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);
52 void GetXCoherentInfoGdcmReader::Process()
54 // Read the *first* image file (a SET of file names is given as input)
55 f = GDCM_NAME_SPACE::File::New();
56 f->SetFileName( bbGetInputIn()[0] );
64 // Get info from the first image file
66 std::vector<double> v_iop;
68 f->GetImageOrientationPatient(iop);
71 v_iop.push_back(iop[i]);
72 bbSetOutputIOP(v_iop );
74 std::vector<double> v_ipp;
76 f->GetImagePositionPatient(ipp);
79 v_ipp.push_back(ipp[i]);
80 bbSetOutputIPP(v_ipp );
82 // Add *all the files* to the SerieHelper
83 sh = GDCM_NAME_SPACE::SerieHelper::New();
84 std::vector<std::string> gii = bbGetInputIn();
86 for(std::vector<std::string>::iterator it = gii.begin();
93 GDCM_NAME_SPACE::FileList::const_iterator it;
94 GDCM_NAME_SPACE::FileList *l;
96 // Should only contain one!
97 l = sh->GetFirstSingleSerieUIDFileSet();
100 double zspacing = 0.;
101 nbFiles = l->size() ;
102 sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
103 zspacing = sh->GetZSpacing();
104 std::vector<double> v_pixelspacing;
105 v_pixelspacing.push_back( f->GetXSpacing() );
106 v_pixelspacing.push_back( f->GetYSpacing() );
107 v_pixelspacing.push_back( zspacing );
108 // if (f->GetZSize() != 1) {
109 // v_pixelspacing.push_back(f->GetZSpacing());
111 bbSetOutputPixelSpacing(v_pixelspacing);
118 reader = vtkGdcmReader::New();
120 //EED 21 mars 2012 FLIP probleme ..PLOP..
121 reader->SetFlipY(false);
124 //reader->SetFileName( bbGetInputIn().c_str() );
125 reader->SetCoherentFileList(l);
129 bbSetOutputOut( reader->GetOutput() );
134 #if defined USE_GDCM2
135 void GetXCoherentInfoGdcmReader::Process()
137 // Read the *first* image file (a SET of file names is given as input)
138 gdcm::Reader *read = new gdcm::Reader();
139 reader->SetFileName( bbGetInputIn()[0].c_str() );
141 bool res = read->Read();
145 printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
146 bbSetOutputOut(NULL);
152 // Get info from the first image file
153 const gdcm::File &f = read->GetFile();
155 std::vector<double> v_iop;
156 const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
157 std::stringstream ss;
158 deIop.GetValue().Print(ss);
159 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
162 v_iop.push_back((float)(iop[i]));
163 bbSetOutputIOP(v_iop );
165 std::vector<double> v_ipp;
166 const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
167 deIpp.GetValue().Print(ss);
168 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
171 v_ipp.push_back((float)(ipp[i]));
172 bbSetOutputIPP(v_ipp );
174 // Add *all the files* to the IPPsorter
176 s.SetComputeZSpacing( true );
177 s.SetZSpacingTolerance( 1e-3 );
178 std::vector<std::string> gii = bbGetInputIn();
181 //l = sh->GetFirstSingleSerieUIDFileSet();
182 // no Test if we have multiple series
186 double zspacing = 0.;
187 zspacing = s.GetZSpacing();
188 std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
189 v_pixelspacing.push_back( v_pixelspacing[0] );
190 v_pixelspacing.push_back( v_pixelspacing[1] );
191 v_pixelspacing.push_back( zspacing );
192 bbSetOutputPixelSpacing(v_pixelspacing);
199 reader = vtkGDCMImageReader::New();
200 vtkStringArray *files = vtkStringArray::New();
201 std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
202 for( ; it != s.GetFilenames().end(); ++it)
204 const std::string &f = *it;
205 files->InsertNextValue( f.c_str() );
207 reader->SetFileNames(files);
209 bbSetOutputOut( reader->GetOutput() );
214 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
216 std::vector<std::string> init;
219 //reader=NULL; /// \TODO fixme JPR
222 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
228 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
239 #if defined USE_GDCM2
240 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
248 // EO namespace bbgdcmvtk