Merge branch 'release'

Author: malaterre

Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -1159,9 +1159,12 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   {0x2013,0x0007,"BioClinicaImagingSegmentGroup",VR::OB,VM::VM1,"Custom Storage Segment Blob #7",false},
   {0x2013,0x0008,"BioClinicaImagingSegmentGroup",VR::OB,VM::VM1,"Custom Storage Segment Blob #8",false},
   {0x2013,0x0009,"BioClinicaImagingSegmentGroup",VR::OB,VM::VM1,"Custom Storage Segment Blob #9",false},
-  {0x7fe1,0x0001,"Bioclinica",VR::UT,VM::VM1,"??",false},
-  {0x7fe1,0x0002,"Bioclinica",VR::LO,VM::VM1,"??",false},
-  {0x7fe1,0x0003,"Bioclinica",VR::LO,VM::VM1,"??",false},
+  {0x2213,0x0001,"Clario",VR::UT,VM::VM1,"AES tag",false},
+  {0x2213,0x0002,"Clario",VR::LO,VM::VM1,"PX version",false},
+  {0x2213,0x0003,"Clario",VR::LO,VM::VM1,"Mask Name",false},
+  {0x7fe1,0x0001,"Bioclinica",VR::UT,VM::VM1,"AES tag",false},
+  {0x7fe1,0x0002,"Bioclinica",VR::LO,VM::VM1,"PX version",false},
+  {0x7fe1,0x0003,"Bioclinica",VR::LO,VM::VM1,"Mask Name",false},
   {0x5533,0x0033,"Visus Change",VR::SQ,VM::VM1,"Visus Data Save Sequence",false},
   {0x5533,0x0035,"Visus Change",VR::DA,VM::VM1,"Visus Data Save Date",false},
   {0x5533,0x0037,"Visus Change",VR::LO,VM::VM1,"Visus Data Save Originator",false},

Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx

@@ -203,6 +203,11 @@ std::istream &ExplicitDataElement::ReadValue(std::istream &is, bool readvalues)
       gdcm_assert( VRField & VR::OB_OW || VRField == VR::UN );
       ValueField = new SequenceOfFragments;
       }
+    else if( TagField == Tag(0x7fe1,0x1060) && VRField == VR::OB )
+      {
+      gdcmWarningMacro( "IllegalPrivatePixelSequence (7fe1,1060)" );
+      ValueField = new SequenceOfFragments;
+      }
     else
       {
       // Support cp246 conforming file:

Source/DataStructureAndEncodingDefinition/gdcmFileMetaInformation.cxx

@@ -835,7 +835,7 @@ void FileMetaInformation::ComputeDataSetTransferSyntax()
   const ByteValue *bv = de.GetByteValue();
   if( !bv )
     {
-    throw Exception( "Unknown Transfer syntax" );
+    throw Exception( "NULL Transfer syntax" );
     }
   // Pad string with a \0
   ts = std::string(bv->GetPointer(), bv->GetLength());

Source/DataStructureAndEncodingDefinition/gdcmTransferSyntax.cxx

@@ -87,6 +87,8 @@ static const char *TSStrings[] = {
   "1.2.840.10008.1.2.4.202",
   // High-Throughput JPEG 2000 Image Compression
   "1.2.840.10008.1.2.4.203",
+  // Deflated Image Frame Compression
+  "1.2.840.10008.1.2.8.1",
   // Unknown
   "Unknown Transfer Syntax", // Pretty sure we never use this case... until a new transfer syntax is added
   nullptr // Compilers have no obligation to finish by NULL, do it ourselves
@@ -195,6 +197,7 @@ bool TransferSyntax::CanStoreLossy() const
     TSField == JPEGLSLossless ||
     TSField == JPEG2000Lossless ||
     TSField == JPEG2000Part2Lossless ||
+    TSField == DeflatedImageFrameCompression ||
     TSField == RLELossless
   )
     {
@@ -311,6 +314,7 @@ bool TransferSyntax::IsEncapsulated() const
   case HTJ2KLossless:
   case HTJ2KRPCLLossless:
   case HTJ2K:
+  case DeflatedImageFrameCompression:
 
     ret = true;
     break;

