1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
18 #ifndef clitkWriteDicomSeriesGenericFilter_txx
19 #define clitkWriteDicomSeriesGenericFilter_txx
21 /* =================================================
22 * @file clitkWriteDicomSeriesGenericFilter.txx
28 ===================================================*/
31 #include "clitkResampleImageWithOptionsFilter.h"
32 #if GDCM_MAJOR_VERSION >= 2
33 #include "gdcmUIDGenerator.h"
44 //-----------------------------------------------------------
46 //-----------------------------------------------------------
47 template<class args_info_type>
48 WriteDicomSeriesGenericFilter<args_info_type>::WriteDicomSeriesGenericFilter()
55 //-----------------------------------------------------------
57 //-----------------------------------------------------------
58 template<class args_info_type>
59 void WriteDicomSeriesGenericFilter<args_info_type>::Update()
61 // Read the Dimension and PixelType
63 std::string PixelType;
64 ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
68 if(Dimension==2) UpdateWithDim<2>(PixelType);
69 else if(Dimension==3) UpdateWithDim<3>(PixelType);
70 // else if (Dimension==4)UpdateWithDim<4>(PixelType);
72 std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
77 //-------------------------------------------------------------------
78 // Update with the number of dimensions
79 //-------------------------------------------------------------------
80 template<class args_info_type>
81 template<unsigned int Dimension>
83 WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
85 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
87 if(PixelType == "short") {
88 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
89 UpdateWithDimAndPixelType<Dimension, signed short>();
91 else if(PixelType == "unsigned_short"){
92 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
93 UpdateWithDimAndPixelType<Dimension, unsigned short>();
96 else if (PixelType == "unsigned_char") {
97 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
98 UpdateWithDimAndPixelType<Dimension, unsigned char>();
101 // else if (PixelType == "char"){
102 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
103 // UpdateWithDimAndPixelType<Dimension, signed char>();
105 else if (PixelType == "double") {
106 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
107 UpdateWithDimAndPixelType<Dimension, double>();
110 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
111 UpdateWithDimAndPixelType<Dimension, float>();
115 //-------------------------------------------------------------------
116 // Update with the number of dimensions and the pixeltype read from
117 // the dicom files. The MHD files may be resampled to match the
118 // dicom spacing (and number of slices). Rounding errors in resampling
119 // are handled by removing files when generating the output dicom
121 //-------------------------------------------------------------------
122 template<class args_info_type>
123 template <unsigned int Dimension, class PixelType>
125 WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
129 typedef itk::Image<PixelType, Dimension> InputImageType;
130 typedef itk::Image<PixelType, 2> OutputImageType;
132 // Read the dicom directory
133 typedef itk::ImageSeriesReader< InputImageType > ReaderType;
134 typedef itk::GDCMImageIO ImageIOType;
135 typedef itk::GDCMSeriesFileNames NamesGeneratorType;
137 ImageIOType::Pointer gdcmIO = ImageIOType::New();
138 NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
139 namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
140 namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
141 typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
142 typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
144 // Output the dicom files
145 unsigned int numberOfFilenames = filenames_in.size();
147 std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
148 for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
149 std::cout << "filename # " << fni << " = ";
150 std::cout << filenames_in[fni] << std::endl;
155 typename ReaderType::Pointer reader = ReaderType::New();
156 gdcmIO->LoadPrivateTagsOn();
157 gdcmIO->KeepOriginalUIDOn();
158 reader->SetImageIO( gdcmIO );
159 reader->SetFileNames( filenames_in );
162 } catch (itk::ExceptionObject &excp) {
163 std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
