typedef itk::Image<PixelType, Dimension> OutputImageType;
// Read the dicom directory
- typedef itk::ImageSeriesReader< InputImageType > ReaderType;
+ typedef itk::ImageFileReader< 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();
+ std::string filename_out = m_ArgsInfo.outputFilename_arg;
// Output the dicom files
- unsigned int numberOfFilenames = filenames_in.size();
+ unsigned int numberOfFilenames = 1;
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;
- }
+ std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputModelFilename_arg<<"..."<<std::endl<<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();
+ gdcmIO->LoadPrivateTagsOn();
+ gdcmIO->KeepOriginalUIDOn();
#endif
- }
reader->SetImageIO( gdcmIO );
- reader->SetFileNames( filenames_in );
+ reader->SetFileName( m_ArgsInfo.inputModelFilename_arg );
try {
reader->Update();
} catch (itk::ExceptionObject &excp) {
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()))) {
+ if (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->SetVerboseOptions(m_Verbose);
filter->SetGaussianFilteringEnabled(false);
filter->SetDefaultPixelValue(0);
-
- if (!m_ArgsInfo.useSizeAsReference_flag) {
- filter->SetOutputSpacing(input->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;
- }
+
+ const SizeType& input_size = input->GetLargestPossibleRegion().GetSize();
+ SizeType output_size;
+ for (unsigned int i = 0; i < Dimension; i++)
+ output_size[i] = input_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 mhd 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 {
std::cerr << excp << std::endl;
}
}
- std::cout << "RESAMPING FILTER DONE" << 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;
- }
- std::cout << Dimension << volumeSize[2] << numberOfFilenames << 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());
+#if GDCM_MAJOR_VERSION < 2
+ gdcmIO->SetKeepOriginalUID(true);
#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] );
+ //Read the dicom file to find the energy, the head & the steps (TODO: do it on the mhd filetext)
- 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;
+/*
+ // update output dicom keys/tags
+ //std::string seriesUIDkey = "0020|000e";
+ for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
+ std::string entryId(m_ArgsInfo.key_arg[i] );
+ std::string value( m_ArgsInfo.tag_arg[i] );
- 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");
- }
+ itk::EncapsulateMetaData<std::string>(reader->GetMetaDataDictionary(), entryId, value );
}
-
+*/
// Output directory and filenames
- itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
+ //itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputFilename_arg ); // create if it doesn't exist
typedef itk::ImageFileWriter<OutputImageType> SeriesWriterType;
typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput( input );
seriesWriter->SetImageIO( gdcmIO );
- seriesWriter->SetFileName( filenames_out[0] );
- seriesWriter->SetMetaDataDictionary( *((*dictionary)[0]) );
+ seriesWriter->SetFileName( filename_out );
+ seriesWriter->SetMetaDataDictionary(reader->GetMetaDataDictionary());
// Write
try {
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff