Add experimental HTJ2K TransferSyntax for reading to GDCM

Modules/IO/GDCM/include/itkGDCMImageIO.h

@@ -52,7 +52,8 @@ class GDCMImageIOEnums
     JPEG = 0,
     JPEG2000,
     JPEGLS,
-    RLE
+    RLE,
+    HTJ2K
   };
 };
 
@@ -210,6 +211,16 @@ class ITKIOGDCM_EXPORT GDCMImageIO : public ImageIOBase
   static constexpr CompressionEnum RLE = CompressionEnum::RLE;
 #endif
 
+  /** Set the compression type to use for writing.
+   *
+   * Currently only JPEG2000 and JPEG are supported.
+   * These map to the following DICOM standards:
+   *   JPEG2000: JPEG 2000 Image Compression (Lossless Only)
+   *   JPEG:     JPEG Lossless, Non-Hierarchical, First-Order Prediction
+   *
+   *
+   * @param _arg
+   */
   itkSetEnumMacro(CompressionType, CompressionEnum);
   itkGetEnumMacro(CompressionType, CompressionEnum);
 

Modules/IO/GDCM/src/itkGDCMImageIO.cxx

@@ -1475,6 +1475,8 @@ operator<<(std::ostream & out, const GDCMImageIOEnums::Compression value)
         return "itk::GDCMImageIOEnums::Compression::JPEGLS";
       case GDCMImageIOEnums::Compression::RLE:
         return "itk::GDCMImageIOEnums::Compression::RLE";
+      case GDCMImageIOEnums::Compression::HTJ2K:
+        return "itk::GDCMImageIOEnums::Compression::HTJ2K";
       default:
         return "INVALID VALUE FOR itk::GDCMImageIOEnums::Compression";
     }

Modules/IO/GDCM/test/Baseline/Lily_full.mha.cid

@@ -0,0 +1 @@
+bafybeig7pgo3x55bfh47ymckelybsug7rv2nqwjic2gzurvng6o3vqoux4

Modules/IO/GDCM/test/CMakeLists.txt

@@ -392,7 +392,12 @@ itk_add_test(
   ${ITK_TEST_OUTPUT_DIR}/no_preamble.mha
   scalar)
 
+
 function(AddComplianceTest fileName)
+  set(arg_baseline_fileName "Lily.mha")
+  if (ARGV1)
+    set(arg_baseline_fileName ${ARGV1})
+  endif()
   itk_add_test(
     NAME
     itkGDCM_ComplianceTestRGB_${fileName}
@@ -403,7 +408,7 @@ function(AddComplianceTest fileName)
     --compareCoordinateTolerance
     0.001
     --compare
-    DATA{Baseline/Lily.mha}
+    DATA{Baseline/${arg_baseline_fileName}}
     ${ITK_TEST_OUTPUT_DIR}/itkGDCM_ComplianceTestRGB_${fileName}.mha
     itkGDCMImageReadWriteTest
     DATA{Input/Lily/${fileName}.dcm}
@@ -419,3 +424,5 @@ addcompliancetest(raw-RGB)
 addcompliancetest(raw-YBR_FULL)
 addcompliancetest(raw-YBR_FULL_422)
 addcompliancetest(RLE-RGB)
+addcompliancetest(HTJ2K-YBR_ICT Lily_full.mha)
+addcompliancetest(HTJ2K-YBR_RCT Lily_full.mha)

Modules/IO/GDCM/test/Input/Lily/HTJ2K-YBR_ICT.dcm.cid

@@ -0,0 +1 @@
+bafkreib5e6kni2tdbtaxpz2i77k7hp5gzkztppiuws3ov4yx4dswlna6p4

Modules/IO/GDCM/test/Input/Lily/HTJ2K-YBR_RCT.dcm.cid

@@ -0,0 +1 @@
+bafybeifxqqmljz3yrqhrdv7vzrqrfkvs7aq2mx7mo3g3mjykqq3onlgh6i

Modules/ThirdParty/GDCM/UpdateFromUpstream.sh

@@ -8,7 +8,7 @@ readonly name="GDCM"
 readonly ownership="GDCM Upstream <[email protected]>"
 readonly subtree="Modules/ThirdParty/GDCM/src/gdcm"
 readonly repo="https://github.com/malaterre/GDCM.git"
-readonly tag="release"
+readonly tag="v3.0.25"
 readonly shortlog=false
 readonly paths="
   .gitattributes
@@ -31,7 +31,6 @@ readonly paths="
   Utilities/gdcmmd5
   Utilities/gdcm_md5.h
   Utilities/gdcm_openjpeg.h
-  Utilities/gdcmopenjpeg
   Utilities/gdcmrle
   Utilities/gdcmutfcpp
   Utilities/gdcmuuid

Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt

@@ -10,7 +10,7 @@ endif()
 #----------------------------------------------------------------------------
 
 project(GDCM
-  VERSION 3.0.24
+  VERSION 3.0.25
   LANGUAGES CXX C
 )
 ## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0
@@ -180,6 +180,10 @@ macro(CHECK_INCLUDE_FILE_CONCAT FILE VARIABLE)
   endif()
 endmacro()
 
+if(UNIX)
+  include(GNUInstallDirs)
+endif()
+
 #include(${GDCM_SOURCE_DIR}/CMake/gdcmPlatformCxxTests.cmake)
 #
 #GDCM_PLATFORM_CXX_TEST(GDCM_CXX_HAS_FUNCTION
@@ -696,6 +700,7 @@ if(GDCM_STANDALONE)
         HEADERS_DESTINATION   "${GDCM_INSTALL_INCLUDE_DIR}/vtk${vtk_version_suffix}"
         CMAKE_DESTINATION     "${GDCM_INSTALL_PACKAGE_DIR}"
         LICENSE_DESTINATION   "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
+        SPDX_DESTINATION      "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
         HIERARCHY_DESTINATION "${GDCM_INSTALL_LIB_DIR}/vtk${vtk_version_suffix}/hierarchy/vtkgdcm"
         LIBRARY_NAME_SUFFIX   "${vtkgdcm_library_suffix}"
         VERSION               "${GDCM_VERSION}"

Modules/ThirdParty/GDCM/src/gdcm/Source/Common/gdcmFilename.cxx

@@ -17,6 +17,10 @@
 #include <cstdlib> // realpath
 #include <cstring>
 
+#if defined(_WIN32) && (defined(_MSC_VER) || defined(__WATCOMC__) || defined(__BORLANDC__) || defined(__MINGW32__))
+#include <windows.h>
+#endif
+
 namespace gdcm
 {
 
@@ -97,7 +101,6 @@ const char *Filename::ToUnixSlashes()
 }
 
 #if defined(_WIN32) && (defined(_MSC_VER) || defined(__WATCOMC__) || defined(__BORLANDC__) || defined(__MINGW32__))
-#include <windows.h>
 
 inline void Realpath(const char *path, std::string & resolved_path)
 {

Modules/ThirdParty/GDCM/src/gdcm/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -38,6 +38,9 @@ using DICT_ENTRY = struct
 };
 
 static const DICT_ENTRY DICOMV3DataDict [] = {
+  {0x0049,0x0010,"AIR",VR::LO,VM::VM1,"?Possibly PHI?",false },
+  {0x0049,0x0011,"AIR",VR::LO,VM::VM1,"?number?",false },
+  {0x0049,0x0013,"AIR",VR::LT,VM::VM1,"?Long desc possibly PHI?",false },
   {0x0021,0x0010,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },
   {0x0021,0x0011,"SIEMENS MR FMRI",VR::LO,VM::VM1,"?",false },
   {0x0021,0x0012,"SIEMENS MR FMRI",VR::SQ,VM::VM1,"?",false },

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmByteSwapFilter.cxx

@@ -135,7 +135,6 @@ bool ByteSwapFilter::ByteSwap()
       de.SetTag(
         Tag( SwapperDoOp::Swap( tag.GetGroup() ), SwapperDoOp::Swap( tag.GetElement() ) ) );
       copy.Insert( de );
-      DS.Remove( de.GetTag() );
       }
     DS = copy;
     }

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmElement.h

@@ -392,7 +392,7 @@ static void x16printf(char *buf, int size, Float f) {
       strcpy(buf, mant);
       return;
     }
-    strncpy(buf, mant, iexp + 1);
+    memcpy(buf, mant, iexp + 1);
     buf[iexp + 1] = '.';
     strncpy(buf + iexp + 2, mant + iexp + 1, size - iexp - 1);
     buf[size] = 0;
@@ -409,7 +409,7 @@ static void x16printf(char *buf, int size, Float f) {
     for(j=0; j< -1 - iexp; j++) {
       buf[j+1] = '0';
     }
-    strncpy(buf - iexp, mant, size + 1 + iexp);
+    memcpy(buf - iexp, mant, size + 1 + iexp);
     buf[size] = 0;
     clean(buf);
   }

