+/*
+# ---------------------------------------------------------------------
+#
+# 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);
+
+
+vtkImageData* GetXCoherentInfoGdcmReader::CreateDefaultImage()
+{
+ int i;
+ int sizeX, sizeY, sizeZ;
+ sizeX = 200;
+ sizeY = sizeX;
+ sizeZ = 1;
+ vtkImageData *newImage = vtkImageData::New();
+ newImage->Initialize();
+ newImage->SetSpacing( 1,1,1 );
+ newImage->SetDimensions( sizeX,sizeY,sizeZ );
+ newImage->SetExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+ newImage->SetWholeExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
+ newImage->SetScalarTypeToUnsignedChar();
+ newImage->SetNumberOfScalarComponents(1);
+ newImage->AllocateScalars();
+ newImage->Update();
+#else
+ newImage->AllocateScalars(VTK_UNSIGNED_CHAR,1);
+#endif
+
+ memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
+ for (i=0; i<sizeX; i++)
+ {
+ newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
+ newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
+ } // for i
+ return newImage;
+}
+
+
+#if defined USE_GDCM
+
+void GetXCoherentInfoGdcmReader::Process2()
+{
+ printf("EED GetXCoherentInfoGdcmReader::Process >>>>>> \n" );
+ GDCM_NAME_SPACE::FileList lstFiles;
+ int i,size=bbGetInputIn().size();
+ for (i=0;i<size;i++)
+ {
+ printf("a: %s\n",bbGetInputIn()[i].c_str() );
+ f = GDCM_NAME_SPACE::File::New();
+ f->SetFileName( bbGetInputIn()[i] );
+ bool res = f->Load();
+ if ( res==true )
+ {
+ lstFiles.push_back(f);
+ }
+ } // for
+ sh = GDCM_NAME_SPACE::SerieHelper::New();
+ sh->ImagePositionPatientOrdering( &lstFiles );
+ size=lstFiles.size();
+ for (i=0;i<size;i++)
+ {
+ printf("d: %s\n", lstFiles[i]->GetFileName().c_str() );
+ } // for
+}
+
+
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] );
+
+ if ( bbGetInputIn().size()!=0 )
+ {
+ f->SetFileName( bbGetInputIn()[0] );
+ } else {
+ f->SetFileName( "" );
+ } // if
+
bool res = f->Load();
if ( !res )
{
- f->Delete();
- bbSetOutputOut(0);
- return;
- }
+ printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
+ f->Delete();
+ bbSetOutputOut( CreateDefaultImage() );
+ return;
+ } // if res
+
// Get info from the first image file
int i;
std::vector<double> v_iop;
float iop[6];
f->GetImageOrientationPatient(iop);
+
for(i=0; i< 6; i++)
+ {
v_iop.push_back(iop[i]);
+ } // for 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 );
+
+// EED 2022-12-15
+// std::vector<double> v_ipp;
+// float ipp[3];
+// f->GetImagePositionPatient(ipp);
+// for(i=0; i< 3; i++)
+// {
+// v_ipp.push_back(ipp[i]);
+// } // for i
+// bbSetOutputIPP(v_ipp );
+
+// EED 2023-01-13
+ GDCM_NAME_SPACE::FileList lstFiles;
+ GDCM_NAME_SPACE::FileList *l;
+ if (bbGetInputRespectSerieUID()==false)
+ {
+ int i,size=bbGetInputIn().size();
+ for (i=0;i<size;i++)
+ {
+ f = GDCM_NAME_SPACE::File::New();
+ f->SetFileName( bbGetInputIn()[i] );
+ bool res = f->Load();
+ if ( res==true )
+ {
+ lstFiles.push_back(f);
+ }
+ } // for i
+ sh = GDCM_NAME_SPACE::SerieHelper::New();
+ l = &lstFiles;
+ sh->ImagePositionPatientOrdering( l );
+ } else{
+ // 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)
+ {
+ sh->AddFileName(*it);
+ } //for vector
+ GDCM_NAME_SPACE::FileList::const_iterator it;
+ // Should only contain one!
