// 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 {
// Get keys
unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
+ if (m_ArgsInfo.verbose_flag)
+ DD(numberOfKeysGiven);
std::string seriesUID;
std::string frameOfReferenceUID;
// 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);
- if (seriesUIDGiven)
- {
- if (entryId == seriesUIDkey)
- seriesUID = m_ArgsInfo.tag_arg[i];
- else
- frameOfReferenceUID = m_ArgsInfo.tag_arg[i];
- }
- else if (m_ArgsInfo.newSeriesUID_flag) {
+ 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;
- seriesUID = suid.Generate();
- gdcm::UIDGenerator fuid;
- frameOfReferenceUID = fuid.Generate();
+ gdcm::UIDGenerator suid;
+ studyUID = suid.Generate();
#else
- seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
- frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+ studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
#endif
- if (m_ArgsInfo.verbose_flag)
- {
- DD(seriesUID);
- DD(frameOfReferenceUID);
- }
- }
-
- studyUIDGiven = (entryId == studyUIDKey);
- if (studyUIDGiven)
- studyUID = m_ArgsInfo.tag_arg[i];
- else if (m_ArgsInfo.newStudyUID_flag) {
+ }
+
+ if (!seriesUIDGiven && m_ArgsInfo.newSeriesUID_flag) {
#if GDCM_MAJOR_VERSION >= 2
- gdcm::UIDGenerator suid;
- studyUID = suid.Generate();
+ gdcm::UIDGenerator suid;
+ seriesUID = suid.Generate();
+ gdcm::UIDGenerator fuid;
+ frameOfReferenceUID = fuid.Generate();
#else
- studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
-#endif
- if (m_ArgsInfo.verbose_flag)
- DD(studyUID);
- }
-#if GDCM_MAJOR_VERSION < 2
- else
- gdcmIO->KeepOriginalUID();
+ 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;
+ 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 = namesGenerator->GetOutputFileNames();
}
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++) {
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 );
}
}
+ // 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;
#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");
}
}
// 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;