Applications/Cxx/gdcmdump.cxx

@@ -816,7 +816,7 @@ static int PrintPDB(const std::string & filename, bool verbose)
     }
   if( !found )
     {
-    std::cout << "no pdb tag found" << std::endl;
+    std::cerr << "no pdb tag found" << std::endl;
     ret = 1;
     }
 
@@ -901,7 +901,7 @@ static int PrintCSA(const std::string & filename)
     found = true;
     if( csa.GetFormat() == gdcm::CSAHeader::ZEROED_OUT )
       {
-      std::cout << "CSA Header has been zero-out (contains only 0)" << std::endl;
+      std::cerr << "CSA Header has been zero-out (contains only 0)" << std::endl;
       ret = 1;
       }
     else if( csa.GetFormat() == gdcm::CSAHeader::DATASET_FORMAT )
@@ -920,7 +920,7 @@ static int PrintCSA(const std::string & filename)
     found = true;
     if( csa.GetFormat() == gdcm::CSAHeader::ZEROED_OUT )
       {
-      std::cout << "CSA Header has been zero-out (contains only 0)" << std::endl;
+      std::cerr << "CSA Header has been zero-out (contains only 0)" << std::endl;
       ret = 1;
       }
     else if( csa.GetFormat() == gdcm::CSAHeader::DATASET_FORMAT )
@@ -939,7 +939,7 @@ static int PrintCSA(const std::string & filename)
     found = true;
     if( csa.GetFormat() == gdcm::CSAHeader::ZEROED_OUT )
       {
-      std::cout << "CSA Header has been zero-out (contains only 0)" << std::endl;
+      std::cerr << "CSA Header has been zero-out (contains only 0)" << std::endl;
       ret = 1;
       }
     else if( csa.GetFormat() == gdcm::CSAHeader::INTERFILE )
@@ -958,7 +958,7 @@ static int PrintCSA(const std::string & filename)
     }
   if( !found )
     {
-    std::cout << "no csa tag found" << std::endl;
+    std::cerr << "no csa tag found" << std::endl;
     ret = 1;
     }
 

Applications/Cxx/gdcmscu.cxx

@@ -283,6 +283,7 @@ int main(int argc, char *argv[])
             std::string str;
             //ss >> str;
             std::getline(ss, str); // do not skip whitespace
+            if( str.size() % 2 == 1 ) str += " ";
             keys.push_back( std::make_pair(tag, str) );
           }
           else if( option_index == 20 ) /* port-scp */

CMakeLists.txt

@@ -40,7 +40,7 @@ set(GDCM_PACKAGE_CONTACT "GDCM Developers <gdcm-developers@lists.sourceforge.net
 #----------------------------------------------------------------------------
 set(GDCM_MAJOR_VERSION 2)
 set(GDCM_MINOR_VERSION 8)
-set(GDCM_BUILD_VERSION 6)
+set(GDCM_BUILD_VERSION 7)
 set(GDCM_VERSION
   "${GDCM_MAJOR_VERSION}.${GDCM_MINOR_VERSION}.${GDCM_BUILD_VERSION}")
 # let advanced user the option to define GDCM_API_VERSION:

Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -1723,6 +1723,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x07a1,0x002b,"ELSCINT1",VR::CS,VM::VM1,"?",false },
   {0x07a1,0x0036,"ELSCINT1",VR::AE,VM::VM1,"Tamar Source Ae",false },
   {0x07a1,0x0040,"ELSCINT1",VR::CS,VM::VM1,"Tamar Study Body Part",false },
+  {0x07a1,0x0042,"ELSCINT1",VR::SH,VM::VM1,"?",false },
   {0x07a1,0x0043,"ELSCINT1",VR::IS,VM::VM1,"?",false },
   {0x07a1,0x0047,"ELSCINT1",VR::CS,VM::VM1,"?orientation?",false },
   {0x07a1,0x0050,"ELSCINT1",VR::US,VM::VM1,"Tamar Site Id",false },
@@ -1737,6 +1738,7 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x07a1,0x0088,"ELSCINT1",VR::US,VM::VM1,"?",false },
   {0x07a1,0x0098,"ELSCINT1",VR::US,VM::VM1,"?",false },
   {0x07a1,0x009f,"ELSCINT1",VR::CS,VM::VM1,"?",false },
+  {0x07a1,0x00d0,"ELSCINT1",VR::LO,VM::VM1,"?",false },
   {0x07a3,0x0001,"ELSCINT1",VR::LO,VM::VM1,"Tamar Exe Software Version",false },
   {0x07a3,0x0003,"ELSCINT1",VR::CS,VM::VM1,"Tamar Study Has Sticky Note",false },
   {0x07a3,0x0005,"ELSCINT1",VR::CS,VM::VM1,"?",false },
@@ -1750,16 +1752,22 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x07a3,0x001c,"ELSCINT1",VR::ST,VM::VM1,"?patient name?",false },
   {0x07a3,0x001d,"ELSCINT1",VR::ST,VM::VM1,"?radiologist name?",false },
   {0x07a3,0x001e,"ELSCINT1",VR::ST,VM::VM1,"?num?",false },
+  {0x07a3,0x001f,"ELSCINT1",VR::ST,VM::VM1,"?",false },
+  {0x07a3,0x0022,"ELSCINT1",VR::ST,VM::VM1,"?",false },
   {0x07a3,0x0023,"ELSCINT1",VR::ST,VM::VM1,"?+sign?",false },
+  {0x07a3,0x0024,"ELSCINT1",VR::ST,VM::VM1,"?",false },
   {0x07a3,0x0034,"ELSCINT1",VR::SH,VM::VM1,"Tamar Study Age",false },
   {0x07a3,0x0043,"ELSCINT1",VR::DS,VM::VM1_n,"?",false },
+  {0x07a3,0x0052,"ELSCINT1",VR::LO,VM::VM1,"?",false },
   {0x07a3,0x0055,"ELSCINT1",VR::SH,VM::VM1,"?",false },
+  {0x07a3,0x005c,"ELSCINT1",VR::ST,VM::VM1,"?",false },
   {0x07a3,0x0061,"ELSCINT1",VR::LT,VM::VM1,"?",false },
   {0x07a3,0x0062,"ELSCINT1",VR::SQ,VM::VM1,"?",false },
   {0x07a3,0x0063,"ELSCINT1",VR::SQ,VM::VM1,"?",false },
   {0x07a3,0x0064,"ELSCINT1",VR::IS,VM::VM1_n,"?",false },
   {0x07a3,0x0065,"ELSCINT1",VR::CS,VM::VM1_n,"?yes/no bool?",false },
   {0x07a3,0x0066,"ELSCINT1",VR::IS,VM::VM1,"?",false },
+  {0x07a3,0x008f,"ELSCINT1",VR::CS,VM::VM1,"?",false },
   {0x07a3,0x0099,"ELSCINT1",VR::CS,VM::VM1,"?yes/no bool?",false },
   {0x07a3,0x009c,"ELSCINT1",VR::CS,VM::VM1,"?yes/no bool?",false },
   {0x07a3,0x009f,"ELSCINT1",VR::CS,VM::VM1,"?",false },
@@ -1779,8 +1787,11 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x07a3,0x00cb,"ELSCINT1",VR::SQ,VM::VM1,"?network seq11?",false },
   {0x07a3,0x00cc,"ELSCINT1",VR::LO,VM::VM1,"Tamar Grid Token Version",false },
   {0x07a5,0x0000,"ELSCINT1",VR::LO,VM::VM1,"?",false },
+  {0x07a5,0x0054,"ELSCINT1",VR::DT,VM::VM1,"?",false },
   {0x07a5,0x0056,"ELSCINT1",VR::CS,VM::VM1,"?",false },
+  {0x07a5,0x0063,"ELSCINT1",VR::CS,VM::VM1_n,"?",false },
   {0x07a5,0x0069,"ELSCINT1",VR::LO,VM::VM1,"?",false },
+  {0x07a5,0x00c8,"ELSCINT1",VR::CS,VM::VM1,"?",false },
   {0x5001,0x0070,"ELSCINT1",VR::SQ,VM::VM1,"?",false },
   {0x5001,0x0071,"ELSCINT1",VR::SH,VM::VM1,"?",false },
   {0x5001,0x0080,"ELSCINT1",VR::SQ,VM::VM1,"?",false },
@@ -6045,7 +6056,9 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x200b,0x0099,"Philips RAD Imaging DD 097",VR::SH,VM::VM1,"?",false },
   {0x200b,0x009a,"Philips RAD Imaging DD 097",VR::FD,VM::VM1,"?",false },
   {0x200b,0x009b,"Philips RAD Imaging DD 097",VR::FD,VM::VM1,"?",false },
+  {0x200b,0x009f,"Philips RAD Imaging DD 097",VR::SQ,VM::VM1,"?",false },
   {0x200b,0x00a0,"Philips RAD Imaging DD 097",VR::LT,VM::VM1,"?",false },
+  {0x200b,0x00a1,"Philips RAD Imaging DD 097",VR::CS,VM::VM1,"?bool?",false },
   {0x0031,0x0030,"Philips US Imaging 60",VR::UL,VM::VM1,"Private data",false },
   {0x0031,0x0031,"Philips US Imaging 60",VR::UL,VM::VM1,"Private data",false },
   {0x200d,0x0005,"Philips US Imaging DD 017",VR::LO,VM::VM1,"?",false },

