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 clitkImage2DicomDoseGenericFilter_txx
19 #define clitkImage2DicomDoseGenericFilter_txx
21 /* =================================================
22 * @file clitkImage2DicomDosemGenericFilter.txx
28 ===================================================*/
32 #include "clitkImage2DicomDoseGenericFilter.h"
33 #include "clitkCommon.h"
34 #if GDCM_MAJOR_VERSION >= 2
35 #include "gdcmUIDGenerator.h"
36 #include <gdcmImageHelper.h>
37 #include <gdcmAttribute.h>
38 #include <gdcmReader.h>
39 #include <gdcmWriter.h>
45 //#include "gdcmBase.h"
46 //#include "gdcmDocEntry.h"
54 //-----------------------------------------------------------
56 //-----------------------------------------------------------
57 template<class args_info_type>
58 Image2DicomDoseGenericFilter<args_info_type>::Image2DicomDoseGenericFilter()
65 //-----------------------------------------------------------
67 //-----------------------------------------------------------
68 template<class args_info_type>
69 void Image2DicomDoseGenericFilter<args_info_type>::Update()
71 // Read the Dimension and PixelType
73 std::string PixelType;
74 ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
78 if(Dimension==2) UpdateWithDim<2>(PixelType);
79 else if(Dimension==3) UpdateWithDim<3>(PixelType);
80 // else if (Dimension==4)UpdateWithDim<4>(PixelType);
82 std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
87 //-------------------------------------------------------------------
88 // Update with the number of dimensions
89 //-------------------------------------------------------------------
90 template<class args_info_type>
91 template<unsigned int Dimension>
93 Image2DicomDoseGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
95 if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
97 if(PixelType == "short") {
98 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
99 UpdateWithDimAndPixelType<Dimension, signed short>();
101 else if(PixelType == "unsigned_short"){
102 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
103 UpdateWithDimAndPixelType<Dimension, unsigned short>();
106 else if (PixelType == "unsigned_char") {
107 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
108 UpdateWithDimAndPixelType<Dimension, unsigned char>();
111 // else if (PixelType == "char"){
112 // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
113 // UpdateWithDimAndPixelType<Dimension, signed char>();
115 else if (PixelType == "double") {
116 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
117 UpdateWithDimAndPixelType<Dimension, double>();
120 if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
121 UpdateWithDimAndPixelType<Dimension, float>();
125 //-------------------------------------------------------------------
126 // Update with the number of dimensions and the pixeltype read from
127 // the dicom files. The MHD files may be resampled to match the
128 // dicom spacing (and number of slices). Rounding errors in resampling
129 // are handled by removing files when generating the output dicom
131 //-------------------------------------------------------------------
132 template<class args_info_type>
133 template <unsigned int Dimension, class PixelType>
135 Image2DicomDoseGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
138 #if GDCM_MAJOR_VERSION == 2
140 typedef itk::Image<PixelType, Dimension> InputImageType;
141 typedef itk::Image<PixelType, Dimension> OutputImageType;
142 typedef itk::ImageFileReader< InputImageType > ReaderType;
143 typedef itk::ImageSeriesReader< InputImageType > ReaderSeriesType;
144 typedef itk::ImageRegionIterator< InputImageType > IteratorType;
145 typedef itk::GDCMImageIO ImageIOType;
147 // Read Dicom model file
148 typename ReaderSeriesType::Pointer readerSeries = ReaderSeriesType::New();
149 ImageIOType::Pointer gdcmIO = ImageIOType::New();
150 std::string filename_out = m_ArgsInfo.output_arg;
151 gdcmIO->LoadPrivateTagsOn();
