view OrthancFramework/Sources/DicomParsing/DcmtkTranscoder.cpp @ 5911:bfae0fc2ea1b get-scu-test

Started to work on handling errors as warnings when trying to store instances whose SOPClassUID has not been accepted during the negotiation. Work to be finalized later
author Alain Mazy <am@orthanc.team>
date Mon, 09 Dec 2024 10:07:19 +0100
parents f7adfb22e20e
children
line wrap: on
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/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2023 Osimis S.A., Belgium
 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this program. If not, see
 * <http://www.gnu.org/licenses/>.
 **/


#include "../PrecompiledHeaders.h"
#include "DcmtkTranscoder.h"


#if !defined(ORTHANC_ENABLE_DCMTK_JPEG)
#  error Macro ORTHANC_ENABLE_DCMTK_JPEG must be defined
#endif

#if !defined(ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS)
#  error Macro ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS must be defined
#endif


#include "FromDcmtkBridge.h"
#include "../Logging.h"
#include "../OrthancException.h"
#include "../Toolbox.h"

#include <dcmtk/dcmdata/dcdeftag.h>
#include <dcmtk/dcmjpeg/djrploss.h>  // for DJ_RPLossy
#include <dcmtk/dcmjpeg/djrplol.h>   // for DJ_RPLossless
#include <dcmtk/dcmjpls/djrparam.h>  // for DJLSRepresentationParameter

#include <boost/lexical_cast.hpp>


namespace Orthanc
{
  DcmtkTranscoder::DcmtkTranscoder() :
    lossyQuality_(90)
  {
  }


  static bool GetBitsStored(uint16_t& bitsStored,
                            DcmDataset& dataset)
  {
    return dataset.findAndGetUint16(DCM_BitsStored, bitsStored).good();
  }

  
  void DcmtkTranscoder::SetLossyQuality(unsigned int quality)
  {
    if (quality == 0 ||
        quality > 100)
    {
      throw OrthancException(
        ErrorCode_ParameterOutOfRange,
        "The quality for lossy transcoding must be an integer between 1 and 100, received: " +
        boost::lexical_cast<std::string>(quality));
    }
    else
    {
      LOG(INFO) << "Quality for lossy transcoding using DCMTK is set to: " << quality;
      lossyQuality_ = quality;
    }
  }

  unsigned int DcmtkTranscoder::GetLossyQuality() const
  {
    return lossyQuality_;
  }

  bool TryTranscode(std::vector<std::string>& failureReasons, /* out */
                    DicomTransferSyntax& selectedSyntax, /* out*/
                    DcmFileFormat& dicom, /* in/out */
                    const std::set<DicomTransferSyntax>& allowedSyntaxes,
                    DicomTransferSyntax trySyntax)
  {
    if (allowedSyntaxes.find(trySyntax) != allowedSyntaxes.end())
    {
      if (FromDcmtkBridge::Transcode(dicom, trySyntax, NULL))
      {
        selectedSyntax = trySyntax;
        return true;
      }

      failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(trySyntax));
    }
    return false;
  }

  bool DcmtkTranscoder::InplaceTranscode(DicomTransferSyntax& selectedSyntax /* out */,
                                         std::string& failureReason /* out */,
                                         DcmFileFormat& dicom, /* in/out */
                                         const std::set<DicomTransferSyntax>& allowedSyntaxes,
                                         bool allowNewSopInstanceUid) 
  {
    std::vector<std::string> failureReasons;

    if (dicom.getDataset() == NULL)
    {
      throw OrthancException(ErrorCode_InternalError);
    }

    DicomTransferSyntax syntax;
    if (!FromDcmtkBridge::LookupOrthancTransferSyntax(syntax, dicom))
    {
      throw OrthancException(ErrorCode_BadFileFormat,
                             "Cannot determine the transfer syntax");
    }

    uint16_t bitsStored;
    bool hasBitsStored = GetBitsStored(bitsStored, *dicom.getDataset());
    
    if (allowedSyntaxes.find(syntax) != allowedSyntaxes.end())
    {
      // No transcoding is needed
      return true;
    }
    
    if (TryTranscode(failureReasons, selectedSyntax, dicom, allowedSyntaxes, DicomTransferSyntax_LittleEndianImplicit))
    {
      return true;
    }

    if (TryTranscode(failureReasons, selectedSyntax, dicom, allowedSyntaxes, DicomTransferSyntax_LittleEndianExplicit))
    {
      return true;
    }

    if (TryTranscode(failureReasons, selectedSyntax, dicom, allowedSyntaxes, DicomTransferSyntax_BigEndianExplicit))
    {
      return true;
    }

    if (TryTranscode(failureReasons, selectedSyntax, dicom, allowedSyntaxes, DicomTransferSyntax_DeflatedLittleEndianExplicit))
    {
      return true;
    }