Source/MediaStorageAndFileFormat/gdcmIPPSorter.cxx

@@ -37,6 +37,25 @@ inline double spacing_round(double n, int d) /* pow is defined as pow( double, d
   return floor(n * pow(10., d) + .5) / pow(10., d);
 }
 
+struct dircos_key {
+  double dircos[6];
+  void read( const std::string & str ) {
+    DirectionCosines dc;
+    dc.SetFromString( str.c_str() );
+    const double * ptr = dc;
+    memcpy( dircos, ptr, sizeof(dircos) );
+  }
+};
+
+struct dircos_comp {
+  bool operator()( dircos_key const & lhs, dircos_key const & rhs ) {
+    const double *iop1 = lhs.dircos;
+    const double *iop2 = rhs.dircos;
+    return std::lexicographical_compare(iop1, iop1+6,
+        iop2, iop2+6);
+  }
+};
+
 bool IPPSorter::Sort(std::vector<std::string> const & filenames)
 {
   // BUG: I cannot clear Filenames since input filenames could also be the output of ourself...
@@ -88,11 +107,22 @@ bool IPPSorter::Sort(std::vector<std::string> const & filenames)
     {
     if( iops.size() != 1 )
       {
-      gdcmDebugMacro( "More than one IOP (or no IOP): " << iops.size() );
-      //std::copy(iops.begin(), iops.end(), std::ostream_iterator<std::string>(std::cout, "\n"));
+      std::set< dircos_key, dircos_comp > s;
+      for( Scanner::ValuesType::const_iterator it = iops.begin(); it != iops.end(); ++it )
+      {
+        dircos_key dk;
+        dk.read( *it );
+        s.insert( dk );
+      }
+      // sometime we want to handle:
+      // iops = {[0] = "1\\0\\0\\0\\1\\-0", [1] = "1\\0\\0\\0\\1\\0 "} 
+      if( s.size() != 1 )
+        {
+        gdcmDebugMacro( "More than one IOP (or no IOP): " << iops.size() << ". Try changing DirCosTolerance"  );
         return false;
         }
       }
+    }
   const size_t fsize = frames.size(); // Should I really tolerate issue with Frame of Reference UID ?
   if( fsize == 1 ) // by the book
     {

Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx

@@ -773,12 +773,12 @@ std::vector<unsigned int> ImageHelper::GetDimensionsValue(const File& f)
 #endif
     {
       {
-      Attribute<0x0028,0x0011> at = { 0 };
+      Attribute<0x0028,0x0011> at = { 0 }; // Columns
       at.SetFromDataSet( ds );
       theReturn[0] = at.GetValue();
       }
       {
-      Attribute<0x0028,0x0010> at = { 0 };
+      Attribute<0x0028,0x0010> at = { 0 }; // Rows
       at.SetFromDataSet( ds );
       theReturn[1] = at.GetValue();
       }

Source/MediaStorageAndFileFormat/gdcmJPEG2000Codec.cxx

@@ -1032,7 +1032,7 @@ opj_image_t* rawtoimage(const char *inputbuffer, opj_cparameters_t *parameters,
     }
   assert( bitsallocated % 8 == 0 );
   // eg. fragment_size == 63532 and 181 * 117 * 3 * 8 == 63531 ...
-  assert( ((fragment_size + 1)/2 ) * 2 == ((image_height * image_width * numcomps * (bitsallocated/8) + 1)/ 2 )* 2 );
+  assert( ((fragment_size + 1)/2 ) * 2 == (((size_t)image_height * image_width * numcomps * (bitsallocated/8) + 1)/ 2 )* 2 );
   int subsampling_dx = parameters->subsampling_dx;
   int subsampling_dy = parameters->subsampling_dy;
 

Source/MediaStorageAndFileFormat/gdcmSplitMosaicFilter.cxx

@@ -16,7 +16,6 @@
 #include "gdcmAttribute.h"
 #include "gdcmImageHelper.h"
 #include "gdcmDirectionCosines.h"
-#include "gdcmAnonymizer.h"
 
 #include <math.h>
 
@@ -48,7 +47,6 @@ static bool reorganize_mosaic(const unsigned short *input, const unsigned int *i
   return true;
 }
 
-#ifdef SNVINVERT
 static bool reorganize_mosaic_invert(const unsigned short *input, const unsigned int *inputdims,
   unsigned int square, const unsigned int *outputdims, unsigned short *output )
 {
@@ -67,7 +65,6 @@ static bool reorganize_mosaic_invert(const unsigned short *input, const unsigned
     }
   return true;
 }
-#endif
 
 }
 
@@ -76,13 +73,60 @@ void SplitMosaicFilter::SetImage(const Image& image)
   I = image;
 }
 
-bool SplitMosaicFilter::ComputeMOSAICDimensions( unsigned int dims[3] )
+bool SplitMosaicFilter::GetAcquisitionSize(unsigned int size[2], DataSet const & ds)
 {
+  bool found = true;
+  /*
+  Dimensions of the acquired frequency /phase data before reconstruction.
+  Multi-valued: frequency rows\frequency columns\phase rows\phase columns.
+   */
+  Attribute<0x0018, 0x1310> acquisitionMatrix;
+  acquisitionMatrix.SetFromDataSet( ds );
+  const unsigned short *pMat = acquisitionMatrix.GetValues();
+  /*
+  The axis of phase encoding with respect to the image.
+
+  Enumerated Values:
+
+  ROW
+  phase encoded in rows.
+
+  COL
+  phase encoded in columns.
+   */
+  Attribute<0x0018, 0x1312> inPlanePhaseEncodingDirection;
+  inPlanePhaseEncodingDirection.SetFromDataSet( ds );
+  CSComp val = inPlanePhaseEncodingDirection.GetValue();
+  std::string dir = val.Trim();
+  // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.3.html
+  if( dir == "COL" )
+    {
+    /* pay attention that size is: { columns  , rows } */
+    // [256\0\0\134]
+    size[0] = pMat[3];
+    size[1] = pMat[0];
+    }
+  else if( dir == "ROW" )
+    {
+    // [0\512\213\0]
+    size[0] = pMat[1];
+    size[1] = pMat[2];
+    }
+  else
+    {
+    size[0] = size[1] = 0;
+    }
+  found = size[0] && size[1];
+  return found;
+}
+
+unsigned int SplitMosaicFilter::GetNumberOfImagesInMosaic( File const & file )
+{
+  unsigned int numberOfImagesInMosaic = 0;
+  DataSet const &ds = file.GetDataSet();
   CSAHeader csa;
-  DataSet& ds = GetFile().GetDataSet();
 
   const PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
-  int numberOfImagesInMosaic = 0;
   if( csa.LoadFromDataElement( ds.GetDataElement( t1 ) ) )
   {
     if( csa.FindCSAElementByName( "NumberOfImagesInMosaic" ) )
@@ -96,7 +140,8 @@ bool SplitMosaicFilter::ComputeMOSAICDimensions( unsigned int dims[3] )
       }
     }
   }
-  else
+  // try harder:
+  if( !numberOfImagesInMosaic )
   {
     // Some weird anonymizer remove the private creator but leave the actual element.
     // oh well, let try harder:
@@ -116,14 +161,62 @@ bool SplitMosaicFilter::ComputeMOSAICDimensions( unsigned int dims[3] )
       }
     }
   }
+
+  std::vector<unsigned int> colrow =
+    ImageHelper::GetDimensionsValue( file );
+
+  // try super harder. Pay attention that trailing black image cannot be removed here.
+  if( !numberOfImagesInMosaic )
+  {
+    unsigned int mosaicSize[2];
+    if( GetAcquisitionSize(mosaicSize, ds) )
+    {
+      if( colrow[0] % mosaicSize[0] == 0 &&
+       colrow[1] % mosaicSize[1] == 0 )
+      {
+        numberOfImagesInMosaic = 
+          colrow[0] / mosaicSize[0] *
+          colrow[1] / mosaicSize[1];
+        // MultiFrame will contain trailing empty slices:
+        gdcmWarningMacro( "NumberOfImagesInMosaic was not found. Volume will be padded with black image." );
+      }
+      else
+      {
+        // assume interpolation:
+        unsigned int mosSize = std::max( mosaicSize[0], mosaicSize[1] );
+        if( colrow[0] % mosSize == 0 &&
+         colrow[1] % mosSize == 0 )
+        {
+          gdcmDebugMacro( "Matrix Acquisition does not match exactly. Using max value." );
+          numberOfImagesInMosaic = 
+            colrow[0] / mosSize *
+            colrow[1] / mosSize;
+          // MultiFrame will contain trailing empty slices:
+          gdcmWarningMacro( "NumberOfImagesInMosaic was not found. Volume will be padded with black image." );
+        }
+        else
+        {
+           gdcmErrorMacro( "NumberOfImagesInMosaic cannot be computed from Img Acq: " << mosaicSize[0] << "," << mosaicSize[1] );
+        }
+      }
+    }
+  }
+  return numberOfImagesInMosaic;
+}
+
+bool SplitMosaicFilter::ComputeMOSAICDimensions( unsigned int dims[3] )
+{
+  unsigned int numberOfImagesInMosaic = GetNumberOfImagesInMosaic( GetFile() );
+
   if( !numberOfImagesInMosaic )
   {
-    gdcmErrorMacro( "Could not find NumberOfImagesInMosaic" );
+    gdcmErrorMacro( "Could not find/compute NumberOfImagesInMosaic" );
     return false;
   }
 