164 std::cerr << excp << std::endl;
167 // Read the input (MHD file)
168 typedef typename InputImageType::RegionType RegionType;
169 typedef typename RegionType::SizeType SizeType;
170 typedef itk::ImageFileReader<InputImageType> InputReaderType;
171 typename InputReaderType::Pointer volumeReader = InputReaderType::New();
172 volumeReader->SetFileName( m_InputFileName);
173 volumeReader->Update();
175 typename InputImageType::Pointer input = volumeReader->GetOutput();
176 if ((!m_ArgsInfo.useSizeAsReference_flag && (input->GetSpacing() != reader->GetOutput()->GetSpacing())) ||
177 (m_ArgsInfo.useSizeAsReference_flag && (input->GetLargestPossibleRegion().GetSize() != reader->GetOutput()->GetLargestPossibleRegion().GetSize()))) {
179 // resampling is carried out on the fly if resolution or size between
180 // the input mhd and input dicom series is different
183 typedef clitk::ResampleImageWithOptionsFilter<InputImageType, InputImageType> ResampleImageFilterType;
184 typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
185 filter->SetInput(input);
186 filter->SetVerboseOptions(m_Verbose);
187 filter->SetGaussianFilteringEnabled(false);
188 filter->SetDefaultPixelValue(0);
190 if (!m_ArgsInfo.useSizeAsReference_flag) {
191 filter->SetOutputSpacing(reader->GetOutput()->GetSpacing());
193 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;
194 std::cout << "MHD -> " << input->GetSpacing() << std::endl;
195 std::cout << "dicom -> " << reader->GetOutput()->GetSpacing() << std::endl;
199 const SizeType& dicom_size = reader->GetOutput()->GetLargestPossibleRegion().GetSize();
200 SizeType output_size;
201 for (unsigned int i = 0; i < Dimension; i++)
202 output_size[i] = dicom_size[i];
203 filter->SetOutputSize(output_size);
205 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;
206 std::cout << "MHD -> " << input->GetLargestPossibleRegion().GetSize() << std::endl;
207 std::cout << "dicom -> " << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;
213 input = filter->GetOutput();
214 } catch( itk::ExceptionObject & excp ) {
215 std::cerr << "Error: Exception thrown while resampling!!" << std::endl;
216 std::cerr << excp << std::endl;
220 // In some cases, due to resampling approximation issues,
221 // the number of slices in the MHD file may be different (smaller)
222 // from the number of files in the template dicom directory.
223 // To avoid ITK generating an exception, we reduce the number
224 // of DCM files to be considered, and a warning is printed
226 const RegionType volumeRegion = input->GetLargestPossibleRegion();
227 const SizeType& volumeSize = volumeRegion.GetSize();
229 std::cout << volumeRegion << volumeSize << std::endl;
231 if (Dimension == 3 && volumeSize[2] < numberOfFilenames) {
233 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;
235 filenames_in.resize(volumeSize[2]);
236 filenames_out.resize(filenames_in.size());
237 numberOfFilenames = filenames_in.size();
240 // Modify the meta dictionary
241 typedef itk::MetaDataDictionary DictionaryType;
242 const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
245 unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
246 if (m_ArgsInfo.verbose_flag)
247 DD(numberOfKeysGiven);
249 std::string seriesUID;
250 std::string frameOfReferenceUID;
251 std::string studyUID;
253 // one pass through the keys given on the cmd-line, to check what will be recreated
254 std::string seriesUIDkey = "0020|000e";
255 std::string seriesNumberKey = "0020|0011";
256 std::string seriesDescriptionKey = "0008|103e";
257 std::string frameOfReferenceUIDKey = "0020|0052";
258 std::string studyUIDKey = "0020|000d";
259 std::string studyIDKey = "0020|0010";
260 std::string studyDescriptionKey = "0008|1030";
261 bool seriesUIDGiven = false;
262 bool seriesNumberGiven = false;
263 bool seriesDescriptionGiven = false;
264 bool studyUIDGiven = false;
265 bool studyIDGiven = false;
266 bool studyDescriptionGiven = false;
267 for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
268 std::string entryId( m_ArgsInfo.key_arg[i] );
269 if (m_ArgsInfo.verbose_flag)
272 seriesUIDGiven |= (entryId == seriesUIDkey || entryId == frameOfReferenceUIDKey);
273 seriesNumberGiven |= (entryId == seriesNumberKey);
274 seriesDescriptionGiven |= (entryId == seriesDescriptionKey);
275 studyUIDGiven |= (entryId == studyUIDKey);
