view Framework/Deprecated/Toolbox/MessagingToolbox.cpp @ 925:4639d0bf6390

Added support for Grayscale16 in the multiframe loader (Victor)
author Benjamin Golinvaux <bgo@osimis.io>
date Mon, 22 Jul 2019 16:00:03 +0200
parents 4fe4b221a31f
children 2d8ab34c8c91
line wrap: on
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/**
 * Stone of Orthanc
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2019 Osimis S.A., Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Affero 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
 * Affero General Public License for more details.
 * 
 * You should have received a copy of the GNU Affero General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 **/


#include "MessagingToolbox.h"

#include <Core/Images/Image.h>
#include <Core/Images/ImageProcessing.h>
#include <Core/Images/JpegReader.h>
#include <Core/Images/PngReader.h>
#include <Core/OrthancException.h>
#include <Core/Toolbox.h>
#include <Core/Logging.h>

#include <boost/lexical_cast.hpp>
#include <json/reader.h>
#include <json/writer.h>

namespace Deprecated
{
  namespace MessagingToolbox
  {
    static bool ParseVersion(std::string& version,
                             unsigned int& major,
                             unsigned int& minor,
                             unsigned int& patch,
                             const Json::Value& info)
    {
      if (info.type() != Json::objectValue ||
          !info.isMember("Version") ||
          info["Version"].type() != Json::stringValue)
      {
        return false;
      }

      version = info["Version"].asString();
      if (version == "mainline")
      {
        // Some arbitrary high values Orthanc versions will never reach ;)
        major = 999;
        minor = 999;
        patch = 999;
        return true;
      }

      std::vector<std::string> tokens;
      Orthanc::Toolbox::TokenizeString(tokens, version, '.');
      
      if (tokens.size() != 2 &&
          tokens.size() != 3)
      {
        return false;
      }

      int a, b, c;
      try
      {
        a = boost::lexical_cast<int>(tokens[0]);
        b = boost::lexical_cast<int>(tokens[1]);

        if (tokens.size() == 3)
        {
          c = boost::lexical_cast<int>(tokens[2]);
        }
        else
        {
          c = 0;
        }
      }
      catch (boost::bad_lexical_cast&)
      {
        return false;
      }

      if (a < 0 ||
          b < 0 ||
          c < 0)
      {
        return false;
      }
      else
      {
        major = static_cast<unsigned int>(a);
        minor = static_cast<unsigned int>(b);
        patch = static_cast<unsigned int>(c);
        return true;
      }         
    }


    bool ParseJson(Json::Value& target,
                   const void* content,
                   size_t size)
    {
      Json::Reader reader;
      return reader.parse(reinterpret_cast<const char*>(content),
                          reinterpret_cast<const char*>(content) + size,
                          target);
    }

    void JsonToString(std::string& target,
                      const Json::Value& source)
    {
      Json::FastWriter writer;
      target = writer.write(source);
    }

    static void ParseJsonException(Json::Value& target,
                                   const std::string& source)
    {
      Json::Reader reader;
      if (!reader.parse(source, target))
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
      }
    }


    void RestApiGet(Json::Value& target,
                    OrthancPlugins::IOrthancConnection& orthanc,
                    const std::string& uri)
    {
      std::string tmp;
      orthanc.RestApiGet(tmp, uri);
      ParseJsonException(target, tmp);
    }


    void RestApiPost(Json::Value& target,
                     OrthancPlugins::IOrthancConnection& orthanc,
                     const std::string& uri,
                     const std::string& body)
    {
      std::string tmp;
      orthanc.RestApiPost(tmp, uri, body);
      ParseJsonException(target, tmp);
    }


    bool HasWebViewerInstalled(OrthancPlugins::IOrthancConnection& orthanc)
    {
      try
      {
        Json::Value json;
        RestApiGet(json, orthanc, "/plugins/web-viewer");
        return json.type() == Json::objectValue;
      }
      catch (Orthanc::OrthancException&)
      {
        return false;
      }
    }


    bool CheckOrthancVersion(OrthancPlugins::IOrthancConnection& orthanc)
    {
      Json::Value json;
      std::string version;
      unsigned int major, minor, patch;

      try
      {
        RestApiGet(json, orthanc, "/system");
      }
      catch (Orthanc::OrthancException&)
      {
        LOG(ERROR) << "Cannot connect to your Orthanc server";
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
      }
        
      if (!ParseVersion(version, major, minor, patch, json))
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
      }