#if ORTHANC_ENABLE_DCMTK_JPEG == 1
    if (allowedSyntaxes.find(DicomTransferSyntax_JPEGProcess1) != allowedSyntaxes.end())
    {
      if (!allowNewSopInstanceUid)
      {
        failureReasons.push_back(std::string("Can not transcode to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess1) + " without generating new SOPInstanceUID");
      }
      else if (hasBitsStored && bitsStored != 8)
      {
        failureReasons.push_back(std::string("Can not transcode to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess1) + " if BitsStored != 8");
      }
      else
      {
        // Check out "dcmjpeg/apps/dcmcjpeg.cc"
        DJ_RPLossy parameters(lossyQuality_);
          
        if (FromDcmtkBridge::Transcode(dicom, DicomTransferSyntax_JPEGProcess1, &parameters))
        {
          selectedSyntax = DicomTransferSyntax_JPEGProcess1;
          return true;
        }
        failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess1));
      }
    }
#endif
      
#if ORTHANC_ENABLE_DCMTK_JPEG == 1
    if (allowedSyntaxes.find(DicomTransferSyntax_JPEGProcess2_4) != allowedSyntaxes.end())
    {
      if (!allowNewSopInstanceUid)
      {
        failureReasons.push_back(std::string("Can not transcode to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess2_4) + " without generating new SOPInstanceUID");
      }
      else if (hasBitsStored && bitsStored > 12)
      {
        failureReasons.push_back(std::string("Can not transcode to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess2_4) + " if BitsStored != 8");
      }
      else
      {
        // Check out "dcmjpeg/apps/dcmcjpeg.cc"
        DJ_RPLossy parameters(lossyQuality_);
        if (FromDcmtkBridge::Transcode(dicom, DicomTransferSyntax_JPEGProcess2_4, &parameters))
        {
          selectedSyntax = DicomTransferSyntax_JPEGProcess2_4;
          return true;
        }
        failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess2_4));
      }
    }
#endif
      
#if ORTHANC_ENABLE_DCMTK_JPEG == 1
    if (allowedSyntaxes.find(DicomTransferSyntax_JPEGProcess14) != allowedSyntaxes.end())
    {
      // Check out "dcmjpeg/apps/dcmcjpeg.cc"
      DJ_RPLossless parameters(6 /* opt_selection_value */,
                               0 /* opt_point_transform */);
      if (FromDcmtkBridge::Transcode(dicom, DicomTransferSyntax_JPEGProcess14, &parameters))
      {
        selectedSyntax = DicomTransferSyntax_JPEGProcess14;
        return true;
      }
      failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess14));
    }
#endif
      
#if ORTHANC_ENABLE_DCMTK_JPEG == 1
    if (allowedSyntaxes.find(DicomTransferSyntax_JPEGProcess14SV1) != allowedSyntaxes.end())
    {
      // Check out "dcmjpeg/apps/dcmcjpeg.cc"
      DJ_RPLossless parameters(6 /* opt_selection_value */,
                               0 /* opt_point_transform */);
      if (FromDcmtkBridge::Transcode(dicom, DicomTransferSyntax_JPEGProcess14SV1, &parameters))
      {
        selectedSyntax = DicomTransferSyntax_JPEGProcess14SV1;
        return true;
      }
      failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGProcess14SV1));
    }
#endif
      
#if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1
    if (allowedSyntaxes.find(DicomTransferSyntax_JPEGLSLossless) != allowedSyntaxes.end())
    {
      // Check out "dcmjpls/apps/dcmcjpls.cc"
      DJLSRepresentationParameter parameters(2 /* opt_nearlossless_deviation */,
                                             OFTrue /* opt_useLosslessProcess */);

      /**
       * WARNING: This call results in a segmentation fault if using
       * the DCMTK package 3.6.2 from Ubuntu 18.04.
       **/              
      if (FromDcmtkBridge::Transcode(dicom, DicomTransferSyntax_JPEGLSLossless, &parameters))
      {
        selectedSyntax = DicomTransferSyntax_JPEGLSLossless;
        return true;
      }
      failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGLSLossless));
    }
#endif
      
#if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1
    if (allowNewSopInstanceUid &&
        allowedSyntaxes.find(DicomTransferSyntax_JPEGLSLossy) != allowedSyntaxes.end())
    {
      // Check out "dcmjpls/apps/dcmcjpls.cc"
      DJLSRepresentationParameter parameters(2 /* opt_nearlossless_deviation */,
                                             OFFalse /* opt_useLosslessProcess */);