276 studyIDGiven |= (entryId == studyIDKey);
277 studyDescriptionGiven |= (entryId == studyDescriptionKey);
280 // force the creation of a new series if a new study was specified
281 if (!studyUIDGiven && m_ArgsInfo.newStudyUID_flag) {
282 m_ArgsInfo.newSeriesUID_flag = true;
283 #if GDCM_MAJOR_VERSION >= 2
284 gdcm::UIDGenerator suid;
285 studyUID = suid.Generate();
287 studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
291 if (!seriesUIDGiven && m_ArgsInfo.newSeriesUID_flag) {
292 #if GDCM_MAJOR_VERSION >= 2
293 gdcm::UIDGenerator suid;
294 seriesUID = suid.Generate();
295 gdcm::UIDGenerator fuid;
296 frameOfReferenceUID = fuid.Generate();
298 seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
299 frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
303 if (m_ArgsInfo.verbose_flag) {
305 DD(frameOfReferenceUID);
309 // check if file UIDs will be be preserved
310 bool useInputFileUID = true;
311 if (m_ArgsInfo.newSeriesUID_flag || m_ArgsInfo.newStudyUID_flag || seriesUIDGiven || studyUIDGiven) {
312 useInputFileUID = false;
315 #if GDCM_MAJOR_VERSION < 2
316 gdcmIO->SetKeepOriginalUID(true);
318 namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
321 filenames_out.resize(numberOfFilenames);
325 struct tm* instanceDateTimeTm = localtime(&t);
327 strftime(datetime, 16, "%Y%m%d", instanceDateTimeTm);
328 std::ostringstream instanceDate;
329 instanceDate << datetime;
330 std::ostringstream instanceTime;
331 strftime(datetime, 16, "%H%M%S", instanceDateTimeTm);
332 instanceTime << datetime;
334 // update output dicom keys/tags
335 for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
336 for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
337 std::string entryId(m_ArgsInfo.key_arg[i] );
338 std::string value( m_ArgsInfo.tag_arg[i] );
340 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
344 if (!seriesUIDGiven) {
345 if (m_ArgsInfo.newSeriesUID_flag) {
346 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesUIDkey, seriesUID );
347 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID );
352 if (!studyUIDGiven) {
353 if (m_ArgsInfo.newStudyUID_flag)
354 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyUIDKey, studyUID );
358 if (studyUIDGiven || m_ArgsInfo.newStudyUID_flag) {
360 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyIDKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
361 if (!studyDescriptionGiven)
362 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyDescriptionKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
364 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0020", instanceDate.str() );
365 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0030", instanceTime.str() );
368 // series description/number
369 if (seriesUIDGiven || m_ArgsInfo.newSeriesUID_flag) {
370 if (!seriesDescriptionGiven)
371 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesDescriptionKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
372 if (!seriesNumberGiven)
373 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesNumberKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
375 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0012", instanceDate.str() );
376 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0013", instanceTime.str() );
379 // file UIDs are recreated for new studies or series
380 if (!useInputFileUID)
382 if (m_ArgsInfo.verbose_flag)
383 std::cout << "Recreating file UIDs" << std::endl;
386 #if GDCM_MAJOR_VERSION >= 2
387 gdcm::UIDGenerator fid;
388 fileUID = fid.Generate();
390 fileUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
392 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0018", fileUID );
393 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0002|0003", fileUID );
395 filenames_out[fni] = itksys::SystemTools::CollapseFullPath(fileUID.c_str(), m_ArgsInfo.outputDir_arg) + std::string(".dcm");
399 // Output directory and filenames
400 itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
401 typedef itk::ImageSeriesWriter<InputImageType, OutputImageType > SeriesWriterType;
402 typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
404 seriesWriter->SetInput( input );
405 seriesWriter->SetImageIO( gdcmIO );
407 seriesWriter->SetFileNames( filenames_out );
408 seriesWriter->SetMetaDataDictionaryArray( dictionary );
412 if (m_ArgsInfo.verbose_flag)