+ l = sh->GetFirstSingleSerieUIDFileSet();
+ if (l==NULL)
+ {
+ return;
+ }
+ } // if bbGetInputForceRead
+
+ double zspacing = 0.;
+ 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());
- if (f->GetZSize() != 1) {
- v_pixelspacing.push_back(f->GetZSpacing());
- }
+ 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);
-// 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)
- {
- sh->AddFileName(*it);
- }
+ VectorMapInfoDicom vectormapinfodicom;
+ uint16_t group;
+ uint16_t elem;
+ std::string key;
+ std::string strTagValue; // read on disc
+ int iTag,sizeDicomTagsVector=bbGetInputDicomTags().size();
+ GDCM_NAME_SPACE::FileList::const_iterator iitt = l->begin();
+ float px,py,pz;
+
+ std::vector<std::string> lstFileNames;
+
+ for ( ; iitt != l->end(); ++iitt)
+ {
+ lstFileNames.push_back( (*iitt)->GetFileName() );
+ // EED 2022-12-15
+ if ( iitt == l->begin() ) // The first ordered element IPP
+ {
+ group = 0;
+ elem = 0;
+ strTagValue = std::string("void");
+ sscanf("D0020_0032","D%04hx_%04hx",&group,&elem);
+ strTagValue = (*iitt)->GetEntryString(group,elem);
+ sscanf(strTagValue.c_str(),"%f\\%f\\%f\\%f", &px , &py , &pz);
+ std::vector<double> v_ipp;
+ v_ipp.push_back( (double)px );
+ v_ipp.push_back( (double)py );
+ v_ipp.push_back( (double)pz );
+ bbSetOutputIPP(v_ipp );
+ } // if first elemetn get IPP
+
+ MapInfoDicom mapinfodicom;
+ for (iTag=0; iTag<sizeDicomTagsVector; iTag++)
+ {
+ key = bbGetInputDicomTags()[iTag];
+ group = elem = 0;
+ if ( (key.size()==10) && (key[0] == 'D') && (key[5] == '_') )
+ {
+ sscanf(key.c_str(),"D%04hx_%04hx ",&group,&elem);
+ }// if key
+ strTagValue = (*iitt)->GetEntryString(group,elem);
+ mapinfodicom.insert ( std::pair<std::string,std::string>(key,strTagValue) );
+ } // for iTag
+ vectormapinfodicom.push_back( mapinfodicom );
+ } // for iitt
+ bbSetOutputDicomInfo( vectormapinfodicom );
+ bbSetOutputOutFileNames( lstFileNames );
- GDCM_NAME_SPACE::FileList::const_iterator it;
- GDCM_NAME_SPACE::FileList *l;
+ if (bbGetInputReadRaw()==true)
+ {
+ if (reader!=NULL)
+ {
+ reader->Delete();
+ reader = NULL;
+ }
+ reader = vtkGdcmReader::New();
+ //EED 21 mars 2012 FLIP probleme ..PLOP..
+ reader->SetFlipY(false);
+ //reader->SetFileName( bbGetInputIn().c_str() );
+ reader->SetCoherentFileList(l);
+ reader->Update();
+ reader->GetOutput();
+ bbSetOutputOut( reader->GetOutput() );
+ } // if bGetInputReadRaw
+}
+#endif
+// endif USE_GDCM
- // ==================== Just to see ==============================
- std::cout << std::endl << " ---------------------------------------- Recap"
- << std::endl;
- l = sh->GetFirstSingleSerieUIDFileSet();
- while (l)
+#if defined USE_GDCM2
+void GetXCoherentInfoGdcmReader::Process()
+{
+// printf("GetXCoherentInfoGdcmReader %d files.\n", bbGetInputIn().size() );
+ // 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(NULL);
+ 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++)
{
- it = l->begin();
- std::cout << "SerieUID [" << (*it)->GetEntryString(0x0020,0x000e) <<"] Serie Description ["
- << (*it)->GetEntryString(0x0008,0x103e) << "] "
- << " : " << l->size() << " files" << std::endl;
- l = sh->GetNextSingleSerieUIDFileSet();
+ v_iop.push_back((float)(iop[i]));
}
- std::cout << " ----------------------------------------End Recap"
- << std::endl << std::endl;
-
- if(l->size() > 1)
- std::cout << " --------------------------- More than ONE Serie UID ?!?"
- << std::endl << std::endl;
- // ============================================================
+ 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]));
+ } // for 3
+ bbSetOutputIPP(v_ipp );
- // Should only contain one!
- l = sh->GetFirstSingleSerieUIDFileSet();
+// 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);
- int nbFiles;
- double zspacing = 0.;
- nbFiles = l->size() ;
- sh->OrderFileList(l);
- zspacing = sh->GetZSpacing();
+ //l = sh->GetFirstSingleSerieUIDFileSet();
+ // no Test if we have multiple series
+ //s.GetFilenames();
+ //int nbFiles;
- std::cout << "GetZSpacing() of sorted SingleSerieUIDFileSet "
- << "from GDCM_NAME_SPACE::SerieHelper: " << zspacing << std::endl;
- std::cout << " ('-1' means all the files have the same position)" << std::endl;
+ 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);
- bbSetOutputInterSlice(zspacing);
-
-
- reader = vtkGdcmReader::New();
- //reader->SetFileName( bbGetInputIn().c_str() );
- reader->SetCoherentFileList(l);
+ 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();
-
- vtkIndent indent ;
- reader->GetOutput()->PrintSelf(std::cout, indent);
bbSetOutputOut( reader->GetOutput() );
}
+#endif
+// endif USE_GDCM2
-void GetXCoherentInfoGdcmReader::bbUserConstructor()
+void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
{
- std::vector<std::string> init;
- init.push_back("");
- bbSetInputIn(init);
+ reader=NULL;
+ std::vector<std::string> init;
+ init.push_back("");
+ bbSetInputIn(init);
+ bbSetInputReadRaw(true);
+ bbSetInputRespectSerieUID(true);
+ //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 reader
if(f)
+ {
f->Delete();
+ } // if f
if(sh)
+ {
sh->Delete();
+ } // if sh
}
+#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