputDir_arg << " (" << filenames_in.size() << " files) is greater than the number of slices in MHD (" << volumeSize[2] << " slices). Using only " << volumeSize[2] << " files." << std::endl;
+
+ filenames_in.resize(volumeSize[2]);
+ filenames_out.resize(filenames_in.size());
+ numberOfFilenames = filenames_in.size();
+ }
+
+ // Modify the meta dictionary
+ typedef itk::MetaDataDictionary DictionaryType;
+ const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
+
+ // Get keys
+ unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
+ if (m_ArgsInfo.verbose_flag)
+ DD(numberOfKeysGiven);
+
+ std::string seriesUID;
+ std::string frameOfReferenceUID;
+ std::string studyUID;
+
+ // one pass through the keys given on the cmd-line, to check what will be recreated
+ std::string seriesUIDkey = "0020|000e";
+ std::string seriesNumberKey = "0020|0011";
+ std::string seriesDescriptionKey = "0008|103e";
+ std::string frameOfReferenceUIDKey = "0020|0052";
+ std::string studyUIDKey = "0020|000d";
+ std::string studyIDKey = "0020|0010";
+ std::string studyDescriptionKey = "0008|1030";
+ bool seriesUIDGiven = false;
+ bool seriesNumberGiven = false;
+ bool seriesDescriptionGiven = false;
+ bool studyUIDGiven = false;
+ bool studyIDGiven = false;
+ bool studyDescriptionGiven = false;
+ for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
+ std::string entryId( m_ArgsInfo.key_arg[i] );
+ if (m_ArgsInfo.verbose_flag)
+ DD(entryId);
+
+ seriesUIDGiven |= (entryId == seriesUIDkey || entryId == frameOfReferenceUIDKey);
+ seriesNumberGiven |= (entryId == seriesNumberKey);
+ seriesDescriptionGiven |= (entryId == seriesDescriptionKey);
+ studyUIDGiven |= (entryId == studyUIDKey);
+ studyIDGiven |= (entryId == studyIDKey);
+ studyDescriptionGiven |= (entryId == studyDescriptionKey);
+ }
+ // force the creation of a new series if a new study was specified
+ if (!studyUIDGiven && m_ArgsInfo.newStudyUID_flag) {
+ m_ArgsInfo.newSeriesUID_flag = true;
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::UIDGenerator suid;
+ studyUID = suid.Generate();
+#else
+ studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+ }
+
+ if (!seriesUIDGiven && m_ArgsInfo.newSeriesUID_flag) {
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::UIDGenerator suid;
+ seriesUID = suid.Generate();
+ gdcm::UIDGenerator fuid;
+ frameOfReferenceUID = fuid.Generate();
+#else
+ seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+ frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+ }
+
+ if (m_ArgsInfo.verbose_flag) {
+ DD(seriesUID);
+ DD(frameOfReferenceUID);
+ DD(studyUID);
+ }
+
+ // check if file UIDs will be be preserved
+ bool useInputFileUID = true;
+ if (m_ArgsInfo.newSeriesUID_flag || m_ArgsInfo.newStudyUID_flag || seriesUIDGiven || studyUIDGiven) {
+ useInputFileUID = false;
+ }
+ else {
+#if GDCM_MAJOR_VERSION < 2
+ gdcmIO->SetKeepOriginalUID(true);
+#endif
+ namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
+ }
+
+ filenames_out.resize(numberOfFilenames);
+
+ time_t t;
+ t = time(&t);
+ struct tm* instanceDateTimeTm = localtime(&t);
+ char datetime[16];
+ strftime(datetime, 16, "%Y%m%d", instanceDateTimeTm);
+ std::ostringstream instanceDate;
+ instanceDate << datetime;
+ std::ostringstream instanceTime;
+ strftime(datetime, 16, "%H%M%S", instanceDateTimeTm);
+ instanceTime << datetime;
+
+ // update output dicom keys/tags
+ for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
+ for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
+ std::string entryId(m_ArgsInfo.key_arg[i] );
+ std::string value( m_ArgsInfo.tag_arg[i] );
+
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
+ }
+
+ // series UID
+ if (!seriesUIDGiven) {
+ if (m_ArgsInfo.newSeriesUID_flag) {
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesUIDkey, seriesUID );
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID );
+ }
+ }
+
+ // study UID
+ if (!studyUIDGiven) {
+ if (m_ArgsInfo.newStudyUID_flag)
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyUIDKey, studyUID );
+ }
+
+ // study description
+ if (studyUIDGiven || m_ArgsInfo.newStudyUID_flag) {
+ if (!studyIDGiven)
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyIDKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
+ if (!studyDescriptionGiven)
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyDescriptionKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
+
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0020", instanceDate.str() );
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0030", instanceTime.str() );
