--- a/Core/DicomParsing/FromDcmtkBridge.cpp	Wed May 06 08:40:48 2020 +0200
+++ b/Core/DicomParsing/FromDcmtkBridge.cpp	Wed May 20 16:42:44 2020 +0200
@@ -121,6 +121,13 @@
 #endif
 
 
+#include <dcmtk/dcmdata/dcrledrg.h>
+#if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1
+#  include <dcmtk/dcmdata/dcrleerg.h>
+#  include <dcmtk/dcmimage/diregist.h>  // include to support color images
+#endif
+
+
 namespace Orthanc
 {
   static bool IsBinaryTag(const DcmTag& key)
@@ -1198,51 +1205,30 @@
     }
   }
 
-  bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
-                                           DcmDataset& dataSet)
+
+  
+  static bool SaveToMemoryBufferInternal(std::string& buffer,
+                                         DcmFileFormat& dicom,
+                                         E_TransferSyntax xfer)
   {
-    // Determine the transfer syntax which shall be used to write the
-    // information to the file. We always switch to the Little Endian
-    // syntax, with explicit length.
-
-    // http://support.dcmtk.org/docs/dcxfer_8h-source.html
-
-
-    /**
-     * Note that up to Orthanc 0.7.1 (inclusive), the
-     * "EXS_LittleEndianExplicit" was always used to save the DICOM
-     * dataset into memory. We now keep the original transfer syntax
-     * (if available).
-     **/
-    E_TransferSyntax xfer = dataSet.getOriginalXfer();
-    if (xfer == EXS_Unknown)
-    {
-      // No information about the original transfer syntax: This is
-      // most probably a DICOM dataset that was read from memory.
-      xfer = EXS_LittleEndianExplicit;
-    }
-
     E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength;
 
-    // Create the meta-header information
-    DcmFileFormat ff(&dataSet);
-    ff.validateMetaInfo(xfer);
-    ff.removeInvalidGroups();
-
     // Create a memory buffer with the proper size
     {
-      const uint32_t estimatedSize = ff.calcElementLength(xfer, encodingType);  // (*)
+      const uint32_t estimatedSize = dicom.calcElementLength(xfer, encodingType);  // (*)
       buffer.resize(estimatedSize);
     }
 
     DcmOutputBufferStream ob(&buffer[0], buffer.size());
 
     // Fill the memory buffer with the meta-header and the dataset
-    ff.transferInit();
-    OFCondition c = ff.write(ob, xfer, encodingType, NULL,
-                             /*opt_groupLength*/ EGL_recalcGL,
-                             /*opt_paddingType*/ EPD_withoutPadding);
-    ff.transferEnd();
+    dicom.transferInit();
+    OFCondition c = dicom.write(ob, xfer, encodingType, NULL,
+                                /*opt_groupLength*/ EGL_recalcGL,
+                                /*opt_paddingType*/ EPD_noChange,
+                                /*padlen*/ 0, /*subPadlen*/ 0, /*instanceLength*/ 0,
+                                EWM_updateMeta /* creates new SOP instance UID on lossy */);
+    dicom.transferEnd();
 
     if (c.good())
     {
@@ -1265,6 +1251,81 @@
       return false;
     }
   }
+  
+
+  bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer,
+                                           DcmDataset& dataSet)
+  {
+    // Determine the transfer syntax which shall be used to write the
+    // information to the file. If not possible, switch to the Little
+    // Endian syntax, with explicit length.
+
+    // http://support.dcmtk.org/docs/dcxfer_8h-source.html
+
+
+    /**
+     * Note that up to Orthanc 0.7.1 (inclusive), the
+     * "EXS_LittleEndianExplicit" was always used to save the DICOM
+     * dataset into memory. We now keep the original transfer syntax
+     * (if available).
+     **/
+    E_TransferSyntax xfer = dataSet.getCurrentXfer();
+    if (xfer == EXS_Unknown)
+    {
+      // No information about the original transfer syntax: This is
+      // most probably a DICOM dataset that was read from memory.
+      xfer = EXS_LittleEndianExplicit;
+    }
+
+    // Create the meta-header information
+    DcmFileFormat ff(&dataSet);
+    ff.validateMetaInfo(xfer);
+    ff.removeInvalidGroups();
+
+    return SaveToMemoryBufferInternal(buffer, ff, xfer);
+  }
+
+
+  bool FromDcmtkBridge::Transcode(DcmFileFormat& dicom,
+                                  DicomTransferSyntax syntax,
+                                  const DcmRepresentationParameter* representation)
+  {
+    E_TransferSyntax xfer;
+    if (!LookupDcmtkTransferSyntax(xfer, syntax))
+    {
+      throw OrthancException(ErrorCode_InternalError);
+    }
+    else
+    {
+      DicomTransferSyntax sourceSyntax;
+      bool known = LookupOrthancTransferSyntax(sourceSyntax, dicom);
+      
+      if (!dicom.chooseRepresentation(xfer, representation).good() ||
+          !dicom.canWriteXfer(xfer) ||
+          !dicom.validateMetaInfo(xfer, EWM_updateMeta).good())
+      {
+        return false;
+      }
+      else
+      {
+        dicom.removeInvalidGroups();
+
+        if (known)
+        {
+          LOG(INFO) << "Transcoded an image from transfer syntax "
+                    << GetTransferSyntaxUid(sourceSyntax) << " to "
+                    << GetTransferSyntaxUid(syntax);
+        }
+        else
+        {
+          LOG(INFO) << "Transcoded an image from unknown transfer syntax to "
+                    << GetTransferSyntaxUid(syntax);
+        }
+        
+        return true;
+      }
+    }
+  }
 