   std::vector<unsigned int> colrow =
     ImageHelper::GetDimensionsValue( GetFile() );
+
   dims[0] = colrow[0];
   dims[1] = colrow[1];
 
@@ -171,12 +264,12 @@ bool SplitMosaicFilter::ComputeMOSAICSliceNormal( double slicenormalvector[3], b
     double z[3];
     dc.Cross (z);
     const double snv_dot = dc.Dot( normal, z );
-    if( (1. - snv_dot) < 1e-6 )
+    if( fabs(1. - snv_dot) < 1e-6 )
     {
       gdcmDebugMacro("Same direction");
       inverted = false;
     }
-    else if( (-1. - snv_dot) < 1e-6 )
+    else if( fabs(-1. - snv_dot) < 1e-6 )
     {
       gdcmWarningMacro("SliceNormalVector is opposite direction");
       inverted = true;
@@ -251,14 +344,19 @@ bool SplitMosaicFilter::Split()
   const unsigned int div = (unsigned int )ceil(sqrt( (double)dims[2]) );
   bool inverted;
   double normal[3];
+  bool hasOriginCSA = true;
+  bool hasNormalCSA = true;
   if( !ComputeMOSAICSliceNormal( normal, inverted ) )
   {
-    return false;
+    gdcmDebugMacro( "Normal will not be accurate" );
+    hasNormalCSA = false;
   }
+  (void)hasNormalCSA;
   double origin[3];
   if( !ComputeMOSAICSlicePosition( origin, inverted ) )
   {
-    return false;
+    gdcmWarningMacro( "Origin will not be accurate" );
+    hasOriginCSA = false;
   }
 
   const Image &inputimage = GetImage();
@@ -277,7 +375,6 @@ bool SplitMosaicFilter::Split()
   outbuf.resize(l);
 
   bool b;
-#ifdef SNVINVERT
   if( inverted )
   {
     b = details::reorganize_mosaic_invert(
@@ -285,7 +382,6 @@ bool SplitMosaicFilter::Split()
         (unsigned short*)&outbuf[0] );
   }
   else
-#endif
   {
     b = details::reorganize_mosaic(
         (unsigned short*)&buf[0], inputimage.GetDimensions(), div, dims,
@@ -312,6 +408,7 @@ bool SplitMosaicFilter::Split()
   image.SetDimension(2, dims[2] );
 
   // Fix origin (direction is ok since we reorganize the tiles):
+  if( hasOriginCSA )
   image.SetOrigin( origin );
 
   PhotometricInterpretation pi;

Source/MediaStorageAndFileFormat/gdcmSplitMosaicFilter.h

@@ -33,6 +33,12 @@ namespace gdcm
  * Siemens CSA Image Header
  * CSA:= Common Siemens Architecture, sometimes also known as Common syngo Architecture
  *
+ * \warning when private attributes are not found, the acquisition matrix is
+ * used to compute the NumberOfImagesInMosaic. This means trailing black slices
+ * will be considered in the volume (instead of discarded).
+ * CSA 0029,1010 is needed for correct NumberOfImagesInMosaic
+ * CSA 0029,1020 is needed to compute the correct origin
+ * without above info default are taken (may not be accurate).
  */
 class GDCM_EXPORT SplitMosaicFilter
 {
@@ -61,6 +67,12 @@ public:
   File &GetFile() { return *F; }
   const File &GetFile() const { return *F; }
 
+  /// Get the Acquisition Matrix (non zero value):
+  static bool GetAcquisitionSize(unsigned int size[2], DataSet const & ds);
+
+  /// Return the value for NumberOfImagesInMosaic, or compute it from Acquisition Size
+  static unsigned int GetNumberOfImagesInMosaic( File const & file );
+
 protected:
 
 private:

