2 # ---------------------------------------------------------------------
4 # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
6 # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
7 # Previous Authors : Laurent Guigues, Jean-Pierre Roux
8 # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
10 # This software is governed by the CeCILL-B license under French law and
11 # abiding by the rules of distribution of free software. You can use,
12 # modify and/ or redistribute the software under the terms of the CeCILL-B
13 # license as circulated by CEA, CNRS and INRIA at the following URL
14 # http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
15 # or in the file LICENSE.txt.
17 # As a counterpart to the access to the source code and rights to copy,
18 # modify and redistribute granted by the license, users are provided only
19 # with a limited warranty and the software's author, the holder of the
20 # economic rights, and the successive licensors have only limited
23 # The fact that you are presently reading this means that you have had
24 # knowledge of the CeCILL-B license and that you accept its terms.
25 # ------------------------------------------------------------------------ */
27 #include "bbgdcmvtkGetXCoherentInfoGdcmReader.h"
28 #include "bbgdcmvtkPackage.h"
31 #include "vtkImageData.h"
32 #include <vtkIndent.h>
35 #include "gdcmFileHelper.h"
39 #include <gdcmReader.h>
40 #include <gdcmImageHelper.h>
41 #include <gdcmIPPSorter.h>
42 #include <vtkGDCMImageReader.h>
43 #include "vtkStringArray.h"
49 BBTK_ADD_BLACK_BOX_TO_PACKAGE(gdcmvtk,GetXCoherentInfoGdcmReader)
50 BBTK_BLACK_BOX_IMPLEMENTATION(GetXCoherentInfoGdcmReader,bbtk::AtomicBlackBox);
53 vtkImageData* GetXCoherentInfoGdcmReader::CreateDefaultImage()
56 int sizeX, sizeY, sizeZ;
60 vtkImageData *newImage = vtkImageData::New();
61 newImage->Initialize();
62 newImage->SetSpacing( 1,1,1 );
63 newImage->SetDimensions( sizeX,sizeY,sizeZ );
64 newImage->SetExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
66 //EED 2017-01-01 Migration VTK7
67 #if VTK_MAJOR_VERSION <= 5
68 newImage->SetWholeExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
69 newImage->SetScalarTypeToUnsignedChar();
70 newImage->SetNumberOfScalarComponents(1);
71 newImage->AllocateScalars();
74 newImage->AllocateScalars(VTK_UNSIGNED_CHAR,1);
77 memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
78 for (i=0; i<sizeX; i++)
80 newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
81 newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
89 void GetXCoherentInfoGdcmReader::Process2()
91 printf("EED GetXCoherentInfoGdcmReader::Process >>>>>> \n" );
92 GDCM_NAME_SPACE::FileList lstFiles;
93 int i,size=bbGetInputIn().size();
96 printf("a: %s\n",bbGetInputIn()[i].c_str() );
97 f = GDCM_NAME_SPACE::File::New();
98 f->SetFileName( bbGetInputIn()[i] );
102 lstFiles.push_back(f);
105 sh = GDCM_NAME_SPACE::SerieHelper::New();
106 sh->ImagePositionPatientOrdering( &lstFiles );
107 size=lstFiles.size();
110 printf("d: %s\n", lstFiles[i]->GetFileName().c_str() );
115 void GetXCoherentInfoGdcmReader::Process()
117 // Read the *first* image file (a SET of file names is given as input)
118 f = GDCM_NAME_SPACE::File::New();
120 if ( bbGetInputIn().size()!=0 )
122 f->SetFileName( bbGetInputIn()[0] );
124 f->SetFileName( "" );
127 bool res = f->Load();
130 printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
132 bbSetOutputOut( CreateDefaultImage() );
136 // Get info from the first image file
138 std::vector<double> v_iop;
140 f->GetImageOrientationPatient(iop);
144 v_iop.push_back(iop[i]);
146 bbSetOutputIOP(v_iop );
149 // std::vector<double> v_ipp;
151 // f->GetImagePositionPatient(ipp);
152 // for(i=0; i< 3; i++)
154 // v_ipp.push_back(ipp[i]);
156 // bbSetOutputIPP(v_ipp );
159 GDCM_NAME_SPACE::FileList lstFiles;
160 GDCM_NAME_SPACE::FileList *l;
162 if (bbGetInputRespectSerieUID()==false)
164 int i,size=bbGetInputIn().size();
167 f = GDCM_NAME_SPACE::File::New();
168 f->SetFileName( bbGetInputIn()[i] );
169 bool res = f->Load();
172 lstFiles.push_back(f);
175 sh = GDCM_NAME_SPACE::SerieHelper::New();
177 sh->ImagePositionPatientOrdering( l );
179 // Add *all the files* to the SerieHelper
180 sh = GDCM_NAME_SPACE::SerieHelper::New();
181 std::vector<std::string> gii = bbGetInputIn();
182 for(std::vector<std::string>::iterator it = gii.begin();
186 sh->AddFileName(*it);
188 GDCM_NAME_SPACE::FileList::const_iterator it;
189 // Should only contain one!