152 gdcmIO->KeepOriginalUIDOn();
153 typename ReaderSeriesType::FileNamesContainer fileNames;
154 fileNames.push_back(m_ArgsInfo.DicomInputFile_arg);
155 readerSeries->SetImageIO( gdcmIO );
156 readerSeries->SetFileNames( fileNames );
158 readerSeries->Update();
159 } catch (itk::ExceptionObject &excp) {
160 std::cerr << "Error: Exception thrown while reading the DICOM model file !!" << std::endl;
161 std::cerr << excp << std::endl;
166 //-----------------------------------------------------------------------------------
167 // opening dicom input file
168 gdcm::Reader reader2;
169 reader2.SetFileName( m_ArgsInfo.DicomInputFile_arg );
171 gdcm::File &mDCMFile = reader2.GetFile();
172 gdcm::DataSet &ds = mDCMFile.GetDataSet();
173 //mDCMFile.SetMaxSizeLoadEntry(1006384); // important size required, otherwise some data are not loaded
174 //mDCMFile.AddForceLoadElement(0x7fe0,0x0010); //Load pixel data no matter its size
176 std::cout << "File: "<< m_ArgsInfo.DicomInputFile_arg << " loaded !"<< std::endl;
180 //-----------------------------------------------------------------------------
181 // opening image input file
182 typename ReaderType::Pointer reader = ReaderType::New();
183 const char * filename = m_ArgsInfo.input_arg;
184 reader->SetFileName( filename );
186 typename InputImageType::Pointer image = reader->GetOutput();
189 typename InputImageType::PointType origin = image->GetOrigin();
193 typename InputImageType::SizeType imageSize = image->GetLargestPossibleRegion().GetSize();
195 int NbCols=imageSize[0]; // col
196 int NbRows=imageSize[1]; // row
197 int NbFrames=imageSize[2]; // frame
203 typename InputImageType::SpacingType Spacing = image->GetSpacing();
207 float highestValue=pow(10,-10);
208 IteratorType out( image, image->GetRequestedRegion() );
209 for (out.GoToBegin(); !out.IsAtEnd(); ++out){
211 if (out.Get()>highestValue) highestValue=out.Get();
213 double doseScaling = highestValue/(pow(2,16)-1);
217 std::vector<unsigned short int> ImageData;
218 typename InputImageType::IndexType pixelIndex;
220 unsigned short int pixelValue;
222 for (int i=0; i<NbFrames; i++){
224 for (int j=0; j<NbRows; j++){
226 for (int k=0; k<NbCols; k++){
228 pixelValue=image->GetPixel(pixelIndex)/doseScaling;
229 if(float(image->GetPixel(pixelIndex)/doseScaling)>(pow(2,16)-1.)) {
230 std::cout<<"\n!!!!! WARNING !!!!! pixel index: "<<pixelIndex<<"unsigned short int capacity ful or overfuled => Highest value may become 0"<<std::endl;
232 DD(image->GetPixel(pixelIndex));
233 //DD(image->GetPixel(pixelIndex)/doseScaling);
235 std::cout<<"Pixel Value should be equal to "<<(pow(2,16)-1)<<" but should not be 0"<<std::endl;
236 std::cout<<"\n"<<std::endl;
237 //assert(pixelValue<=(pow(2,16)-1)); should work, but do not...
240 ImageData.push_back(pixelValue);
245 DD(ImageData.size());
247 // Relevant parameters inserted in the new dicom file
258 typename ReaderSeriesType::DictionaryRawPointer inputDict = (*(readerSeries->GetMetaDataDictionaryArray()))[0];
259 typename ReaderSeriesType::DictionaryArrayType outputArray;
260 typename ReaderSeriesType::DictionaryRawPointer outputDict = new typename ReaderSeriesType::DictionaryType;
261 CopyDictionary (*inputDict, *outputDict);
262 outputArray.push_back(outputDict);
264 // Output directory and filenames
265 typedef itk::ImageSeriesWriter<OutputImageType, OutputImageType> WriterSerieType;
266 typename WriterSerieType::Pointer writerSerie = WriterSerieType::New();
267 writerSerie->SetInput( image );
268 writerSerie->SetImageIO( gdcmIO );
269 typename ReaderSeriesType::FileNamesContainer fileNamesOutput;
270 fileNamesOutput.push_back(filename_out);
271 writerSerie->SetFileNames( fileNamesOutput );
272 writerSerie->SetMetaDataDictionaryArray(&outputArray);
290 //--------------------------------------------------------------
291 std::cout<<"\nECRITURE DU FICHIER DICOM !"<<std::endl;
294 std::string Value("");
297 gdcm::DataElement DE;
299 DE = gdcm::Tag(0x20, 0x32);
305 DE.SetVR( gdcm::VR::US );
306 DE.SetByteValue(Value.c_str(), 1);
311 DE = gdcm::Tag(0x28, 0x11);
313 DE.SetVR( gdcm::VR::US );
314 DE.SetByteValue(Value.c_str(), 1);
319 DE = gdcm::Tag(0x28, 0x10);
321 DE.SetVR( gdcm::VR::US );
322 DE.SetByteValue(Value.c_str(), 1);
327 DE = gdcm::Tag(0x28, 0x08);
329 DE.SetVR( gdcm::VR::US );
330 DE.SetByteValue(Value.c_str(), 1);
335 DE = gdcm::Tag(0x3004, 0x0e);
337 DE.SetVR( gdcm::VR::US );
338 DE.SetByteValue(Value.c_str(), 1);
343 DE = gdcm::Tag(0x28, 0x30);
347 DE.SetVR( gdcm::VR::US );
348 DE.SetByteValue(Value.c_str(), 1);
353 DE = gdcm::Tag(0x3004, 0x000c);
356 for (int i=1; i<NbFrames ; i++){
362 DE.SetVR( gdcm::VR::US );
363 DE.SetByteValue(Value.c_str(), 1);
370 b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028,0x0011);
372 b->SetValue(Value.str());
377 b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028,0x0010);
379 b->SetValue(Value.str());
385 b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028,0x0008);
387 b->SetValue(Value.str());
392 b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x3004,0x000e);
394 b->SetValue(Value.str());
399 b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x0028, 0x0030);
400 Value<<Spacing[0]<<'\\'<<Spacing[1];
401 b->SetValue(Value.str());
405 // Spacing Z ([Grid Frame Offset Vector])
406 b = ((gdcm::SQItem*)mDCMFile)->GetValEntry(0x3004, 0x000c);
409 for (int i=1; i<NbFrames ; i++){
413 b->SetValue(Value.str());
418 //bool data = mDCMFile->SetBinEntry(reinterpret_cast<uint8_t*>( &(ImageData[0]) ) , (int)(sizeof(unsigned short int) * ImageData.size()) , 0x7fe0, 0x0010);
419 //if (data) std::cout<<"\n DICOM dose data written !"<<std::endl;
421 //---------------------------------------------------------------------------------------
423 /*gdcm::FileType type = mDCMFile->GetFileType();
424 //type=(gdcm::FileType)2;
425 bool ecriture = mDCMFile->Write (args_info.OutputFile_arg, type);
426 if (ecriture) std::cout<<"\n DICOM File written !"<<std::endl;
428 //---------------------------------------------------------------------------------------
430 // The previous way of writting DICOM-RT-DOSE works only for ITK
431 // and resulting RT-DOSE files are not readable by commercial systems.
432 // The nex step is to copy again the output file with another syntax, allowing to make RT-DOSE files readable by commercial systems.
433 // see Jean-Pierre Roux comment below.
435 /*gdcm::FileHelper *fh = new gdcm::FileHelper(args_info.OutputFile_arg);
439 dataSize = fh->GetImageDataRawSize();
440 imageData = fh->GetImageDataRaw();// somewhat important : Loads the Pixels in memory !
442 fh->SetWriteModeToRaw();
443 fh->SetWriteTypeToDcmExplVR();
445 bool res = fh->Write(args_info.OutputFile_arg);
448 std::cout <<"Fail to write [" << args_info.OutputFile_arg << "]" <<std::endl;
449 else std::cout<<"\n DICOM File re-written, using the FileHelper syntax, in order to be processed by commercial systems !"<<std::endl;
454 w.SetFileName(m_ArgsInfo.output_arg);
458 //---------------------------------------------------------------------------------------
459 //---------------------------------------------------------------------------------------
460 // Jean-Pierre Roux help for DICOM-RT-DOSE writting
461 //---------------------------------------------------------------------------------------
462 //---------------------------------------------------------------------------------------
464 // de Jean-Pierre Roux <jpr@creatis.insa-lyon.fr>
465 // répondre à jpr@creatis.insa-lyon.fr
466 // à Loic Grevillot <loic.grevillot@gmail.com>
467 // cc jpr@creatis.insa-lyon.fr,
468 // Joël Schaerer <joel.schaerer@gmail.com>,
469 // David Sarrut <David.Sarrut@creatis.insa-lyon.fr>,
470 // Joel Schaerer <joel.schaerer@creatis.insa-lyon.fr>
471 // date 12 juillet 2010 12:23
472 // objet Re: DICOM RT DOSE
474 // masquer les détails 12:23 (Il y a 21 heures)
478 // J'aurais écrit à peut prèt la même chose.
479 // (Ci après un extrait de mon code -Example/ReWrite.cxx-)
481 // L'utilisation d'un FileHelper (qui ne changera rien dans ce cas précis) est une mesure de précaution, car, l'élément 7FE0|0010 peut être compressé (ce qui n'est pas le cas pour tes images), que la manière de stocker les pixels ainsi compressés était parfois un peu ... curieuse.
482 // Je décompresse, et réécrit non compressé.
484 // ============================
485 // gdcm::File *f = new gdcm::File();
486 // f->SetMaxSizeLoadEntry(0x7fffffff);
487 // f->SetFileName( fileName );
488 // bool res = f->Load();
495 // if (!f->IsReadable())
497 // std::cerr << "Sorry, not a Readable DICOM / ACR File" <<std::endl;
502 // gdcm::FileHelper *fh = new gdcm::FileHelper(f);
506 // dataSize = fh->GetImageDataRawSize();
507 // imageData = fh->GetImageDataRaw();// somewhat important : Loads the Pixels in memory !
509 // fh->SetWriteModeToRaw();
510 // fh->SetWriteTypeToDcmExplVR();
511 // res = fh->Write(outputFileName);
514 // std::cout <<"Fail to write [" << outputFileName << "]" <<std::endl;
519 //---------------------------------------------------------------------------------------
520 //---------------------------------------------------------------------------------------
521 // pour supprimer des tags:
522 //---------------------------------------------------------------------------------------
523 //---------------------------------------------------------------------------------------
524 // SOLUCE 1 QUI MARCHE POUR UN SQItem SIMPLE
527 //a= ((gdcm::SQItem*)mDCMFile)->GetDocEntry(0xfffe,0xe00d);
528 a= ((gdcm::SQItem*)mDCMFile)->GetDocEntry(0x3004,0x000e);
529 ((gdcm::SQItem*)mDCMFile)->RemoveEntry(a);
530 mDCMFile->Write (args_info.OutputFile_arg, type);
533 // SOLUCE 2 QUI MARCHE POUR UNE SeqEntry->SQItem
535 std::cout<<"\ntest correction fichier apres ecriture\n"<<std::endl;
536 gdcm::SeqEntry *seqEntry = mDCMFile->GetSeqEntry(0x300c,0x0002);
537 gdcm::SQItem* currentItem = seqEntry->GetFirstSQItem();
539 //a= currentItem->GetDocEntry(0x0008,0x1155);
540 a= currentItem->GetDocEntry(0xfffe,0xe00d);
541 currentItem->RemoveEntry(a);
542 mDCMFile->Write (args_info.OutputFile_arg, type);
546 //a=GetDocEntry(0x7fe0,0x0000);
547 //((gdcm::SQItem*)mDCMFile)->RemoveEntry(a);
549 //-----------------------------------------------------------------------------------
550 std::cout <<"\n## DICOM Image to RT DOSE application is ended..."<<std::endl;
551 std::cout <<"#########################################################\n" << std::endl;
554 std::cout << "Use GDCM2" << std::endl;
557 //---------------------------------------------------------------------------
560 //---------------------------------------------------------------------------
561 void CopyDictionary (itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict)
563 typedef itk::MetaDataDictionary DictionaryType;
565 DictionaryType::ConstIterator itr = fromDict.Begin();
566 DictionaryType::ConstIterator end = fromDict.End();
567 typedef itk::MetaDataObject< std::string > MetaDataStringType;
571 itk::MetaDataObjectBase::Pointer entry = itr->second;
573 MetaDataStringType::Pointer entryvalue =
574 dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
577 std::string tagkey = itr->first;
578 std::string tagvalue = entryvalue->GetMetaDataObjectValue();
579 itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
584 //---------------------------------------------------------------------------
587 #endif //#define clitkImage2DicomDoseGenericFilter_txx