X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=packages%2Fgdcmvtk%2Fsrc%2FbbgdcmvtkGetXCoherentInfoGdcmReader.cxx;h=25700ecdd80ce3d34c415c07e44265ced2a230d2;hb=d3acb61552eab12e25d95d72b7b7250c984bf22e;hp=faabc03cf6eca63b458e6c3cfe119ddf5864f823;hpb=fef49cf06296bb65a839585dba63f282a89d91fc;p=bbtk.git diff --git a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx index faabc03..25700ec 100644 --- a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx +++ b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx @@ -59,14 +59,21 @@ vtkImageData* GetXCoherentInfoGdcmReader::CreateDefaultImage() sizeZ = 1; vtkImageData *newImage = vtkImageData::New(); newImage->Initialize(); - newImage->SetScalarTypeToUnsignedChar(); newImage->SetSpacing( 1,1,1 ); newImage->SetDimensions( sizeX,sizeY,sizeZ ); - newImage->SetWholeExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 ); 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>>>>> \n" ); + GDCM_NAME_SPACE::FileList lstFiles; + int i,size=bbGetInputIn().size(); + for (i=0;iSetFileName( 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;iGetFileName().c_str() ); + } // for +} + +void GetXCoherentInfoGdcmReader::Process() +{ // Read the *first* image file (a SET of file names is given as input) f = GDCM_NAME_SPACE::File::New(); @@ -89,8 +122,8 @@ void GetXCoherentInfoGdcmReader::Process() f->SetFileName( bbGetInputIn()[0] ); } else { f->SetFileName( "" ); - } - + } // if + bool res = f->Load(); if ( !res ) { @@ -98,7 +131,8 @@ void GetXCoherentInfoGdcmReader::Process() f->Delete(); bbSetOutputOut( CreateDefaultImage() ); return; - } + } // if res + // Get info from the first image file int i; std::vector v_iop; @@ -108,40 +142,61 @@ void GetXCoherentInfoGdcmReader::Process() 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]); - } - bbSetOutputIPP(v_ipp ); - -// 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); - } - - - GDCM_NAME_SPACE::FileList::const_iterator it; - GDCM_NAME_SPACE::FileList *l; - - // Should only contain one! - l = sh->GetFirstSingleSerieUIDFileSet(); - + +// EED 2022-12-15 +// 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 ); + +// 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;iSetFileName( 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 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; + // 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(); + zspacing = sh->GetZSpacing(); std::vector v_pixelspacing; v_pixelspacing.push_back( f->GetXSpacing() ); v_pixelspacing.push_back( f->GetYSpacing() ); @@ -158,11 +213,30 @@ void GetXCoherentInfoGdcmReader::Process() 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) + float px,py,pz; + + std::vector 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 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; iTagGetEntryString(group,elem); mapinfodicom.insert ( std::pair(key,strTagValue) ); } // for iTag - vectormapinfodicom.push_back( mapinfodicom ); } // for iitt bbSetOutputDicomInfo( vectormapinfodicom ); + bbSetOutputOutFileNames( lstFileNames ); - 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(); - bbSetOutputOut( reader->GetOutput() ); + 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() { +// 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 ) { @@ -213,8 +289,6 @@ void GetXCoherentInfoGdcmReader::Process() return; } - - // Get info from the first image file const gdcm::File &f = read->GetFile(); int i; @@ -225,16 +299,20 @@ void GetXCoherentInfoGdcmReader::Process() gdcm::Element iop; iop.Read( ss ); for(i=0; i< 6; i++) - v_iop.push_back((float)(iop[i])); + { + v_iop.push_back((float)(iop[i])); + } bbSetOutputIOP(v_iop ); - std::vector v_ipp; + 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++) + 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 @@ -279,26 +357,34 @@ void GetXCoherentInfoGdcmReader::Process() void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues() { + reader=NULL; std::vector init; init.push_back(""); bbSetInputIn(init); + bbSetInputReadRaw(true); + bbSetInputRespectSerieUID(true); //reader=NULL; /// \TODO fixme JPR } 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 @@ -306,7 +392,9 @@ void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing() void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing() { if(reader) + { reader->Delete(); + } } #endif