// 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>();
// 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 {
const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
// Get keys
- unsigned int numberOfKeysGiven=0;
- if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given)
- std::cerr<<"Error: both keys and midP option are given"<<std::endl;
- else if (m_ArgsInfo.midP_flag)
- numberOfKeysGiven=1;
- else
- numberOfKeysGiven=m_ArgsInfo.key_given;
+ 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] );
- std::string value( m_ArgsInfo.tag_arg[i] );
- std::cout << entryId << " " << value << std::endl;
- for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
- itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
+ 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;
// Write
try {
+ if (m_ArgsInfo.verbose_flag)
+ std::cout << seriesWriter << std::endl;
seriesWriter->Update();
- std::cerr << "filter update" << std::endl;
} catch( itk::ExceptionObject & excp ) {
std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
std::cerr << excp << std::endl;
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff