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()
91 // Read the *first* image file (a SET of file names is given as input)
92 f = GDCM_NAME_SPACE::File::New();
94 if ( bbGetInputIn().size()!=0 )
96 f->SetFileName( bbGetInputIn()[0] );
101 bool res = f->Load();
104 printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
106 bbSetOutputOut( CreateDefaultImage() );
109 // Get info from the first image file
111 std::vector<double> v_iop;
113 f->GetImageOrientationPatient(iop);
116 v_iop.push_back(iop[i]);
117 bbSetOutputIOP(v_iop );
119 std::vector<double> v_ipp;
121 f->GetImagePositionPatient(ipp);
124 v_ipp.push_back(ipp[i]);
125 bbSetOutputIPP(v_ipp );
127 // Add *all the files* to the SerieHelper
128 sh = GDCM_NAME_SPACE::SerieHelper::New();
129 std::vector<std::string> gii = bbGetInputIn();
131 for(std::vector<std::string>::iterator it = gii.begin();
135 sh->AddFileName(*it);
139 GDCM_NAME_SPACE::FileList::const_iterator it;
140 GDCM_NAME_SPACE::FileList *l;
142 // Should only contain one!
143 l = sh->GetFirstSingleSerieUIDFileSet();
146 double zspacing = 0.;
147 nbFiles = l->size() ;
148 sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
149 zspacing = sh->GetZSpacing();
150 std::vector<double> v_pixelspacing;
151 v_pixelspacing.push_back( f->GetXSpacing() );
152 v_pixelspacing.push_back( f->GetYSpacing() );
153 v_pixelspacing.push_back( zspacing );
154 // if (f->GetZSize() != 1) {
155 // v_pixelspacing.push_back(f->GetZSpacing());
157 bbSetOutputPixelSpacing(v_pixelspacing);
164 reader = vtkGdcmReader::New();
166 //EED 21 mars 2012 FLIP probleme ..PLOP..
167 reader->SetFlipY(false);
170 //reader->SetFileName( bbGetInputIn().c_str() );
171 reader->SetCoherentFileList(l);
173 bbSetOutputOut( reader->GetOutput() );
178 #if defined USE_GDCM2
179 void GetXCoherentInfoGdcmReader::Process()
181 // Read the *first* image file (a SET of file names is given as input)
182 gdcm::Reader *read = new gdcm::Reader();
183 reader->SetFileName( bbGetInputIn()[0].c_str() );
185 bool res = read->Read();
189 bbSetOutputOut(NULL);
195 // Get info from the first image file
196 const gdcm::File &f = read->GetFile();
198 std::vector<double> v_iop;
199 const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
200 std::stringstream ss;
201 deIop.GetValue().Print(ss);
202 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
205 v_iop.push_back((float)(iop[i]));
206 bbSetOutputIOP(v_iop );
208 std::vector<double> v_ipp;
209 const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
210 deIpp.GetValue().Print(ss);
211 gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
214 v_ipp.push_back((float)(ipp[i]));
216 bbSetOutputIPP(v_ipp );
218 // Add *all the files* to the IPPsorter
220 s.SetComputeZSpacing( true );
221 s.SetZSpacingTolerance( 1e-3 );
222 std::vector<std::string> gii = bbGetInputIn();
225 //l = sh->GetFirstSingleSerieUIDFileSet();
226 // no Test if we have multiple series
230 double zspacing = 0.;
231 zspacing = s.GetZSpacing();
232 std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
233 v_pixelspacing.push_back( v_pixelspacing[0] );
234 v_pixelspacing.push_back( v_pixelspacing[1] );
235 v_pixelspacing.push_back( zspacing );
236 bbSetOutputPixelSpacing(v_pixelspacing);
243 reader = vtkGDCMImageReader::New();
244 vtkStringArray *files = vtkStringArray::New();
245 std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
246 for( ; it != s.GetFilenames().end(); ++it)
248 const std::string &f = *it;
249 files->InsertNextValue( f.c_str() );
251 reader->SetFileNames(files);
253 bbSetOutputOut( reader->GetOutput() );
258 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
260 std::vector<std::string> init;
263 //reader=NULL; /// \TODO fixme JPR
266 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
272 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
283 #if defined USE_GDCM2
284 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
292 // EO namespace bbgdcmvtk