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 reader->SetImageIO( gdcmIO );
157 reader->SetFileNames( filenames_in );
160 } catch (itk::ExceptionObject &excp) {
161 std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
162 std::cerr << excp << std::endl;
165 // Read the input (MHD file)
166 typedef typename InputImageType::RegionType RegionType;
167 typedef typename RegionType::SizeType SizeType;
168 typedef itk::ImageFileReader<InputImageType> InputReaderType;
169 typename InputReaderType::Pointer volumeReader = InputReaderType::New();
170 volumeReader->SetFileName( m_InputFileName);
171 volumeReader->Update();
173 typename InputImageType::Pointer input = volumeReader->GetOutput();
174 if ((!m_ArgsInfo.useSizeAsReference_flag && (input->GetSpacing() != reader->GetOutput()->GetSpacing())) ||
175 (m_ArgsInfo.useSizeAsReference_flag && (input->GetLargestPossibleRegion().GetSize() != reader->GetOutput()->GetLargestPossibleRegion().GetSize()))) {
177 // resampling is carried out on the fly if resolution or size between
178 // the input mhd and input dicom series is different
181 typedef clitk::ResampleImageWithOptionsFilter<InputImageType, InputImageType> ResampleImageFilterType;
182 typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New();
183 filter->SetInput(input);
184 filter->SetVerboseOptions(m_Verbose);
185 filter->SetGaussianFilteringEnabled(false);
186 filter->SetDefaultPixelValue(0);
188 if (!m_ArgsInfo.useSizeAsReference_flag) {
189 filter->SetOutputSpacing(reader->GetOutput()->GetSpacing());
191 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;
192 std::cout << "MHD -> " << input->GetSpacing() << std::endl;
193 std::cout << "dicom -> " << reader->GetOutput()->GetSpacing() << std::endl;
197 const SizeType& dicom_size = reader->GetOutput()->GetLargestPossibleRegion().GetSize();
198 SizeType output_size;
199 for (unsigned int i = 0; i < Dimension; i++)
200 output_size[i] = dicom_size[i];
201 filter->SetOutputSize(output_size);
203 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;
204 std::cout << "MHD -> " << input->GetLargestPossibleRegion().GetSize() << std::endl;
205 std::cout << "dicom -> " << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;
211 input = filter->GetOutput();
212 } catch( itk::ExceptionObject & excp ) {
213 std::cerr << "Error: Exception thrown while resampling!!" << std::endl;
214 std::cerr << excp << std::endl;
218 // In some cases, due to resampling approximation issues,
219 // the number of slices in the MHD file may be different (smaller)
220 // from the number of files in the template dicom directory.
221 // To avoid ITK generating an exception, we reduce the number
222 // of DCM files to be considered, and a warning is printed
224 const RegionType volumeRegion = input->GetLargestPossibleRegion();
225 const SizeType& volumeSize = volumeRegion.GetSize();
227 std::cout << volumeRegion << volumeSize << std::endl;
229 if (Dimension == 3 && volumeSize[2] < numberOfFilenames) {
231 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;
233 filenames_in.resize(volumeSize[2]);
234 filenames_out.resize(filenames_in.size());
235 numberOfFilenames = filenames_in.size();
238 // Modify the meta dictionary
239 typedef itk::MetaDataDictionary DictionaryType;
240 const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
243 unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
244 if (m_ArgsInfo.verbose_flag)
245 DD(numberOfKeysGiven);
247 std::string seriesUID;
248 std::string frameOfReferenceUID;
249 std::string studyUID;
251 // one pass through the keys given on the cmd-line, to check what will be recreated
252 std::string seriesUIDkey = "0020|000e";
253 std::string seriesNumberKey = "0020|0011";
254 std::string seriesDescriptionKey = "0008|103e";
255 std::string frameOfReferenceUIDKey = "0020|0052";
256 std::string studyUIDKey = "0020|000d";
257 std::string studyIDKey = "0020|0010";
258 std::string studyDescriptionKey = "0008|1030";
259 bool seriesUIDGiven = false;
260 bool seriesNumberGiven = false;
261 bool seriesDescriptionGiven = false;
262 bool studyUIDGiven = false;
263 bool studyIDGiven = false;
264 bool studyDescriptionGiven = false;
265 for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
266 std::string entryId( m_ArgsInfo.key_arg[i] );
267 if (m_ArgsInfo.verbose_flag)
270 seriesUIDGiven |= (entryId == seriesUIDkey || entryId == frameOfReferenceUIDKey);
271 seriesNumberGiven |= (entryId == seriesNumberKey);
