--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancStone/Sources/Loaders/SeriesFramesLoader.cpp	Tue Jul 07 16:21:02 2020 +0200
@@ -0,0 +1,550 @@
+/**
+ * Stone of Orthanc
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2020 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 "SeriesFramesLoader.h"
+
+#include "../Oracle/ParseDicomFromFileCommand.h"
+#include "../Oracle/ParseDicomFromWadoCommand.h"
+
+#if ORTHANC_ENABLE_DCMTK == 1
+#  include <DicomParsing/Internals/DicomImageDecoder.h>
+#endif
+
+#include <DicomFormat/DicomInstanceHasher.h>
+#include <Images/Image.h>
+#include <Images/ImageProcessing.h>
+#include <Images/JpegReader.h>
+
+#include <boost/algorithm/string/predicate.hpp>
+
+namespace OrthancStone
+{  
+  class SeriesFramesLoader::Payload : public Orthanc::IDynamicObject
+  {
+  private:
+    DicomSource   source_;
+    size_t        seriesIndex_;
+    std::string   sopInstanceUid_;  // Only used for debug purpose
+    unsigned int  quality_;
+    bool          hasWindowing_;
+    float         windowingCenter_;
+    float         windowingWidth_;
+    std::unique_ptr<Orthanc::IDynamicObject>  userPayload_;
+
+  public:
+    Payload(const DicomSource& source,
+            size_t seriesIndex,
+            const std::string& sopInstanceUid,
+            unsigned int quality,
+            Orthanc::IDynamicObject* userPayload) :
+      source_(source),
+      seriesIndex_(seriesIndex),
+      sopInstanceUid_(sopInstanceUid),
+      quality_(quality),
+      hasWindowing_(false),
+      userPayload_(userPayload)
+    {
+    }
+
+    size_t GetSeriesIndex() const
+    {
+      return seriesIndex_;
+    }
+
+    const std::string& GetSopInstanceUid() const
+    {
+      return sopInstanceUid_;
+    }
+
+    unsigned int GetQuality() const
+    {
+      return quality_;
+    }
+
+    void SetWindowing(float center,
+                      float width)
+    {
+      hasWindowing_ = true;
+      windowingCenter_ = center;
+      windowingWidth_ = width;
+    }
+
+    bool HasWindowing() const
+    {
+      return hasWindowing_;
+    }
+
+    float GetWindowingCenter() const
+    {
+      if (hasWindowing_)
+      {
+        return windowingCenter_;
+      }
+      else
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+      }
+    }
+
+    float GetWindowingWidth() const
+    {
+      if (hasWindowing_)
+      {
+        return windowingWidth_;
+      }
+      else
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+      }
+    }
+
+    const DicomSource& GetSource() const
+    {
+      return source_;
+    }
+
+    Orthanc::IDynamicObject* GetUserPayload() const
+    {
+      return userPayload_.get();
+    }
+  };
+    
+
+  SeriesFramesLoader::SeriesFramesLoader(ILoadersContext& context,
+                                         LoadedDicomResources& instances,
+                                         const std::string& dicomDirPath,
+                                         boost::shared_ptr<LoadedDicomResources> dicomDir) :
+    context_(context),
+    frames_(instances),
+    dicomDirPath_(dicomDirPath),
+    dicomDir_(dicomDir)
+  {
+  }
+
+
+  void SeriesFramesLoader::EmitMessage(const Payload& payload,
+                                       const Orthanc::ImageAccessor& image)
+  {
+    const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(payload.GetSeriesIndex());
+    const Orthanc::DicomMap& instance = frames_.GetInstance(payload.GetSeriesIndex());
+    size_t frameIndex = frames_.GetFrameIndex(payload.GetSeriesIndex());
+
+    if (frameIndex >= parameters.GetImageInformation().GetNumberOfFrames() ||
+        payload.GetSopInstanceUid() != parameters.GetSopInstanceUid())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+    }      
+
+    LOG(TRACE) << "Decoded instance " << payload.GetSopInstanceUid() << ", frame "
+               << frameIndex << ": " << image.GetWidth() << "x"
+               << image.GetHeight() << ", " << Orthanc::EnumerationToString(image.GetFormat())
+               << ", quality " << payload.GetQuality();
+      
+    FrameLoadedMessage message(*this, frameIndex, payload.GetQuality(), image, instance, parameters, payload.GetUserPayload());
+    BroadcastMessage(message);
+  }
+
+
+#if ORTHANC_ENABLE_DCMTK == 1
+  void SeriesFramesLoader::HandleDicom(const Payload& payload,
+                                       Orthanc::ParsedDicomFile& dicom)
+  {     
+    size_t frameIndex = frames_.GetFrameIndex(payload.GetSeriesIndex());