Utilities/VTK/vtkGDCMPolyDataWriter.cxx

@@ -586,7 +586,11 @@ void vtkGDCMPolyDataWriter::WriteRTSTRUCTData(gdcm::File &file, int pdidx )
   if( darray )
     {
     double tuple[3];
+#if VTK_MAJOR_VERSION > 7 || (VTK_MAJOR_VERSION == 7 && VTK_MINOR_VERSION >= 1)
+    darray->GetTypedTuple( 0, tuple );
+#else
     darray->GetTupleValue( 0, tuple );
+#endif
     intcolor[0] = (int32_t)(tuple[0] * 255.);
     intcolor[1] = (int32_t)(tuple[1] * 255.);
     intcolor[2] = (int32_t)(tuple[2] * 255.);
@@ -594,7 +598,11 @@ void vtkGDCMPolyDataWriter::WriteRTSTRUCTData(gdcm::File &file, int pdidx )
   else if( farray )
     {
     float ftuple[3];
+#if VTK_MAJOR_VERSION > 7 || (VTK_MAJOR_VERSION == 7 && VTK_MINOR_VERSION >= 1)
+    farray->GetTypedTuple( 0, ftuple );
+#else
     farray->GetTupleValue( 0, ftuple );
+#endif
     intcolor[0] = (int32_t)(ftuple[0] * 255.);
     intcolor[1] = (int32_t)(ftuple[1] * 255.);
     intcolor[2] = (int32_t)(ftuple[2] * 255.);

appveyor.yml

@@ -97,6 +97,7 @@ install:
   - cmd: SET PATH=%PATH%;C:\Program Files (x86)\NSIS
 
 on_failure:
+  - ctest -D ExperimentalSubmit -C %CONFIG% -Q
   # Display error log file if generated
   - dir C:\projects\gdcm\bin
   - dir C:\projects\gdcm\bin\Release
@@ -104,7 +105,7 @@ on_failure:
 
 # scripts to run before build
 before_build:
-  - cmake -Wno-dev -G"%VS_GEN%" -DCMAKE_BUILD_TYPE=%CONFIG% -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_EXAMPLES:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DBUILDNAME:STRING=%COMPUTERNAME%-%APPVEYOR_REPO_BRANCH%-%B_NAME% -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_USE_PVRG:BOOL=ON -DGDCM_LEGACY_SILENT:BOOL=ON -DCPACK_SYSTEM_NAME:STRING=%B_NAME% .
+  - cmake -Wno-dev -G"%VS_GEN%" -DCMAKE_BUILD_TYPE=%CONFIG% -DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_EXAMPLES:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DBUILDNAME:STRING=%COMPUTERNAME%-%APPVEYOR_REPO_BRANCH%-%B_NAME% -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_USE_PVRG:BOOL=ON -DGDCM_LEGACY_SILENT:BOOL=ON -DCPACK_SYSTEM_NAME:STRING=%B_NAME% .
   - ctest -D ExperimentalStart -C %CONFIG%
 
 # scripts to run after build

debian/.gitlab-ci.yml

+image: debian:sid
+
+build:
+  stage: build
+  before_script:
+    - apt-get update && apt-get -y install devscripts git-buildpackage 
+    - mk-build-deps --tool "apt -y -o Debug::pkgProblemResolver=yes --no-install-recommends" --install -r debian/control 
+  script:
+    - git checkout pristine-tar 
+    - git pull 
+    - git checkout experimental
+    - git pull 
+    # silence build to not exceed build log size of gitlab-ci
+    - gbp buildpackage -uc -us 2>&1 >../build.log
+    - tail -n 100 ../build.log
+

debian/changelog

+gdcm (2.8.7-2python3exp1) experimental; urgency=medium
+
+  * Experimental upload with python3 support
+
+ -- Gert Wollny <gewo@debian.org>  Sat, 30 Jun 2018 12:02:59 +0200
+
+gdcm (2.8.7-1) unstable; urgency=medium
+
+  * d/control: Change back to default-jdk
+  * New upstream version 2.8.7
+  * d/p/fix-vtkjava-build-dir Closes: #894371
+
+ -- Gert Wollny <gewo@debian.org>  Sat, 30 Jun 2018 11:41:20 +0200
+
+gdcm (2.8.6-2) unstable; urgency=medium
+
+  * d/p/gdcm-fix-xslt-maxdepth.patch set maxdeph Closes: #901519
+  * d/control: remove useless python version field
+
+ -- Gert Wollny <gewo@debian.org>  Tue, 19 Jun 2018 23:58:51 +0200
+
 gdcm (2.8.6-2) unstable; urgency=medium
 
   * d/rules: Add explicit java home path on arm* and 
@@ -18,6 +39,20 @@ gdcm (2.8.6-1) unstable; urgency=medium
 