      LOG(WARNING) << "Version of the Orthanc core (must be above 1.3.1): " << version;

      // Stone is only compatible with Orthanc >= 1.3.1
      if (major < 1 ||
          (major == 1 && minor < 3) ||
          (major == 1 && minor == 3 && patch < 1))
      {
        return false;
      }

      try
      {
        RestApiGet(json, orthanc, "/plugins/web-viewer");       
      }
      catch (Orthanc::OrthancException&)
      {
        // The Web viewer is not installed, this is OK
        LOG(WARNING) << "The Web viewer plugin is not installed, progressive download is disabled";
        return true;
      }

      if (!ParseVersion(version, major, minor, patch, json))
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
      }

      LOG(WARNING) << "Version of the Web viewer plugin (must be above 2.2): " << version;

      return (major >= 3 ||
              (major == 2 && minor >= 2));
    }


    Orthanc::ImageAccessor* DecodeFrame(OrthancPlugins::IOrthancConnection& orthanc,
                                        const std::string& instance,
                                        unsigned int frame,
                                        Orthanc::PixelFormat targetFormat)
    {
      std::string uri = ("instances/" + instance + "/frames/" + 
                         boost::lexical_cast<std::string>(frame));

      std::string compressed;

      switch (targetFormat)
      {
        case Orthanc::PixelFormat_RGB24:
          orthanc.RestApiGet(compressed, uri + "/preview");
          break;

        case Orthanc::PixelFormat_Grayscale16:
          orthanc.RestApiGet(compressed, uri + "/image-uint16");
          break;

        case Orthanc::PixelFormat_SignedGrayscale16:
          orthanc.RestApiGet(compressed, uri + "/image-int16");
          break;

        default:
          throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
      }
      
      std::auto_ptr<Orthanc::PngReader> result(new Orthanc::PngReader);
      result->ReadFromMemory(compressed);

      if (targetFormat == Orthanc::PixelFormat_SignedGrayscale16)
      {
        if (result->GetFormat() == Orthanc::PixelFormat_Grayscale16)
        {
          result->SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
        }
        else
        {
          throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
        }
      }

      return result.release();
    }


    Orthanc::ImageAccessor* DecodeJpegFrame(OrthancPlugins::IOrthancConnection& orthanc,
                                            const std::string& instance,
                                            unsigned int frame,
                                            unsigned int quality,
                                            Orthanc::PixelFormat targetFormat)
    {
      if (quality <= 0 || 
          quality > 100)
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
      }

      // This requires the official Web viewer plugin to be installed!
      std::string uri = ("web-viewer/instances/jpeg" + 
                         boost::lexical_cast<std::string>(quality) + 
                         "-" + instance + "_" + 
                         boost::lexical_cast<std::string>(frame));

      Json::Value encoded;
      RestApiGet(encoded, orthanc, uri);

      if (encoded.type() != Json::objectValue ||
          !encoded.isMember("Orthanc") ||
          encoded["Orthanc"].type() != Json::objectValue)
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
      }

      Json::Value& info = encoded["Orthanc"];
      if (!info.isMember("PixelData") ||
          !info.isMember("Stretched") ||
          !info.isMember("Compression") ||
          info["Compression"].type() != Json::stringValue ||
          info["PixelData"].type() != Json::stringValue ||
          info["Stretched"].type() != Json::booleanValue ||
          info["Compression"].asString() != "Jpeg")
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
      }          

      bool isSigned = false;
      bool isStretched = info["Stretched"].asBool();

      if (info.isMember("IsSigned"))
      {
        if (info["IsSigned"].type() != Json::booleanValue)
        {
          throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
        }          
        else
        {
          isSigned = info["IsSigned"].asBool();
        }
      }

      std::string jpeg;
      Orthanc::Toolbox::DecodeBase64(jpeg, info["PixelData"].asString());

      std::auto_ptr<Orthanc::JpegReader> reader(new Orthanc::JpegReader);
      reader->ReadFromMemory(jpeg);

      if (reader->GetFormat() == Orthanc::PixelFormat_RGB24)  // This is a color image
      {
        if (targetFormat != Orthanc::PixelFormat_RGB24)
        {
          throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
        }