272 seriesDescriptionGiven |= (entryId == seriesDescriptionKey);
273 studyUIDGiven |= (entryId == studyUIDKey);
274 studyIDGiven |= (entryId == studyIDKey);
275 studyDescriptionGiven |= (entryId == studyDescriptionKey);
278 // force the creation of a new series if a new study was specified
279 if (!studyUIDGiven && m_ArgsInfo.newStudyUID_flag) {
280 m_ArgsInfo.newSeriesUID_flag = true;
281 #if GDCM_MAJOR_VERSION >= 2
282 gdcm::UIDGenerator suid;
283 studyUID = suid.Generate();
285 studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
289 if (!seriesUIDGiven && m_ArgsInfo.newSeriesUID_flag) {
290 #if GDCM_MAJOR_VERSION >= 2
291 gdcm::UIDGenerator suid;
292 seriesUID = suid.Generate();
293 gdcm::UIDGenerator fuid;
294 frameOfReferenceUID = fuid.Generate();
296 seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
297 frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
301 if (m_ArgsInfo.verbose_flag) {
303 DD(frameOfReferenceUID);
307 // check if file UIDs will be be preserved
308 bool useInputFileUID = true;
309 if (m_ArgsInfo.newSeriesUID_flag || m_ArgsInfo.newStudyUID_flag || seriesUIDGiven || studyUIDGiven) {
310 useInputFileUID = false;
313 #if GDCM_MAJOR_VERSION < 2
314 gdcmIO->SetKeepOriginalUID(true);
316 namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
319 filenames_out.resize(numberOfFilenames);
323 struct tm* instanceDateTimeTm = localtime(&t);
325 strftime(datetime, 16, "%Y%m%d", instanceDateTimeTm);
326 std::ostringstream instanceDate;
327 instanceDate << datetime;
328 std::ostringstream instanceTime;
329 strftime(datetime, 16, "%H%M%S", instanceDateTimeTm);
330 instanceTime << datetime;
332 // update output dicom keys/tags
333 for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
334 for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
335 std::string entryId(m_ArgsInfo.key_arg[i] );
336 std::string value( m_ArgsInfo.tag_arg[i] );
338 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
342 if (!seriesUIDGiven) {
343 if (m_ArgsInfo.newSeriesUID_flag) {
344 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesUIDkey, seriesUID );
345 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID );
350 if (!studyUIDGiven) {
351 if (m_ArgsInfo.newStudyUID_flag)
352 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyUIDKey, studyUID );
356 if (studyUIDGiven || m_ArgsInfo.newStudyUID_flag) {
358 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyIDKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
359 if (!studyDescriptionGiven)
360 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), studyDescriptionKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg ));
362 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0020", instanceDate.str() );
363 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0030", instanceTime.str() );
366 // series description/number
367 if (seriesUIDGiven || m_ArgsInfo.newSeriesUID_flag) {
368 if (!seriesDescriptionGiven)
369 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesDescriptionKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
370 if (!seriesNumberGiven)
371 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), seriesNumberKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) );
373 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0012", instanceDate.str() );
374 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0013", instanceTime.str() );
377 // file UIDs are recreated for new studies or series
378 if (!useInputFileUID)
380 if (m_ArgsInfo.verbose_flag)
381 std::cout << "Recreating file UIDs" << std::endl;
384 #if GDCM_MAJOR_VERSION >= 2
385 gdcm::UIDGenerator fid;
386 fileUID = fid.Generate();
388 fileUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
390 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0008|0018", fileUID );
391 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), "0002|0003", fileUID );
393 filenames_out[fni] = itksys::SystemTools::CollapseFullPath(fileUID.c_str(), m_ArgsInfo.outputDir_arg) + std::string(".dcm");
397 // Output directory and filenames
398 itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
399 typedef itk::ImageSeriesWriter<InputImageType, OutputImageType > SeriesWriterType;
400 typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
402 seriesWriter->SetInput( input );
403 seriesWriter->SetImageIO( gdcmIO );
405 seriesWriter->SetFileNames( filenames_out );
406 seriesWriter->SetMetaDataDictionaryArray( dictionary );
410 if (m_ArgsInfo.verbose_flag)
411 std::cout << seriesWriter << std::endl;
