#3326 BBTK Feature New Normal - gdcm vtk GetXCoherentInfoGdcmReader box option...

[bbtk.git] / packages / gdcmvtk / src / bbgdcmvtkGetXCoherentInfoGdcmReader.cxx

diff --git a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
index 197ed037997da829b0de5672b6af03575e0bc767..2bbf54205c3d2cb9b3e58a091ea1a840de45d107 100644 (file)
--- 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<sizeX; i++)
        {
@@ -80,7 +87,6 @@ vtkImageData* GetXCoherentInfoGdcmReader::CreateDefaultImage()
 #if defined USE_GDCM
 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 +95,8 @@ void GetXCoherentInfoGdcmReader::Process()
                f->SetFileName( bbGetInputIn()[0] );
        } else {
                f->SetFileName( "" );
-       }
-   
+       } // if
+
    bool res = f->Load();  
    if ( !res )
    {
@@ -98,7 +104,8 @@ void GetXCoherentInfoGdcmReader::Process()
        f->Delete();
        bbSetOutputOut( CreateDefaultImage() );
        return;
-   }
+   } // if res
+
  // Get info from the first image file
    int i;
    std::vector<double> v_iop;
@@ -106,7 +113,9 @@ void GetXCoherentInfoGdcmReader::Process()
    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;
@@ -114,20 +123,21 @@ void GetXCoherentInfoGdcmReader::Process()
    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
    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;
    GDCM_NAME_SPACE::FileList *l;
@@ -135,11 +145,14 @@ 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); // this one should compute the *actual* Z Spacing!
-   zspacing = sh->GetZSpacing();
+   zspacing            = sh->GetZSpacing();
    std::vector<double> v_pixelspacing;
    v_pixelspacing.push_back( f->GetXSpacing() );
    v_pixelspacing.push_back( f->GetYSpacing() );
@@ -149,21 +162,50 @@ void GetXCoherentInfoGdcmReader::Process()
 //   }
    bbSetOutputPixelSpacing(v_pixelspacing);
 
-   if (reader!=NULL)
-   { 
-      reader->Delete();
-      reader=NULL;
-   }
-   reader = vtkGdcmReader::New();
-       
-       //EED 21 mars 2012  FLIP probleme  ..PLOP..
-       reader->SetFlipY(false);
+       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 ++;
 
-       
-   //reader->SetFileName( bbGetInputIn().c_str() );
-   reader->SetCoherentFileList(l);
-   reader->Update();
-   bbSetOutputOut( reader->GetOutput() );
+       for ( ; iitt != l->end(); ++iitt)
+       {
+               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 );
+
+       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
@@ -174,7 +216,6 @@ 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 )
        {
@@ -183,8 +224,6 @@ void GetXCoherentInfoGdcmReader::Process()
        return;
        }
     
-
-
  // Get info from the first image file
    const gdcm::File &f = read->GetFile();
    int i;
@@ -195,16 +234,20 @@ void GetXCoherentInfoGdcmReader::Process()
    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]));
+   {
+       v_iop.push_back((float)(iop[i]));
+   }
    bbSetOutputIOP(v_iop );
  
-  std::vector<double> v_ipp;
+   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++)
+   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
@@ -249,9 +292,11 @@ void GetXCoherentInfoGdcmReader::Process()
 
 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
 {
+   reader=NULL;
    std::vector<std::string> init;
    init.push_back("");
    bbSetInputIn(init);  
+   bbSetInputReadRaw(true);  
    //reader=NULL;   /// \TODO fixme JPR
 }
 
@@ -264,11 +309,17 @@ void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 {
    if(reader)
+       {
       reader->Delete();
+       } // if reader
    if(f)
+       {
       f->Delete();
+       } // if f
    if(sh)
+       {
       sh->Delete();      
+       } // if sh
 }
 #endif
 
@@ -276,7 +327,9 @@ void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 {
    if(reader)
+       {
       reader->Delete();
+       }
 }
 #endif