Source/DataStructureAndEncodingDefinition/gdcmTransferSyntax.h

@@ -89,6 +89,7 @@ class GDCM_EXPORT TransferSyntax
     HTJ2KLossless,
     HTJ2KRPCLLossless,
     HTJ2K,
+    DeflatedImageFrameCompression,
     TS_END
   } TSType;
 

Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx

@@ -631,13 +631,17 @@ bool PixmapReader::ReadImageInternal(MediaStorage const &ms, bool handlepixeldat
     {
     // PHILIPS_Gyroscan-12-MONO2-Jpeg_Lossless.dcm
     // PHILIPS_Gyroscan-12-Jpeg_Extended_Process_2_4.dcm
-    gdcmDebugMacro( "Mixture of ACR NEMA and DICOM file" );
-    isacrnema = true;
     const char *str = ds.GetDataElement( trecognitioncode ).GetByteValue()->GetPointer();
-    gdcm_assert( strncmp( str, "ACR-NEMA", strlen( "ACR-NEMA" ) ) == 0 ||
-      strncmp( str, "ACRNEMA", strlen( "ACRNEMA" ) ) == 0 ||
-      strncmp( str, "MIPS 2.0", strlen( "MIPS 2.0" ) ) == 0 );
-    (void)str;//warning removal
+    if( strncmp( str, "ACR-NEMA", strlen( "ACR-NEMA" ) ) == 0 ||
+        strncmp( str, "ACRNEMA", strlen( "ACRNEMA" ) ) == 0 ||
+        strncmp( str, "MIPS 2.0", strlen( "MIPS 2.0" ) ) == 0) {
+      gdcmDebugMacro("Mixture of ACR NEMA and DICOM file");
+      isacrnema = true;
+      } else {
+        Attribute<0x0008, 0x0010> at;
+        at.SetFromDataSet(ds);
+        gdcmWarningMacro("Junk recognition code: " + at.GetValue());
+      }
     }
 
   std::vector<unsigned int> vdims = ImageHelper::GetDimensionsValue(*F);

Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx

@@ -576,6 +576,12 @@ bool PixmapWriter::PrepareWrite( MediaStorage const & ref_ms )
       }
     else
       {
+      if( ts_orig == TransferSyntax::JPEG2000Lossless )
+        {
+        static const CSComp newvalues2[] = {"ISO_15444_1"};
+        at3.SetValues(  newvalues2, 1 );
+        ds.Replace( at3.GetAsDataElement() );
+        } 
       if( ds.FindDataElement( at1.GetTag() ) ) {
         at1.Set( ds );
         if( atoi(at1.GetValue().c_str()) != 1 ) {
@@ -584,16 +590,13 @@ bool PixmapWriter::PrepareWrite( MediaStorage const & ref_ms )
           ds.Replace( at1.GetAsDataElement() );
         }
       } else {
+        at1.SetValue( "01" );
+        ds.Replace( at1.GetAsDataElement() );
+        // Assume originally JPEGLossy and override previous value ISO_15444_1
         if( pi_orig == PhotometricInterpretation::YBR_FULL_422 ) {
-          at1.SetValue( "01" );
-          ds.Replace( at1.GetAsDataElement() );
-
           static const CSComp newvalues2[] = {"ISO_10918_1"};
           at3.SetValues(  newvalues2, 1 );
           ds.Replace( at3.GetAsDataElement() );
-        } else {
-          gdcmErrorMacro( "Unhandled Lossy flag for Pixel Data" );
-          return false;
         }
       }
       }

Source/MediaStorageAndFileFormat/gdcmPrinter.cxx

@@ -642,7 +642,7 @@ VR Printer::PrintDataElement(std::ostringstream &os, const Dicts &dicts, const D
           }
         else if ( sqf )
           {
-          gdcm_assert( t == Tag(0x7fe0,0x0010) );
+          gdcm_assert( t == Tag(0x7fe0,0x0010) || t == Tag(0x7fe1,0x1060) );
           //os << *sqf;
           }
         else if ( sqi )