413 std::cout << seriesWriter << std::endl;
414 seriesWriter->Update();
415 } catch( itk::ExceptionObject & excp ) {
416 std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
417 std::cerr << excp << std::endl;
423 //-------------------------------------------------------------------
424 // Update with the number of dimensions and the pixeltype
425 //-------------------------------------------------------------------
426 template<class args_info_type>
427 template <unsigned int Dimension, class PixelType>
429 WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
433 typedef itk::Image<PixelType, Dimension> InputImageType;
434 typedef itk::Image<PixelType, 2> OutputImageType;
436 // Read the input (volumetric)
437 typedef itk::ImageFileReader<InputImageType> InputReaderType;
438 typename InputReaderType::Pointer volumeReader = InputReaderType::New();
439 volumeReader->SetFileName( m_InputFileName);
440 volumeReader->Update();
441 typename InputImageType::Pointer input= volumeReader->GetOutput();
443 // Read the dicom directory
444 typedef itk::ImageSeriesReader< InputImageType > ReaderType;
445 typedef itk::GDCMImageIO ImageIOType;
446 typedef itk::GDCMSeriesFileNames NamesGeneratorType;
448 ImageIOType::Pointer gdcmIO = ImageIOType::New();
449 NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
450 namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
451 namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
452 typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
453 typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
455 // Output the dicom files
456 unsigned int numberOfFilenames = filenames_in.size();
458 std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
459 for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
460 std::cout << "filename # " << fni << " = ";
461 std::cout << filenames_in[fni] << std::endl;
466 // In some cases, due to resampling approximation issues,
467 // the number of slices in the MHD file may be different
468 // from the number of slices in the template DCM directory.
469 // To avoid ITK generating an exception, we reduce the number
470 // of DCM files to be considered, provided the --force
472 typedef typename InputImageType::RegionType RegionType;
473 typedef typename RegionType::SizeType SizeType;
474 const RegionType volumeRegion = input->GetLargestPossibleRegion();
475 const SizeType& volumeSize = volumeRegion.GetSize();
476 if (m_ArgsInfo.force_given && Dimension == 3 && volumeSize[2] < numberOfFilenames)
478 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;
479 filenames_in.resize(volumeSize[2]);
480 filenames_out.resize(filenames_in.size());
481 numberOfFilenames = filenames_in.size();
485 typename ReaderType::Pointer reader = ReaderType::New();
486 reader->SetImageIO( gdcmIO );
487 reader->SetFileNames( filenames_in );
490 } catch (itk::ExceptionObject &excp) {
491 std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
492 std::cerr << excp << std::endl;
496 // Modify the meta dictionary
497 typedef itk::MetaDataDictionary DictionaryType;
498 const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
501 unsigned int numberOfKeysGiven=0;
502 if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given)
503 std::cerr<<"Error: both keys and midP option are given"<<std::endl;
504 else if (m_ArgsInfo.midP_flag)
507 numberOfKeysGiven=m_ArgsInfo.key_given;
509 for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
510 std::string entryId(m_ArgsInfo.key_arg[i] );
511 std::string value( m_ArgsInfo.tag_arg[i] );
512 for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
513 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
516 // Output directory and filenames
517 itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
518 typedef itk::ImageSeriesWriter<InputImageType, OutputImageType > SeriesWriterType;
519 typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
521 seriesWriter->SetInput( volumeReader->GetOutput() );
522 seriesWriter->SetImageIO( gdcmIO );
524 seriesWriter->SetFileNames( filenames_out );
525 seriesWriter->SetMetaDataDictionaryArray( dictionary );
529 seriesWriter->Update();
530 } catch( itk::ExceptionObject & excp ) {
531 std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
532 std::cerr << excp << std::endl;
540 #endif //#define clitkWriteDicomSeriesGenericFilter_txx