412 seriesWriter->Update();
413 } catch( itk::ExceptionObject & excp ) {
414 std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
415 std::cerr << excp << std::endl;
421 //-------------------------------------------------------------------
422 // Update with the number of dimensions and the pixeltype
423 //-------------------------------------------------------------------
424 template<class args_info_type>
425 template <unsigned int Dimension, class PixelType>
427 WriteDicomSeriesGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
431 typedef itk::Image<PixelType, Dimension> InputImageType;
432 typedef itk::Image<PixelType, 2> OutputImageType;
434 // Read the input (volumetric)
435 typedef itk::ImageFileReader<InputImageType> InputReaderType;
436 typename InputReaderType::Pointer volumeReader = InputReaderType::New();
437 volumeReader->SetFileName( m_InputFileName);
438 volumeReader->Update();
439 typename InputImageType::Pointer input= volumeReader->GetOutput();
441 // Read the dicom directory
442 typedef itk::ImageSeriesReader< InputImageType > ReaderType;
443 typedef itk::GDCMImageIO ImageIOType;
444 typedef itk::GDCMSeriesFileNames NamesGeneratorType;
446 ImageIOType::Pointer gdcmIO = ImageIOType::New();
447 NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
448 namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg );
449 namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg );
450 typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames();
451 typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames();
453 // Output the dicom files
454 unsigned int numberOfFilenames = filenames_in.size();
456 std::cout << numberOfFilenames <<" were read in the directory "<<m_ArgsInfo.inputDir_arg<<"..."<<std::endl<<std::endl;
457 for(unsigned int fni = 0; fni<numberOfFilenames; fni++) {
458 std::cout << "filename # " << fni << " = ";
459 std::cout << filenames_in[fni] << std::endl;
464 // In some cases, due to resampling approximation issues,
465 // the number of slices in the MHD file may be different
466 // from the number of slices in the template DCM directory.
467 // To avoid ITK generating an exception, we reduce the number
468 // of DCM files to be considered, provided the --force
470 typedef typename InputImageType::RegionType RegionType;
471 typedef typename RegionType::SizeType SizeType;
472 const RegionType volumeRegion = input->GetLargestPossibleRegion();
473 const SizeType& volumeSize = volumeRegion.GetSize();
474 if (m_ArgsInfo.force_given && Dimension == 3 && volumeSize[2] < numberOfFilenames)
476 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;
477 filenames_in.resize(volumeSize[2]);
478 filenames_out.resize(filenames_in.size());
479 numberOfFilenames = filenames_in.size();
483 typename ReaderType::Pointer reader = ReaderType::New();
484 reader->SetImageIO( gdcmIO );
485 reader->SetFileNames( filenames_in );
488 } catch (itk::ExceptionObject &excp) {
489 std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl;
490 std::cerr << excp << std::endl;
494 // Modify the meta dictionary
495 typedef itk::MetaDataDictionary DictionaryType;
496 const std::vector<DictionaryType*>* dictionary = reader->GetMetaDataDictionaryArray();
499 unsigned int numberOfKeysGiven=0;
500 if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given)
501 std::cerr<<"Error: both keys and midP option are given"<<std::endl;
502 else if (m_ArgsInfo.midP_flag)
505 numberOfKeysGiven=m_ArgsInfo.key_given;
507 for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
508 std::string entryId(m_ArgsInfo.key_arg[i] );
509 std::string value( m_ArgsInfo.tag_arg[i] );
510 for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
511 itk::EncapsulateMetaData<std::string>( *((*dictionary)[fni]), entryId, value );
514 // Output directory and filenames
515 itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist
516 typedef itk::ImageSeriesWriter<InputImageType, OutputImageType > SeriesWriterType;
517 typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
519 seriesWriter->SetInput( volumeReader->GetOutput() );
520 seriesWriter->SetImageIO( gdcmIO );
522 seriesWriter->SetFileNames( filenames_out );
523 seriesWriter->SetMetaDataDictionaryArray( dictionary );
527 seriesWriter->Update();
528 } catch( itk::ExceptionObject & excp ) {
529 std::cerr << "Error: Exception thrown while writing the series!!" << std::endl;
530 std::cerr << excp << std::endl;
538 #endif //#define clitkWriteDicomSeriesGenericFilter_txx