+
+    std::unique_ptr<Orthanc::ImageAccessor> decoded;
+    decoded.reset(Orthanc::DicomImageDecoder::Decode(
+      dicom, 
+      static_cast<unsigned int>(frameIndex)));
+
+    if (decoded.get() == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
+    }
+
+    EmitMessage(payload, *decoded);
+  }
+#endif
+
+    
+  void SeriesFramesLoader::HandleDicomWebRendered(const Payload& payload,
+                                                  const std::string& body,
+                                                  const std::map<std::string, std::string>& headers)
+  {
+    assert(payload.GetSource().IsDicomWeb() &&
+           payload.HasWindowing());
+
+    bool ok = false;
+    for (std::map<std::string, std::string>::const_iterator it = headers.begin();
+         it != headers.end(); ++it)
+    {
+      if (boost::iequals("content-type", it->first) &&
+          boost::iequals(Orthanc::MIME_JPEG, it->second))
+      {
+        ok = true;
+        break;
+      }
+    }
+
+    if (!ok)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol,
+                                      "The WADO-RS server has not generated a JPEG image on /rendered");
+    }
+
+    Orthanc::JpegReader reader;
+    reader.ReadFromMemory(body);
+
+    switch (reader.GetFormat())
+    {
+      case Orthanc::PixelFormat_RGB24:
+        EmitMessage(payload, reader);
+        break;
+
+      case Orthanc::PixelFormat_Grayscale8:
+      {
+        const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(payload.GetSeriesIndex());
+
+        Orthanc::Image scaled(parameters.GetExpectedPixelFormat(), reader.GetWidth(), reader.GetHeight(), false);
+        Orthanc::ImageProcessing::Convert(scaled, reader);
+          
+        float w = payload.GetWindowingWidth();
+        if (w <= 0.01f)
+        {
+          w = 0.01f;  // Prevent division by zero
+        }
+
+        const float c = payload.GetWindowingCenter();
+        const float scaling = w / 255.0f;
+        const float offset = (c - w / 2.0f) / scaling;
+
+        Orthanc::ImageProcessing::ShiftScale(scaled, offset, scaling, false /* truncation to speed up */);
+        EmitMessage(payload, scaled);
+        break;
+      }
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+    }
+  }
+
+
+#if ORTHANC_ENABLE_DCMTK == 1
+  void SeriesFramesLoader::Handle(const ParseDicomSuccessMessage& message)
+  {
+    assert(message.GetOrigin().HasPayload());
+
+    const Payload& payload = dynamic_cast<const Payload&>(message.GetOrigin().GetPayload());
+    if ((payload.GetSource().IsDicomDir() ||
+         payload.GetSource().IsDicomWeb()) &&
+        message.HasPixelData())
+    {
+      HandleDicom(dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()), message.GetDicom());
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+    }
+  }
+#endif
+
+
+  void SeriesFramesLoader::Handle(const GetOrthancImageCommand::SuccessMessage& message)
+  {
+    assert(message.GetOrigin().HasPayload());
+
+    const Payload& payload = dynamic_cast<const Payload&>(message.GetOrigin().GetPayload());
+    assert(payload.GetSource().IsOrthanc());
+
+    EmitMessage(payload, message.GetImage());
+  }
+
+
+  void SeriesFramesLoader::Handle(const GetOrthancWebViewerJpegCommand::SuccessMessage& message)
+  {
+    assert(message.GetOrigin().HasPayload());
+
+    const Payload& payload = dynamic_cast<const Payload&>(message.GetOrigin().GetPayload());
+    assert(payload.GetSource().IsOrthanc());
+
+    EmitMessage(payload, message.GetImage());
+  }
+
+
+  void SeriesFramesLoader::Handle(const OrthancRestApiCommand::SuccessMessage& message)
+  {
+    // This is to handle "/rendered" in DICOMweb
+    assert(message.GetOrigin().HasPayload());
+    HandleDicomWebRendered(dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()),
+                           message.GetAnswer(), message.GetAnswerHeaders());
+  }
+
+
+  void SeriesFramesLoader::Handle(const HttpCommand::SuccessMessage& message)
+  {
+    // This is to handle "/rendered" in DICOMweb
+    assert(message.GetOrigin().HasPayload());
+    HandleDicomWebRendered(dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()),
+                           message.GetAnswer(), message.GetAnswerHeaders());
+  }
+
+
+  void SeriesFramesLoader::GetPreviewWindowing(float& center,
+                                               float& width,
+                                               size_t index) const
+  {