 
   ValueRepresentation FromDcmtkBridge::LookupValueRepresentation(const DicomTag& tag)
@@ -1659,7 +1720,7 @@
         DcmTag key(tag.GetGroup(), tag.GetElement());
         if (key.getEVR() != EVR_SQ)
         {
-          throw OrthancException(ErrorCode_BadParameterType);
+          throw OrthancException(ErrorCode_BadParameterType, "Bad Parameter type for tag " + tag.Format());
         }
 
         DcmSequenceOfItems* sequence = new DcmSequenceOfItems(key);
@@ -1703,7 +1764,7 @@
       }
 
       default:
-        throw OrthancException(ErrorCode_BadParameterType);
+        throw OrthancException(ErrorCode_BadParameterType, "Bad Parameter type for tag " + tag.Format());
     }
 
     return element.release();
@@ -1719,9 +1780,13 @@
     }
 
     DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element);
+
+    E_TransferSyntax repType;
+    const DcmRepresentationParameter *repParam = NULL;
+    pixelData.getCurrentRepresentationKey(repType, repParam);
+    
     DcmPixelSequence* pixelSequence = NULL;
-    if (!pixelData.getEncapsulatedRepresentation
-        (dataset.getOriginalXfer(), NULL, pixelSequence).good())
+    if (!pixelData.getEncapsulatedRepresentation(repType, repParam, pixelSequence).good())
     {
       return NULL;
     }
@@ -1974,25 +2039,6 @@
   }
 
 
-  bool FromDcmtkBridge::LookupTransferSyntax(std::string& result,
-                                             DcmFileFormat& dicom)
-  {
-    const char* value = NULL;
-
-    if (dicom.getMetaInfo() != NULL &&
-        dicom.getMetaInfo()->findAndGetString(DCM_TransferSyntaxUID, value).good() &&
-        value != NULL)
-    {
-      result.assign(value);
-      return true;
-    }
-    else
-    {
-      return false;
-    }
-  }
-
-
 #if ORTHANC_ENABLE_LUA == 1
   void FromDcmtkBridge::ExecuteToDicom(DicomMap& target,
                                        LuaFunctionCall& call)
@@ -2073,6 +2119,12 @@
     DJEncoderRegistration::registerCodecs();
 # endif
 #endif
+
+    LOG(INFO) << "Registering RLE codecs in DCMTK";
+    DcmRLEDecoderRegistration::registerCodecs(); 
+#if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1
+    DcmRLEEncoderRegistration::registerCodecs();
+#endif
   }
 
 
@@ -2093,6 +2145,11 @@
     DJEncoderRegistration::cleanup();
 # endif
 #endif
+
+    DcmRLEDecoderRegistration::cleanup(); 
+#if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1
+    DcmRLEEncoderRegistration::cleanup();
+#endif
   }
 
 
@@ -2578,6 +2635,33 @@
     Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding);
     ApplyVisitorToDataset(dataset, visitor, parentTags, parentIndexes, encoding, hasCodeExtensions);
   }
+
+
+
+  bool FromDcmtkBridge::LookupOrthancTransferSyntax(DicomTransferSyntax& target,
+                                                    DcmFileFormat& dicom)
+  {
+    if (dicom.getDataset() == NULL)
+    {
+      throw OrthancException(ErrorCode_InternalError);
+    }
+        
+    DcmDataset& dataset = *dicom.getDataset();
+
+    E_TransferSyntax xfer = dataset.getCurrentXfer();
+    if (xfer == EXS_Unknown)
+    {
+      dataset.updateOriginalXfer();
+      xfer = dataset.getOriginalXfer();
+      if (xfer == EXS_Unknown)
+      {
+        throw OrthancException(ErrorCode_BadFileFormat,
+                               "Cannot determine the transfer syntax of the DICOM instance");
+      }
+    }
+
+    return FromDcmtkBridge::LookupOrthancTransferSyntax(target, xfer);
+  }
 }