      /**
       * WARNING: This call results in a segmentation fault if using
       * the DCMTK package 3.6.2 from Ubuntu 18.04.
       **/              
      if (FromDcmtkBridge::Transcode(dicom, DicomTransferSyntax_JPEGLSLossy, &parameters))
      {
        selectedSyntax = DicomTransferSyntax_JPEGLSLossy;
        return true;
      }
      failureReasons.push_back(std::string("Internal error while transcoding to ") + GetTransferSyntaxUid(DicomTransferSyntax_JPEGLSLossy));
    }
#endif

    Orthanc::Toolbox::JoinStrings(failureReason, failureReasons, ", ");
    return false;
  }

  bool DcmtkTranscoder::IsSupported(DicomTransferSyntax syntax)
  {
    if (syntax == DicomTransferSyntax_LittleEndianImplicit ||
        syntax == DicomTransferSyntax_LittleEndianExplicit ||
        syntax == DicomTransferSyntax_BigEndianExplicit ||
        syntax == DicomTransferSyntax_DeflatedLittleEndianExplicit)
    {
      return true;
    }

#if ORTHANC_ENABLE_DCMTK_JPEG == 1
    if (syntax == DicomTransferSyntax_JPEGProcess1 ||
        syntax == DicomTransferSyntax_JPEGProcess2_4 ||
        syntax == DicomTransferSyntax_JPEGProcess14 ||
        syntax == DicomTransferSyntax_JPEGProcess14SV1)
    {
      return true;
    }
#endif

#if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1
    if (syntax == DicomTransferSyntax_JPEGLSLossless ||
        syntax == DicomTransferSyntax_JPEGLSLossy)
    {
      return true;
    }
#endif
    
    return false;
  }


  bool DcmtkTranscoder::Transcode(DicomImage& target,
                                  DicomImage& source /* in, "GetParsed()" possibly modified */,
                                  const std::set<DicomTransferSyntax>& allowedSyntaxes,
                                  bool allowNewSopInstanceUid)
  {
    target.Clear();
    
    DicomTransferSyntax sourceSyntax;
    if (!FromDcmtkBridge::LookupOrthancTransferSyntax(sourceSyntax, source.GetParsed()))
    {
      LOG(ERROR) << "Unsupport transfer syntax for transcoding";
      return false;
    }

    std::string failureReason;
    std::string s;
    for (std::set<DicomTransferSyntax>::const_iterator
            it = allowedSyntaxes.begin(); it != allowedSyntaxes.end(); ++it)
    {
      if (!s.empty())
      {
        s += ", ";
      }

      s += GetTransferSyntaxUid(*it);
    }

    if (s.empty())
    {
      s = "<none>";
    }

    LOG(INFO) << "DCMTK transcoding from " << GetTransferSyntaxUid(sourceSyntax)
              << " to one of: " << s;

#if !defined(NDEBUG)
    const std::string sourceSopInstanceUid = GetSopInstanceUid(source.GetParsed());
#endif

    DicomTransferSyntax targetSyntax;
    if (allowedSyntaxes.find(sourceSyntax) != allowedSyntaxes.end())
    {
      // No transcoding is needed
      target.AcquireParsed(source);
      target.AcquireBuffer(source);
      return true;
    }
    else if (InplaceTranscode(targetSyntax, failureReason, source.GetParsed(),
                              allowedSyntaxes, allowNewSopInstanceUid))
    {   
      // Sanity check
      DicomTransferSyntax targetSyntax2;
      if (FromDcmtkBridge::LookupOrthancTransferSyntax(targetSyntax2, source.GetParsed()) &&
          targetSyntax == targetSyntax2 &&
          allowedSyntaxes.find(targetSyntax2) != allowedSyntaxes.end())
      {
        target.AcquireParsed(source);
        source.Clear();
        
#if !defined(NDEBUG)
        // Only run the sanity check in debug mode
        CheckTranscoding(target, sourceSyntax, sourceSopInstanceUid,
                         allowedSyntaxes, allowNewSopInstanceUid);
#endif
        
        return true;
      }
      else
      {
        throw OrthancException(ErrorCode_InternalError);
      }  
    }
    else
    {
      // Cannot transcode
      LOG(WARNING) << "DCMTK was unable to transcode from " << GetTransferSyntaxUid(sourceSyntax)
                   << " to one of: " << s << " " << failureReason;
      return false;
    }
  }
}