  -- Gert Wollny <gewo@debian.org>  Sun, 29 Apr 2018 10:30:49 +0200
 
+gdcm (2.8.5-1~exp1) experimental; urgency=medium
+
+  * Move to vtk7 and python3
+  * New upstream version 2.8.5
+  * d/gdcm-doc.doc-base: Update version umber in pdf file
+
+ -- Gert Wollny <gewo@debian.org>  Tue, 10 Apr 2018 09:04:33 +0200
+
+gdcm (2.8.4-2) unstable; urgency=medium
+
+  * d/rules: update default java version on all archs
+
+ -- Gert Wollny <gewo@debian.org>  Mon, 02 Apr 2018 19:12:36 +0200
+
 gdcm (2.8.4-1) unstable; urgency=medium
 
   * New upstream version 2.8.4

debian/control

@@ -8,26 +8,26 @@ Uploaders: Andreas Tille <tille@debian.org>,
  Gert Wollny <gewo@debian.org> 
 Build-Depends: cmake (>= 2.8.9),
                debhelper (>= 11),
-	       openjdk-8-jdk,
+	       default-jdk,
                dh-strip-nondeterminism, 
                dh-python, 
-	       python-all-dev,
+	       python3-all-dev,
 	       pvrg-jpeg,
 	       uuid-dev,
 	       libz-dev,
 	       libexpat-dev,
 	       swig3.0,
 	       javahelper,
-	       libvtk6-dev,
+	       libvtk7-dev,
 	       libcharls-dev (>= 1.1.0),
 	       libopenjp2-7-dev,
-	       libvtk6-java,
+	       libvtk7-java,
 	       libxml2-dev,
 	       libjson-c-dev,
 	       libpoppler-private-dev,
 	       libssl-dev,
 	       ninja-build,
-	       python-vtk6,
+	       python3-vtk7 (>= 7.1.1-1~exp4),
 	       castxml,
 	       libsocket++-dev,
 	       libpapyrus3-dev,
@@ -35,14 +35,13 @@ Build-Depends: cmake (>= 2.8.9),
 	       mono-devel (>= 2.10.5) [amd64 armel armhf i386 mipsel kfreebsd-amd64 kfreebsd-i386 powerpc ppc64 ppc64el s390x arm64],
 	       xsltproc, 
                docbook-xsl-ns
-Build-Depends-Indep: vtk6-doc,
+Build-Depends-Indep: vtk7-doc,
 	       doxygen,
 	       doxygen-latex,
 	       ghostscript, 
                graphviz
 Build-Conflicts: libopenjpeg-dev
 Standards-Version: 4.1.4
-X-Python-Version: 2.7
 Vcs-Browser: https://salsa.debian.org/med-team/gdcm
 Vcs-Git: https://salsa.debian.org/med-team/gdcm.git
 Homepage: http://gdcm.sourceforge.net/
@@ -101,10 +100,10 @@ Description: Grassroots DICOM CLI bindings
  CLI bindings to the GDCM DICOM library. It allows developers to use
  GDCM from C# environment.
 
-Package: python-gdcm
+Package: python3-gdcm
 Section: python
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, libgdcm2.8 (= ${binary:Version})
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python3:Depends}, libgdcm2.8 (= ${binary:Version})
 Provides: ${python:Provides}
 Description: Grassroots DICOM Python bindings
  Grassroots DiCoM is a C++ library for DICOM medical files. It is
@@ -151,12 +150,12 @@ Description: Grassroots DICOM VTK CLI bindings
  .
  VTK CLI bindings to the GDCM DICOM library.
 
-Package: python-vtkgdcm
+Package: python3-vtkgdcm
 Section: python
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, libvtkgdcm2.8 (= ${binary:Version})
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python3:Depends}, libvtkgdcm2.8 (= ${binary:Version})
 Provides: ${python:Provides}
-Suggests: python-gdcm
+Suggests: python3-gdcm
 Description: Grassroots DICOM VTK/Python bindings
  Grassroots DiCoM is a C++ library for DICOM medical files. It is
  automatically wrapped to python/C#/Java (using swig). It supports

debian/control.in

@@ -7,8 +7,8 @@ Uploaders: Andreas Tille <tille@debian.org>,
  Sébastien Jodogne <s.jodogne@gmail.com>, 
  Gert Wollny <gewo@debian.org> 
 Build-Depends: cmake (>= 2.8.9),
-               debhelper (>= 9),
-	       openjdk-8-jdk,
+               debhelper (>= 11),
+	       default-jdk,
                dh-strip-nondeterminism, 
                dh-python, 
 	       python-all-dev,

debian/gdcm-doc.doc-base

@@ -9,4 +9,4 @@ Index: /usr/share/doc/gdcm-doc/html/index.xhtml
 Files: /usr/share/doc/gdcm-doc/html/*
 