+    const Orthanc::DicomMap& instance = frames_.GetInstance(index);
+    const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(index);
+
+    if (parameters.HasDefaultWindowing())
+    {
+      // TODO - Handle multiple presets (take the largest width)
+      center = parameters.GetDefaultWindowingCenter();
+      width = parameters.GetDefaultWindowingWidth();
+    }
+    else
+    {
+      float a, b;
+      if (instance.ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) &&
+          instance.ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) &&
+          a < b)
+      {
+        center = (a + b) / 2.0f;
+        width = (b - a);
+      }
+      else
+      {
+        // Cannot infer a suitable windowing from the available tags
+        center = 128.0f;
+        width = 256.0f;
+      }
+    }
+  }
+
+  
+  Orthanc::IDynamicObject& SeriesFramesLoader::FrameLoadedMessage::GetUserPayload() const
+  {
+    if (userPayload_)
+    {
+      return *userPayload_;
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  void SeriesFramesLoader::Factory::SetDicomDir(const std::string& dicomDirPath,
+                                                boost::shared_ptr<LoadedDicomResources> dicomDir)
+  {
+    dicomDirPath_ = dicomDirPath;
+    dicomDir_ = dicomDir;
+  }
+
+
+  boost::shared_ptr<IObserver> SeriesFramesLoader::Factory::Create(ILoadersContext::ILock& stone)
+  {
+    boost::shared_ptr<SeriesFramesLoader> loader(
+      new SeriesFramesLoader(stone.GetContext(), instances_, dicomDirPath_, dicomDir_));
+    loader->Register<GetOrthancImageCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle);
+    loader->Register<GetOrthancWebViewerJpegCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle);
+    loader->Register<HttpCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle);
+    loader->Register<OrthancRestApiCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle);
+
+#if ORTHANC_ENABLE_DCMTK == 1
+    loader->Register<ParseDicomSuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle);
+#endif
+
+    return loader;
+  }
+
+
+  void SeriesFramesLoader::ScheduleLoadFrame(int priority,
+                                             const DicomSource& source,
+                                             size_t index,
+                                             unsigned int quality,
+                                             Orthanc::IDynamicObject* userPayload)
+  {
+    std::unique_ptr<Orthanc::IDynamicObject> protection(userPayload);
+    
+    if (index >= frames_.GetFramesCount() ||
+        quality >= source.GetQualityCount())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    const Orthanc::DicomMap& instance = frames_.GetInstance(index);
+
+    std::string sopInstanceUid;
+    if (!instance.LookupStringValue(sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
+                                      "Missing SOPInstanceUID in a DICOM instance");
+    }
+      
+    if (source.IsDicomDir())
+    {
+      if (dicomDir_.get() == NULL)
+      {
+        // Should have been set in the factory
+        throw Orthanc::OrthancException(
+          Orthanc::ErrorCode_BadSequenceOfCalls,
+          "SeriesFramesLoader::Factory::SetDicomDir() should have been called");
+      }
+        
+      assert(quality == 0);
+        
+      std::string file;
+      if (dicomDir_->LookupStringValue(file, sopInstanceUid, Orthanc::DICOM_TAG_REFERENCED_FILE_ID))
+      {
+        std::unique_ptr<ParseDicomFromFileCommand> command(new ParseDicomFromFileCommand(source, dicomDirPath_, file));
+        command->SetPixelDataIncluded(true);
+        command->AcquirePayload(new Payload(source, index, sopInstanceUid, quality, protection.release()));
+
+        {
+          std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock());
+          lock->Schedule(GetSharedObserver(), priority, command.release());
+        }
+      }
+      else
+      {
+        LOG(WARNING) << "Missing tag ReferencedFileID in a DICOMDIR entry";
+      }
+    }
+    else if (source.IsDicomWeb())
+    {
+      std::string studyInstanceUid, seriesInstanceUid;
+      if (!instance.LookupStringValue(studyInstanceUid, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
+          !instance.LookupStringValue(seriesInstanceUid, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
+                                        "Missing StudyInstanceUID or SeriesInstanceUID in a DICOM instance");
+      }
+
+      const std::string uri = ("/studies/" + studyInstanceUid +
