+# ---------------------------------------------------------------------
+#
+# Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
+# pour la SantÈ)
+# Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
+# Previous Authors : Laurent Guigues, Jean-Pierre Roux
+# CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
+#
+# This software is governed by the CeCILL-B license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL-B
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+# or in the file LICENSE.txt.
+#
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL-B license and that you accept its terms.
+# ------------------------------------------------------------------------ */
+
#include "bbgdcmvtkGetXCoherentInfoGdcmReader.h"
#include "bbgdcmvtkPackage.h"
#include "gdcmFile.h"
-#include "gdcmFileHelper.h"
#include "vtkImageData.h"
-#include "vtkGdcmReader.h"
#include <vtkIndent.h>
+#if defined USE_GDCM
+ #include "gdcmFileHelper.h"
+#endif
+
+#if defined USE_GDCM2
+ #include <gdcmReader.h>
+ #include <gdcmImageHelper.h>
+ #include <gdcmIPPSorter.h>
+ #include <vtkGDCMImageReader.h>
+ #include "vtkStringArray.h"
+#endif
+
namespace bbgdcmvtk
{
BBTK_ADD_BLACK_BOX_TO_PACKAGE(gdcmvtk,GetXCoherentInfoGdcmReader)
BBTK_BLACK_BOX_IMPLEMENTATION(GetXCoherentInfoGdcmReader,bbtk::AtomicBlackBox);
+#if defined USE_GDCM
void GetXCoherentInfoGdcmReader::Process()
{
- // Read the first image file
+ // Read the *first* image file (a SET of file names is given as input)
f = GDCM_NAME_SPACE::File::New();
f->SetFileName( bbGetInputIn()[0] );
bool res = f->Load();
std::vector<double> v_iop;
float iop[6];
f->GetImageOrientationPatient(iop);
+
for(i=0; i< 6; i++)
v_iop.push_back(iop[i]);
bbSetOutputIOP(v_iop );
std::vector<double> v_ipp;
float ipp[3];
f->GetImagePositionPatient(ipp);
+
for(i=0; i< 3; i++)
v_ipp.push_back(ipp[i]);
bbSetOutputIPP(v_ipp );
-
-// Add all the files to the SerieHelper
+// Add *all the files* to the SerieHelper
sh = GDCM_NAME_SPACE::SerieHelper::New();
std::vector<std::string> gii = bbGetInputIn();
+
for(std::vector<std::string>::iterator it = gii.begin();
it != gii.end();
++it)
int nbFiles;
double zspacing = 0.;
nbFiles = l->size() ;
- sh->OrderFileList(l);
+ sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
zspacing = sh->GetZSpacing();
-
- std::vector<double> v_pixelspacing;
- v_pixelspacing.push_back( f->GetXSpacing() );
- v_pixelspacing.push_back( f->GetYSpacing() );
- v_pixelspacing.push_back( zspacing );
-// if (f->GetZSize() != 1) {
-// v_pixelspacing.push_back(f->GetZSpacing());
-// }
- bbSetOutputPixelSpacing(v_pixelspacing);
-
+ std::vector<double> v_pixelspacing;
+ v_pixelspacing.push_back( f->GetXSpacing() );
+ v_pixelspacing.push_back( f->GetYSpacing() );
+ v_pixelspacing.push_back( zspacing );
+// if (f->GetZSize() != 1) {
+// v_pixelspacing.push_back(f->GetZSpacing());
+// }
+ bbSetOutputPixelSpacing(v_pixelspacing);
+
+ if (reader!=NULL)
+ {
+ reader->Delete();
+ reader=NULL;
+ }
+ reader = vtkGdcmReader::New();
+ //EED 21 mars 2012 FLIP probleme ..PLOP..
+ reader->SetFlipY(false);
-
- reader = vtkGdcmReader::New();
+
//reader->SetFileName( bbGetInputIn().c_str() );
reader->SetCoherentFileList(l);
reader->Update();
bbSetOutputOut( reader->GetOutput() );
}
+#endif
+// endif USE_GDCM
+
+#if defined USE_GDCM2
+void GetXCoherentInfoGdcmReader::Process()
+{
+ // Read the *first* image file (a SET of file names is given as input)
+ gdcm::Reader *read = new gdcm::Reader();
+ reader->SetFileName( bbGetInputIn()[0].c_str());
+
+ bool res = read->Read();
+ if ( !res )
+ {
+ delete read;
+ bbSetOutputOut(0);
+ return;
+ }
+
+ // Get info from the first image file
+ const gdcm::File &f = read->GetFile();
+ int i;
+ std::vector<double> v_iop;
+ const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
+ std::stringstream ss;
+ deIop.GetValue().Print(ss);
+ gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
+ iop.Read( ss );
+ for(i=0; i< 6; i++)
+ v_iop.push_back((float)(iop[i]));
+ bbSetOutputIOP(v_iop );
+
+ std::vector<double> v_ipp;
+ const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
+ deIpp.GetValue().Print(ss);
+ gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
+ ipp.Read( ss );
+ for(i=0; i< 3; i++)
+ v_ipp.push_back((float)(ipp[i]));
+ bbSetOutputIPP(v_ipp );
+
+// Add *all the files* to the IPPsorter
+ gdcm::IPPSorter s;
+ s.SetComputeZSpacing( true );
+ s.SetZSpacingTolerance( 1e-3 );
+ std::vector<std::string> gii = bbGetInputIn();
+ s.Sort(gii);
+
+ //l = sh->GetFirstSingleSerieUIDFileSet();
+ // no Test if we have multiple series
+ //s.GetFilenames();
+ //int nbFiles;
+
+ double zspacing = 0.;
+ zspacing = s.GetZSpacing();
+ std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
+ v_pixelspacing.push_back( v_pixelspacing[0] );
+ v_pixelspacing.push_back( v_pixelspacing[1] );
+ v_pixelspacing.push_back( zspacing );
+ bbSetOutputPixelSpacing(v_pixelspacing);
+
+ if (reader!=NULL)
+ {
+ reader->Delete();
+ reader=NULL;
+ }
+ reader = vtkGDCMImageReader::New();
+ vtkStringArray *files = vtkStringArray::New();
+ std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
+ for( ; it != s.GetFilenames().end(); ++it)
+ {
+ const std::string &f = *it;
+ files->InsertNextValue( f.c_str() );
+ }
+ reader->SetFileNames(files);
+ reader->Update();
+ reader->GetOutput();
+ bbSetOutputOut( reader->GetOutput() );
+}
+#endif
+// endif USE_GDCM2
-void GetXCoherentInfoGdcmReader::bbUserConstructor()
+void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
{
- std::vector<std::string> init;
- init.push_back("");
- bbSetInputIn(init);
+ std::vector<std::string> init;
+ init.push_back("");
+ bbSetInputIn(init);
+ //reader=NULL; /// \TODO fixme JPR
}
-void GetXCoherentInfoGdcmReader::bbUserCopyConstructor(bbtk::BlackBox::Pointer)
+void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
{
-
+
}
-void GetXCoherentInfoGdcmReader::bbUserDestructor()
+#if defined USE_GDCM
+void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
{
if(reader)
reader->Delete();
if(sh)
sh->Delete();
}
+#endif
+#if defined USE_GDCM2
+void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
+{
+ if(reader)
+ reader->Delete();
}
-// EO namespace bbgdcmvtk
-
+#endif
+}
+// EO namespace bbgdcmvtk
git://git.creatis.insa-lyon.fr / bbtk.git / blobdiff