+ }
+
+ // series description/number
+ if (seriesUIDGiven || m_ArgsInfo.newSeriesUID_flag) {
+ if (!seriesDescriptionGiven)
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesDescriptionKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
+ if (!seriesNumberGiven)
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesNumberKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
+
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0012", instanceDate.str() );
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0013", instanceTime.str() );
+ }
+
+ // file UIDs are recreated for new studies or series
+ if (!useInputFileUID)
+ {
+ if (m_ArgsInfo.verbose_flag)
+ std::cout << "Recreating file UIDs" << std::endl;
+
+ std::string fileUID;
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::UIDGenerator fid;
+ fileUID = fid.Generate();
+#else
+ fileUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0018", fileUID );
+ itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0002|0003", fileUID );
+
+ filenames_out[fni] = itksys::SystemTools::CollapseFullPath(fileUID.c_str(), m_ArgsInfo.outputDir_arg) + std::string(".dcm");
+ }
+ }
+
+ // Output directory and filenames
+ itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
+ typedef itk::ImageSeriesWriter<InputImageType, OutputImageType > SeriesWriterType;
+ typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
+
+ seriesWriter->SetInput( input );
+ seriesWriter->SetImageIO( gdcmIO );
+
+ seriesWriter->SetFileNames( filenames_out );
+ seriesWriter->SetMetaDataDictionaryArray( dictionary );
+
+ // Write
+ try {
+ if (m_ArgsInfo.verbose_flag)
+ std::cout << seriesWriter << std::endl;
+ seriesWriter->Update();
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
+ std::cerr << excp << std::endl;
+ }
+
+}
+
+/*
//-------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
//-------------------------------------------------------------------
ImageIOType::Pointer gdcmIO = ImageIOType::New();
NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
- typename ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames();
+ namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
+ typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
+ typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
// Output the dicom files
- unsigned int numberOfFilenames = filenames.size();
+ unsigned int numberOfFilenames = filenames_in.size();
if (m_Verbose) {
std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
std::cout << "filename # " << fni << " = ";
- std::cout << filenames[fni] << std::endl;
+ std::cout << filenames_in[fni] << std::endl;
}
}
+
+ // RP: 16/03/2011
+ // In some cases, due to resampling approximation issues,
+ // the number of slices in the MHD file may be different
+ // from the number of slices in the template DCM directory.
+ // To avoid ITK generating an exception, we reduce the number
+ // of DCM files to be considered, provided the --force
+ // option is set.
+ typedef typename InputImageType::RegionType RegionType;
+ typedef typename RegionType::SizeType SizeType;
+ const RegionType volumeRegion = input->GetLargestPossibleRegion();
+ const SizeType& volumeSize = volumeRegion.GetSize();
+ if (m_ArgsInfo.force_given && Dimension == 3 && volumeSize[2] < numberOfFilenames)
+ {
+ std::cout << "Warning: Number of files in " << m_ArgsInfo.inputDir_arg << " is greater than the number of slices in MHD. Using only " << volumeSize[2] << " files." << std::endl;
+ filenames_in.resize(volumeSize[2]);
+ filenames_out.resize(filenames_in.size());
+ numberOfFilenames = filenames_in.size();
+ }
// Read the series
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO( gdcmIO );
- reader->SetFileNames( filenames );
+ reader->SetFileNames( filenames_in );
try {
reader->Update();
} catch (itk::ExceptionObject &excp) {
- std::cerr << "Error: Exception thrown while writing the DICOM series!!" << std::endl;
+ std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
std::cerr << excp << std::endl;
}
seriesWriter->SetInput( volumeReader->GetOutput() );
seriesWriter->SetImageIO( gdcmIO );
- namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
- seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );
- //seriesWriter->SetMetaDataDictionaryArray( dictionary );
+
+ seriesWriter->SetFileNames( filenames_out );
seriesWriter->SetMetaDataDictionaryArray( dictionary );
// Write
}
}
-
+*/
}//end clitk
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff