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 );
88 void GetXCoherentInfoGdcmReader::Process()
90 // Read the *first* image file (a SET of file names is given as input)
91 f = GDCM_NAME_SPACE::File::New();
93 if ( bbGetInputIn().size()!=0 )
95 f->SetFileName( bbGetInputIn()[0] );
100 bool res = f->Load();
103 printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
105 bbSetOutputOut( CreateDefaultImage() );
109 // Get info from the first image file
111 std::vector<double> v_iop;
113 f->GetImageOrientationPatient(iop);
117 v_iop.push_back(iop[i]);
119 bbSetOutputIOP(v_iop );
121 std::vector<double> v_ipp;
123 f->GetImagePositionPatient(ipp);
127 v_ipp.push_back(ipp[i]);
129 bbSetOutputIPP(v_ipp );
131 // Add *all the files* to the SerieHelper
132 sh = GDCM_NAME_SPACE::SerieHelper::New();
133 std::vector<std::string> gii = bbGetInputIn();
135 for(std::vector<std::string>::iterator it = gii.begin();
139 sh->AddFileName(*it);
142 GDCM_NAME_SPACE::FileList::const_iterator it;
143 GDCM_NAME_SPACE::FileList *l;
145 // Should only contain one!
146 l = sh->GetFirstSingleSerieUIDFileSet();
153 double zspacing = 0.;
154 sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
155 zspacing = sh->GetZSpacing();
156 std::vector<double> v_pixelspacing;
157 v_pixelspacing.push_back( f->GetXSpacing() );
158 v_pixelspacing.push_back( f->GetYSpacing() );
159 v_pixelspacing.push_back( zspacing );
160 // if (f->GetZSize() != 1) {
161 // v_pixelspacing.push_back(f->GetZSpacing());
163 bbSetOutputPixelSpacing(v_pixelspacing);
165 VectorMapInfoDicom vectormapinfodicom;
169 std::string strTagValue; // read on disc
170 int iTag,sizeDicomTagsVector=bbGetInputDicomTags().size();
171 GDCM_NAME_SPACE::FileList::const_iterator iitt = l->begin();
174 for ( ; iitt != l->end(); ++iitt)
176 MapInfoDicom mapinfodicom;
177 for (iTag=0; iTag<sizeDicomTagsVector; iTag++)
179 key = bbGetInputDicomTags()[iTag];
181 if ( (key.size()==10) && (key[0] == 'D') && (key[5] == '_') )
183 sscanf(key.c_str(),"D%04hx_%04hx ",&group,&elem);
185 strTagValue = (*iitt)->GetEntryString(group,elem);
186 mapinfodicom.insert ( std::pair<std::string,std::string>(key,strTagValue) );
189 vectormapinfodicom.push_back( mapinfodicom );
191 bbSetOutputDicomInfo( vectormapinfodicom );
193 if (bbGetInputReadRaw()==true)
200 reader = vtkGdcmReader::New();
201 //EED 21 mars 2012 FLIP probleme ..PLOP..
202 reader->SetFlipY(false);
203 //reader->SetFileName( bbGetInputIn().c_str() );
204 reader->SetCoherentFileList(l);
207 bbSetOutputOut( reader->GetOutput() );
208 } // if bGetInputReadRaw
213 #if defined USE_GDCM2
214 void GetXCoherentInfoGdcmReader::Process()
216 // Read the *first* image file (a SET of file names is given as input)
217 gdcm::Reader *read = new gdcm::Reader();
218 reader->SetFileName( bbGetInputIn()[0].c_str() );
219 bool res = read->Read();
223 bbSetOutputOut(NULL);
227 // Get info from the first image file
228 const gdcm::File &f = read->GetFile();
230 std::vector<double> v_iop;
231 const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
232 std::stringstream ss;
233 deIop.GetValue().Print(ss);
234 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
238 v_iop.push_back((float)(iop[i]));
240 bbSetOutputIOP(v_iop );
242 std::vector<double> v_ipp;
243 const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
244 deIpp.GetValue().Print(ss);
245 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
249 v_ipp.push_back((float)(ipp[i]));
251 bbSetOutputIPP(v_ipp );
253 // Add *all the files* to the IPPsorter
255 s.SetComputeZSpacing( true );
256 s.SetZSpacingTolerance( 1e-3 );
257 std::vector<std::string> gii = bbGetInputIn();
260 //l = sh->GetFirstSingleSerieUIDFileSet();
261 // no Test if we have multiple series
265 double zspacing = 0.;
266 zspacing = s.GetZSpacing();
267 std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
268 v_pixelspacing.push_back( v_pixelspacing[0] );
269 v_pixelspacing.push_back( v_pixelspacing[1] );
270 v_pixelspacing.push_back( zspacing );
271 bbSetOutputPixelSpacing(v_pixelspacing);
278 reader = vtkGDCMImageReader::New();
279 vtkStringArray *files = vtkStringArray::New();
280 std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
281 for( ; it != s.GetFilenames().end(); ++it)
283 const std::string &f = *it;
284 files->InsertNextValue( f.c_str() );
286 reader->SetFileNames(files);
288 bbSetOutputOut( reader->GetOutput() );
293 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
296 std::vector<std::string> init;
299 bbSetInputReadRaw(true);
300 //reader=NULL; /// \TODO fixme JPR
303 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
309 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
326 #if defined USE_GDCM2
327 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
337 // EO namespace bbgdcmvtk