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmTransferSyntax.cxx

@@ -81,9 +81,15 @@ static const char *TSStrings[] = {
   "1.2.840.10008.1.2.4.102",
   // MPEG-4 AVC/H.264 BD-compatible High Profile / Level 4.1
   "1.2.840.10008.1.2.4.103",
+  // High-Throughput JPEG 2000 Image Compression (Lossless Only)
+  "1.2.840.10008.1.2.4.201",
+  // High-Throughput JPEG 2000 with RPCL Options Image Compression (Lossless Only)
+  "1.2.840.10008.1.2.4.202",
+  // High-Throughput JPEG 2000 Image Compression
+  "1.2.840.10008.1.2.4.203",
   // Unknown
-  "Unknown Transfer Syntax", // Pretty sure we never use this case...
-  nullptr // Compilers have no obligation to finish by NULL, do it ourself
+  "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
 };
 
 TransferSyntax::TSType TransferSyntax::GetTSType(const char *cstr)
@@ -162,7 +168,8 @@ bool TransferSyntax::IsLossy() const
     TSField == MPEG2MainProfile ||
     TSField == MPEG2MainProfileHighLevel ||
     TSField == MPEG4AVCH264HighProfileLevel4_1 ||
-    TSField == MPEG4AVCH264BDcompatibleHighProfileLevel4_1
+    TSField == MPEG4AVCH264BDcompatibleHighProfileLevel4_1 ||
+    TSField == HTJ2K
   )
     {
     return true;
@@ -211,7 +218,8 @@ bool TransferSyntax::IsLossless() const
     TSField == MPEG2MainProfile ||
     TSField == MPEG2MainProfileHighLevel ||
     TSField == MPEG4AVCH264HighProfileLevel4_1 ||
-    TSField == MPEG4AVCH264BDcompatibleHighProfileLevel4_1
+    TSField == MPEG4AVCH264BDcompatibleHighProfileLevel4_1 ||
+    TSField == HTJ2K
   )
     {
     return false;
@@ -300,6 +308,10 @@ bool TransferSyntax::IsEncapsulated() const
   case MPEG4AVCH264BDcompatibleHighProfileLevel4_1:
   //case ImplicitVRBigEndianACRNEMA:
   //case WeirdPapryus:
+  case HTJ2KLossless:
+  case HTJ2KRPCLLossless:
+  case HTJ2K:
+
     ret = true;
     break;
   default:

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmTransferSyntax.h

@@ -86,6 +86,9 @@ class GDCM_EXPORT TransferSyntax
     MPEG2MainProfileHighLevel,
     MPEG4AVCH264HighProfileLevel4_1,
     MPEG4AVCH264BDcompatibleHighProfileLevel4_1,
+    HTJ2KLossless,
+    HTJ2KRPCLLossless,
+    HTJ2K,
     TS_END
   } TSType;
 

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmDataSetHelper.cxx

@@ -213,7 +213,7 @@ VR DataSetHelper::ComputeVR(File const &file, DataSet const &ds, const Tag& tag)
       {
       // For Pixel Data:
       // if( !ds.FindDataElement( bitsallocated ) ) return VR::UN;
-      Attribute<0x0028,0x0100> at;
+      // Attribute<0x0028,0x0100> at;
       // at.SetFromDataElement( ds.GetDataElement( bitsallocated ) );
       }
     (void)v;

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmFileChangeTransferSyntax.cxx

@@ -454,6 +454,7 @@ bool FileChangeTransferSyntax::InitializeCopy()
         ISO_14495_1 = JPEG-LS Near-lossless Compression
         ISO_15444_1 = JPEG 2000 Irreversible Compression
         ISO_13818_2 = MPEG2 Compression
+        ISO_15444_15 = High-Throughput JPEG 2000 Irreversible Compression
          */
         Attribute<0x0028,0x2114> at3;
         const TransferSyntax ts_orig = Internals->TS;
@@ -467,6 +468,14 @@ bool FileChangeTransferSyntax::InitializeCopy()
           static const CSComp newvalues2[] = {"ISO_14495_1"};
           at3.SetValues( newvalues2, 1 );
           }
+        else if (
+          ts_orig == TransferSyntax::HTJ2KLossless ||
+          ts_orig == TransferSyntax::HTJ2KRPCLLossless ||
+          ts_orig == TransferSyntax::HTJ2K )
+          {
+          static const CSComp newvalues2[] = {"ISO_15444_15"};
+          at3.SetValues( newvalues2, 1 );
+          }
         else if (
           ts_orig == TransferSyntax::JPEGBaselineProcess1 ||
           ts_orig == TransferSyntax::JPEGExtendedProcess2_4 ||