        if (isSigned || isStretched)
        {
          throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
        }
        else
        {
          return reader.release();
        }
      }

      if (reader->GetFormat() != Orthanc::PixelFormat_Grayscale8)
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
      }

      if (!isStretched)
      {
        if (targetFormat != reader->GetFormat())
        {
          throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
        }

        return reader.release();
      }

      int32_t stretchLow = 0;
      int32_t stretchHigh = 0;

      if (!info.isMember("StretchLow") ||
          !info.isMember("StretchHigh") ||
          info["StretchLow"].type() != Json::intValue ||
          info["StretchHigh"].type() != Json::intValue)
      {
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
      }

      stretchLow = info["StretchLow"].asInt();
      stretchHigh = info["StretchHigh"].asInt();

      if (stretchLow < -32768 ||
          stretchHigh > 65535 ||
          (stretchLow < 0 && stretchHigh > 32767))
      {
        // This range cannot be represented with a uint16_t or an int16_t
        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);          
      }

      // Decode a grayscale JPEG 8bpp image coming from the Web viewer
      std::auto_ptr<Orthanc::ImageAccessor> image
        (new Orthanc::Image(targetFormat, reader->GetWidth(), reader->GetHeight(), false));

      float scaling = static_cast<float>(stretchHigh - stretchLow) / 255.0f;
      float offset = static_cast<float>(stretchLow) / scaling;
      
      Orthanc::ImageProcessing::Convert(*image, *reader);
      Orthanc::ImageProcessing::ShiftScale(*image, offset, scaling, true);

#if 0
      /*info.removeMember("PixelData");
        std::cout << info.toStyledString();*/
      
      int64_t a, b;
      Orthanc::ImageProcessing::GetMinMaxValue(a, b, *image);
      std::cout << stretchLow << "->" << stretchHigh << " = " << a << "->" << b << std::endl;
#endif

      return image.release();
    }


    static void AddTag(Orthanc::DicomMap& target,
                       const OrthancPlugins::IDicomDataset& source,
                       const Orthanc::DicomTag& tag)
    {
      OrthancPlugins::DicomTag key(tag.GetGroup(), tag.GetElement());
      
      std::string value;
      if (source.GetStringValue(value, key))
      {
        target.SetValue(tag, value, false);
      }
    }

    
    void ConvertDataset(Orthanc::DicomMap& target,
                        const OrthancPlugins::IDicomDataset& source)
    {
      target.Clear();

      AddTag(target, source, Orthanc::DICOM_TAG_BITS_ALLOCATED);
      AddTag(target, source, Orthanc::DICOM_TAG_BITS_STORED);
      AddTag(target, source, Orthanc::DICOM_TAG_COLUMNS);
      AddTag(target, source, Orthanc::DICOM_TAG_DOSE_GRID_SCALING);
      AddTag(target, source, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER);
      AddTag(target, source, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR);
      AddTag(target, source, Orthanc::DICOM_TAG_HIGH_BIT);
      AddTag(target, source, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT);
      AddTag(target, source, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT);
      AddTag(target, source, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES);
      AddTag(target, source, Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION);
      AddTag(target, source, Orthanc::DICOM_TAG_PIXEL_REPRESENTATION);
      AddTag(target, source, Orthanc::DICOM_TAG_PIXEL_SPACING);
      AddTag(target, source, Orthanc::DICOM_TAG_PLANAR_CONFIGURATION);
      AddTag(target, source, Orthanc::DICOM_TAG_RESCALE_INTERCEPT);
      AddTag(target, source, Orthanc::DICOM_TAG_RESCALE_SLOPE);
      AddTag(target, source, Orthanc::DICOM_TAG_ROWS);
      AddTag(target, source, Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL);
      AddTag(target, source, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID);
      AddTag(target, source, Orthanc::DICOM_TAG_SLICE_THICKNESS);
      AddTag(target, source, Orthanc::DICOM_TAG_SOP_CLASS_UID);
      AddTag(target, source, Orthanc::DICOM_TAG_SOP_INSTANCE_UID);
      AddTag(target, source, Orthanc::DICOM_TAG_WINDOW_CENTER);
      AddTag(target, source, Orthanc::DICOM_TAG_WINDOW_WIDTH);
    }
  }
}