 Format: PDF
-Files: /usr/share/doc/gdcm-doc/gdcm-2.8.6.pdf
+Files: /usr/share/doc/gdcm-doc/gdcm-2.8.7.pdf

debian/patches/03_linkvtkdoc.patch

-Description: Correct use of scripts from vtk6-doc 
- In vtk6-doc these scripts are installed compresses. The patch
- takes care of providing uncompressed versions.  
+Description: Correct use of scripts from vtk7-doc 
+ In vtk7-doc these scripts are installed uncompressed. 
  In addition the patch changes the vtk doxygen source directory and
  incorporates an patch to link to the VTK doc and replace PNG by SVG,
  Merged to one patch because they overlap partially. 
@@ -25,8 +24,8 @@ Author: Gert Wollny <gw.fossdev@gmail.com>, Mathieu Malaterre <malat@debian.org>
 -  set(DOXYGEN_SOURCE_DIR "/usr/share/doc/vtk-doc/html")
 -  elseif(EXISTS "/usr/share/doc/vtk6-doc/doxygen")
 -  set(DOXYGEN_SOURCE_DIR "/usr/share/doc/vtk6-doc/doxygen")
-+  if(EXISTS "/usr/share/vtk-6.3/doxygen")
-+  set(DOXYGEN_SOURCE_DIR "/usr/share/vtk-6.3/doxygen")
++  if(EXISTS "/usr/share/vtk-7.1/doxygen")
++  set(DOXYGEN_SOURCE_DIR "/usr/share/vtk-7.1/doxygen")
    else()
 -  message(WARNING "DOXYGEN_SOURCE_DIR need to be set.")
 +  message("DOXYGEN_SOURCE_DIR need to be set.")

debian/patches/add_cxx11_vtk_defines.patch

+Author: Gert Wollny <gewo@debian.org>
+Description: Add VTK defines for C++11 constructs to the swig interface file
+--- a/Utilities/VTK/vtkgdcm.i
++++ b/Utilities/VTK/vtkgdcm.i
+@@ -31,12 +31,17 @@
+ #endif
+ 
+ %{
+-//#define VTK_MAJOR_VERSION 6
+-//#define VTK_MINOR_VERSION 2
+-//#define VTK_BUILD_VERSION 0
+-//#define VTK_VERSION "6.2.0"
++//#define VTK_MAJOR_VERSION 7
++//#define VTK_MINOR_VERSION 1
++//#define VTK_BUILD_VERSION 1
++//#define VTK_VERSION "7.1.1"
+ %}
+ 
++#define VTK_OVERRIDE override
++#define VTK_FINAL final
++#define VTK_DELETE_FUNCTION = delete
++#define VTK_NEWINSTANCE
++#define VTK_LEGACY(X)
+ 
+ %{
+ // Let's reproduce the stack of include, when one would include vtkSetGet:
+@@ -118,7 +123,6 @@
+ #endif
+ 
+ 
+-
+ #define GDCM_EXPORT
+ #define VTK_EXPORT
+ #define VTK_COMMON_EXPORT

debian/patches/fix-vtkjava-build-dir.patch

+Author: Gert Wollny <gewo@debian.org>
+Description: Newer java compiler versions need some output dir specification
+Debian-Bug: https://bugs.debian.org/894371
+--- a/Utilities/VTK/CMakeLists.txt
++++ b/Utilities/VTK/CMakeLists.txt
+@@ -691,7 +691,7 @@
+       #COMMAND ${Java_JAVAC_EXECUTABLE} ARGS -cp ${GDCM_VTK_JAVA_JAR} "vtk/*.java"
+       # No such thing as -cp for javac only java is listed:
+       # http://java.sun.com/j2se/1.5.0/docs/tooldocs/windows/classpath.html
+-      COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${jflags} -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} -classpath ${GDCM_VTK_JAVA_JAR} "vtk/*.java"
++      COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${jflags} -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} -classpath ${GDCM_VTK_JAVA_JAR} -d . "vtk/*.java"
+       COMMAND ${Java_JAR_EXECUTABLE} ARGS -cvfm ${LIBRARY_OUTPUT_PATH}/${PROJECT_NAME}.jar ${CMAKE_CURRENT_SOURCE_DIR}/manifest.txt vtk/*.class
+       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/java
+       DEPENDS ${VTKGDCM_NAME}Java