+                               "/series/" + seriesInstanceUid +
+                               "/instances/" + sopInstanceUid);
+
+      if (source.HasDicomWebRendered() &&
+          quality == 0)
+      {
+        float c, w;
+        GetPreviewWindowing(c, w, index);
+
+        std::map<std::string, std::string> arguments, headers;
+        arguments["window"] = (boost::lexical_cast<std::string>(c) + "," +
+                               boost::lexical_cast<std::string>(w) + ",linear");
+        headers["Accept"] = "image/jpeg";
+
+        std::unique_ptr<Payload> payload(new Payload(source, index, sopInstanceUid, quality, protection.release()));
+        payload->SetWindowing(c, w);
+
+        {
+          std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock());
+          lock->Schedule(GetSharedObserver(), priority,
+                         source.CreateDicomWebCommand(uri + "/rendered", arguments, headers, payload.release()));
+        }
+      }
+      else
+      {
+        assert((source.HasDicomWebRendered() && quality == 1) ||
+               (!source.HasDicomWebRendered() && quality == 0));
+
+#if ORTHANC_ENABLE_DCMTK == 1
+        std::unique_ptr<Payload> payload(new Payload(source, index, sopInstanceUid, quality, protection.release()));
+
+        const std::map<std::string, std::string> empty;
+
+        std::unique_ptr<ParseDicomFromWadoCommand> command(
+          new ParseDicomFromWadoCommand(source, sopInstanceUid, source.CreateDicomWebCommand(uri, empty, empty, NULL)));
+        command->AcquirePayload(payload.release());
+
+        {
+          std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock());
+          lock->Schedule(GetSharedObserver(), priority, command.release());
+        }
+#else
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented,
+                                        "DCMTK is not enabled, cannot parse a DICOM instance");
+#endif
+      }
+    }
+    else if (source.IsOrthanc())
+    {
+      std::string orthancId;
+
+      {
+        std::string patientId, studyInstanceUid, seriesInstanceUid;
+        if (!instance.LookupStringValue(patientId, Orthanc::DICOM_TAG_PATIENT_ID, false) ||
+            !instance.LookupStringValue(studyInstanceUid, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
+            !instance.LookupStringValue(seriesInstanceUid, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
+        {
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
+                                          "Missing StudyInstanceUID or SeriesInstanceUID in a DICOM instance");
+        }
+
+        Orthanc::DicomInstanceHasher hasher(patientId, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
+        orthancId = hasher.HashInstance();
+      }
+
+      const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(index);
+
+      if (quality == 0 && source.HasOrthancWebViewer1())
+      {
+        std::unique_ptr<GetOrthancWebViewerJpegCommand> command(new GetOrthancWebViewerJpegCommand);
+        command->SetInstance(orthancId);
+        command->SetExpectedPixelFormat(parameters.GetExpectedPixelFormat());
+        command->AcquirePayload(new Payload(source, index, sopInstanceUid, quality, protection.release()));
+
+        {
+          std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock());
+          lock->Schedule(GetSharedObserver(), priority, command.release());
+        }
+      }
+      else if (quality == 0 && source.HasOrthancAdvancedPreview())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+      }
+      else
+      {
+        assert(quality <= 1);
+        assert(quality == 0 || 
+               source.HasOrthancWebViewer1() || 
+               source.HasOrthancAdvancedPreview());
+
+        std::unique_ptr<GetOrthancImageCommand> command(new GetOrthancImageCommand);
+        command->SetFrameUri(orthancId, frames_.GetFrameIndex(index), parameters.GetExpectedPixelFormat());
+        command->SetExpectedPixelFormat(parameters.GetExpectedPixelFormat());
+        command->SetHttpHeader("Accept", Orthanc::MIME_PAM);
+        command->AcquirePayload(new Payload(source, index, sopInstanceUid, quality, protection.release()));
+
+        {
+          std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock());
+          lock->Schedule(GetSharedObserver(), priority, command.release());
+        }
+      }
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+    }
+  }
+}