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->SetScalarTypeToUnsignedChar();
63 newImage->SetSpacing( 1,1,1 );
64 newImage->SetDimensions( sizeX,sizeY,sizeZ );
65 newImage->SetWholeExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
66 newImage->SetExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
67 newImage->SetNumberOfScalarComponents(1);
68 newImage->AllocateScalars();
70 memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
71 for (i=0; i<sizeX; i++)
73 newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
74 newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
81 void GetXCoherentInfoGdcmReader::Process()
84 // Read the *first* image file (a SET of file names is given as input)
85 f = GDCM_NAME_SPACE::File::New();
87 if ( bbGetInputIn().size()!=0 )
89 f->SetFileName( bbGetInputIn()[0] );
97 printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
99 bbSetOutputOut( CreateDefaultImage() );
102 // Get info from the first image file
104 std::vector<double> v_iop;
106 f->GetImageOrientationPatient(iop);
110 v_iop.push_back(iop[i]);
112 bbSetOutputIOP(v_iop );
114 std::vector<double> v_ipp;
116 f->GetImagePositionPatient(ipp);
120 v_ipp.push_back(ipp[i]);
122 bbSetOutputIPP(v_ipp );
124 // Add *all the files* to the SerieHelper
125 sh = GDCM_NAME_SPACE::SerieHelper::New();
126 std::vector<std::string> gii = bbGetInputIn();
128 for(std::vector<std::string>::iterator it = gii.begin();
132 sh->AddFileName(*it);
136 GDCM_NAME_SPACE::FileList::const_iterator it;
137 GDCM_NAME_SPACE::FileList *l;
139 // Should only contain one!
140 l = sh->GetFirstSingleSerieUIDFileSet();
142 double zspacing = 0.;
143 sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
144 zspacing = sh->GetZSpacing();
145 std::vector<double> v_pixelspacing;
146 v_pixelspacing.push_back( f->GetXSpacing() );
147 v_pixelspacing.push_back( f->GetYSpacing() );
148 v_pixelspacing.push_back( zspacing );
149 // if (f->GetZSize() != 1) {
150 // v_pixelspacing.push_back(f->GetZSpacing());
152 bbSetOutputPixelSpacing(v_pixelspacing);
154 VectorMapInfoDicom vectormapinfodicom;
158 std::string strTagValue; // read on disc
159 int iTag,sizeDicomTagsVector=bbGetInputDicomTags().size();
160 GDCM_NAME_SPACE::FileList::const_iterator iitt = l->begin();
162 for ( ; iitt != l->end(); ++iitt)
164 MapInfoDicom mapinfodicom;
166 for (iTag=0; iTag<sizeDicomTagsVector; iTag++)
168 key = bbGetInputDicomTags()[iTag];
170 if ( (key.size()==10) && (key[0] == 'D') && (key[5] == '_') )
172 sscanf(key.c_str(),"D%04hx_%04hx ",&group,&elem);
174 strTagValue = (*iitt)->GetEntryString(group,elem);
175 mapinfodicom.insert ( std::pair<std::string,std::string>(key,strTagValue) );
178 vectormapinfodicom.push_back( mapinfodicom );
180 bbSetOutputDicomInfo( vectormapinfodicom );
187 reader = vtkGdcmReader::New();
189 //EED 21 mars 2012 FLIP probleme ..PLOP..
190 reader->SetFlipY(false);
193 //reader->SetFileName( bbGetInputIn().c_str() );
194 reader->SetCoherentFileList(l);
196 bbSetOutputOut( reader->GetOutput() );
201 #if defined USE_GDCM2
202 void GetXCoherentInfoGdcmReader::Process()
204 // Read the *first* image file (a SET of file names is given as input)
205 gdcm::Reader *read = new gdcm::Reader();
206 reader->SetFileName( bbGetInputIn()[0].c_str() );
208 bool res = read->Read();
212 bbSetOutputOut(NULL);
218 // Get info from the first image file
219 const gdcm::File &f = read->GetFile();
221 std::vector<double> v_iop;
222 const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
223 std::stringstream ss;
224 deIop.GetValue().Print(ss);
225 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
228 v_iop.push_back((float)(iop[i]));
229 bbSetOutputIOP(v_iop );
231 std::vector<double> v_ipp;
232 const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
233 deIpp.GetValue().Print(ss);
234 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
237 v_ipp.push_back((float)(ipp[i]));
238 bbSetOutputIPP(v_ipp );
240 // Add *all the files* to the IPPsorter
242 s.SetComputeZSpacing( true );
243 s.SetZSpacingTolerance( 1e-3 );
244 std::vector<std::string> gii = bbGetInputIn();
247 //l = sh->GetFirstSingleSerieUIDFileSet();
248 // no Test if we have multiple series
252 double zspacing = 0.;
253 zspacing = s.GetZSpacing();
254 std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
255 v_pixelspacing.push_back( v_pixelspacing[0] );
256 v_pixelspacing.push_back( v_pixelspacing[1] );
257 v_pixelspacing.push_back( zspacing );
258 bbSetOutputPixelSpacing(v_pixelspacing);
265 reader = vtkGDCMImageReader::New();
266 vtkStringArray *files = vtkStringArray::New();
267 std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
268 for( ; it != s.GetFilenames().end(); ++it)
270 const std::string &f = *it;
271 files->InsertNextValue( f.c_str() );
273 reader->SetFileNames(files);
275 bbSetOutputOut( reader->GetOutput() );
280 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
282 std::vector<std::string> init;
285 //reader=NULL; /// \TODO fixme JPR
288 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
294 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
305 #if defined USE_GDCM2
306 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
314 // EO namespace bbgdcmvtk