X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=packages%2Fgdcmvtk%2Fsrc%2FbbgdcmvtkGetXCoherentInfoGdcmReader.cxx;h=2bbf54205c3d2cb9b3e58a091ea1a840de45d107;hb=1709248f43dcb7745909d1d59109f553ee0ae700;hp=924048da37c094762fd710d6d33e8ef065af8275;hpb=64953af6e7389a36c4fb533b58bf720ba1342cd7;p=bbtk.git diff --git a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx index 924048d..2bbf542 100644 --- a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx +++ b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx @@ -1,55 +1,143 @@ +/* +# --------------------------------------------------------------------- +# +# 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 +#if defined USE_GDCM + #include "gdcmFileHelper.h" +#endif + +#if defined USE_GDCM2 + #include + #include + #include + #include + #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; iSetScalarComponentFromDouble(i,i,0, 0, 255 ); + newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 ); + } // for i + return newImage; +} + + +#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] ); + + 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 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 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 ); - -// Add all the files to the SerieHelper +// Add *all the files* to the SerieHelper sh = GDCM_NAME_SPACE::SerieHelper::New(); std::vector gii = bbGetInputIn(); + for(std::vector::iterator it = gii.begin(); it != gii.end(); ++it) { sh->AddFileName(*it); - } + } //for vector GDCM_NAME_SPACE::FileList::const_iterator it; GDCM_NAME_SPACE::FileList *l; @@ -57,43 +145,159 @@ void GetXCoherentInfoGdcmReader::Process() // Should only contain one! l = sh->GetFirstSingleSerieUIDFileSet(); - int nbFiles; + if (l==NULL) + { + return; + } + double zspacing = 0.; - nbFiles = l->size() ; - sh->OrderFileList(l); - zspacing = sh->GetZSpacing(); + sh->OrderFileList(l); // this one should compute the *actual* Z Spacing! + zspacing = sh->GetZSpacing(); + std::vector 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); + + 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(); + //iitt ++; + + for ( ; iitt != l->end(); ++iitt) + { + MapInfoDicom mapinfodicom; + for (iTag=0; iTagGetEntryString(group,elem); + mapinfodicom.insert ( std::pair(key,strTagValue) ); + } // for iTag + + vectormapinfodicom.push_back( mapinfodicom ); + } // for iitt + bbSetOutputDicomInfo( vectormapinfodicom ); + + 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 + +#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(NULL); + return; + } + + // Get info from the first image file + const gdcm::File &f = read->GetFile(); + int i; + std::vector v_iop; + const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037)); + std::stringstream ss; + deIop.GetValue().Print(ss); + gdcm::Element iop; + iop.Read( ss ); + for(i=0; i< 6; i++) + { + v_iop.push_back((float)(iop[i])); + } + bbSetOutputIOP(v_iop ); + + std::vector v_ipp; + const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032))); + deIpp.GetValue().Print(ss); + gdcm::Element ipp; + ipp.Read( ss ); + for(i=0; i< 3; i++) + { + v_ipp.push_back((float)(ipp[i])); + } // for 3 + bbSetOutputIPP(v_ipp ); + +// Add *all the files* to the IPPsorter + gdcm::IPPSorter s; + s.SetComputeZSpacing( true ); + s.SetZSpacingTolerance( 1e-3 ); + std::vector gii = bbGetInputIn(); + s.Sort(gii); + + //l = sh->GetFirstSingleSerieUIDFileSet(); + // no Test if we have multiple series + //s.GetFilenames(); + //int nbFiles; - std::vector v_pixelspacing; - v_pixelspacing.push_back( f->GetXSpacing() ); - v_pixelspacing.push_back( f->GetYSpacing() ); + double zspacing = 0.; + zspacing = s.GetZSpacing(); + std::vector 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 ); -// if (f->GetZSize() != 1) { -// v_pixelspacing.push_back(f->GetZSpacing()); -// } bbSetOutputPixelSpacing(v_pixelspacing); - - - if (reader!=NULL) - { - reader->Delete(); - reader=NULL; - } - 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(); - bbSetOutputOut( reader->GetOutput() ); } +#endif +// endif USE_GDCM2 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues() { - std::vector init; - init.push_back(""); - bbSetInputIn(init); - reader=NULL; + reader=NULL; + std::vector init; + init.push_back(""); + bbSetInputIn(init); + bbSetInputReadRaw(true); + //reader=NULL; /// \TODO fixme JPR } void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing() @@ -101,17 +305,33 @@ void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing() } +#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(); + } } +#endif } // EO namespace bbgdcmvtk - -