190 l = sh->GetFirstSingleSerieUIDFileSet();
195 } // if bbGetInputForceRead
197 double zspacing = 0.;
198 sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
199 zspacing = sh->GetZSpacing();
200 std::vector<double> v_pixelspacing;
201 v_pixelspacing.push_back( f->GetXSpacing() );
202 v_pixelspacing.push_back( f->GetYSpacing() );
203 v_pixelspacing.push_back( zspacing );
204 // if (f->GetZSize() != 1) {
205 // v_pixelspacing.push_back(f->GetZSpacing());
207 bbSetOutputPixelSpacing(v_pixelspacing);
209 VectorMapInfoDicom vectormapinfodicom;
213 std::string strTagValue; // read on disc
214 int iTag,sizeDicomTagsVector=bbGetInputDicomTags().size();
215 GDCM_NAME_SPACE::FileList::const_iterator iitt = l->begin();
218 std::vector<std::string> lstFileNames;
220 for ( ; iitt != l->end(); ++iitt)
222 lstFileNames.push_back( (*iitt)->GetFileName() );
224 if ( iitt == l->begin() ) // The first ordered element IPP
228 strTagValue = std::string("void");
229 sscanf("D0020_0032","D%04hx_%04hx",&group,&elem);
230 strTagValue = (*iitt)->GetEntryString(group,elem);
231 sscanf(strTagValue.c_str(),"%f\\%f\\%f\\%f", &px , &py , &pz);
232 std::vector<double> v_ipp;
233 v_ipp.push_back( (double)px );
234 v_ipp.push_back( (double)py );
235 v_ipp.push_back( (double)pz );
236 bbSetOutputIPP(v_ipp );
237 } // if first elemetn get IPP
239 MapInfoDicom mapinfodicom;
240 for (iTag=0; iTag<sizeDicomTagsVector; iTag++)
242 key = bbGetInputDicomTags()[iTag];
244 if ( (key.size()==10) && (key[0] == 'D') && (key[5] == '_') )
246 sscanf(key.c_str(),"D%04hx_%04hx ",&group,&elem);
248 strTagValue = (*iitt)->GetEntryString(group,elem);
249 mapinfodicom.insert ( std::pair<std::string,std::string>(key,strTagValue) );
251 vectormapinfodicom.push_back( mapinfodicom );
253 bbSetOutputDicomInfo( vectormapinfodicom );
254 bbSetOutputOutFileNames( lstFileNames );
256 if (bbGetInputReadRaw()==true)
263 reader = vtkGdcmReader::New();
264 //EED 21 mars 2012 FLIP probleme ..PLOP..
265 reader->SetFlipY(false);
266 //reader->SetFileName( bbGetInputIn().c_str() );
267 reader->SetCoherentFileList(l);
270 bbSetOutputOut( reader->GetOutput() );
271 } // if bGetInputReadRaw
277 #if defined USE_GDCM2
278 void GetXCoherentInfoGdcmReader::Process()
280 // printf("GetXCoherentInfoGdcmReader %d files.\n", bbGetInputIn().size() );
281 // Read the *first* image file (a SET of file names is given as input)
282 gdcm::Reader *read = new gdcm::Reader();
283 reader->SetFileName( bbGetInputIn()[0].c_str() );
284 bool res = read->Read();
288 bbSetOutputOut(NULL);
292 // Get info from the first image file
293 const gdcm::File &f = read->GetFile();
295 std::vector<double> v_iop;
296 const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
297 std::stringstream ss;
298 deIop.GetValue().Print(ss);
299 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
303 v_iop.push_back((float)(iop[i]));
305 bbSetOutputIOP(v_iop );
307 std::vector<double> v_ipp;
308 const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
309 deIpp.GetValue().Print(ss);
310 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
314 v_ipp.push_back((float)(ipp[i]));
316 bbSetOutputIPP(v_ipp );
318 // Add *all the files* to the IPPsorter
320 s.SetComputeZSpacing( true );
321 s.SetZSpacingTolerance( 1e-3 );
322 std::vector<std::string> gii = bbGetInputIn();
325 //l = sh->GetFirstSingleSerieUIDFileSet();
326 // no Test if we have multiple series
330 double zspacing = 0.;
331 zspacing = s.GetZSpacing();
332 std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
333 v_pixelspacing.push_back( v_pixelspacing[0] );
334 v_pixelspacing.push_back( v_pixelspacing[1] );
335 v_pixelspacing.push_back( zspacing );
336 bbSetOutputPixelSpacing(v_pixelspacing);
343 reader = vtkGDCMImageReader::New();
344 vtkStringArray *files = vtkStringArray::New();
345 std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
346 for( ; it != s.GetFilenames().end(); ++it)
348 const std::string &f = *it;
349 files->InsertNextValue( f.c_str() );
351 reader->SetFileNames(files);
353 bbSetOutputOut( reader->GetOutput() );
358 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
361 std::vector<std::string> init;
364 bbSetInputReadRaw(true);
365 bbSetInputRespectSerieUID(true);
366 //reader=NULL; /// \TODO fixme JPR
369 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
374 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
391 #if defined USE_GDCM2
392 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
402 // EO namespace bbgdcmvtk