--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ViewerPlugin/Plugin.cpp	Sat Oct 22 21:48:33 2016 +0200
@@ -0,0 +1,390 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, 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 "../Framework/Inputs/DicomPyramid.h"
+#include "../Framework/Jpeg2000Reader.h"
+#include "../Framework/Messaging/PluginOrthancConnection.h"
+#include "../Framework/Orthanc/Core/Images/PngWriter.h"
+#include "../Framework/Orthanc/Core/MultiThreading/Semaphore.h"
+#include "../Framework/Orthanc/Core/OrthancException.h"
+#include "../Framework/Orthanc/Plugins/Samples/Common/OrthancPluginCppWrapper.h"
+
+#include <EmbeddedResources.h>
+
+#include <cassert>
+
+
+
+namespace OrthancWSI
+{
+  // TODO Add LRU recycling policy
+  class DicomPyramidCache : public boost::noncopyable
+  {
+  private:
+    boost::mutex                  mutex_;
+    IOrthancConnection&           orthanc_;
+    std::auto_ptr<DicomPyramid>   pyramid_;
+
+    DicomPyramid& GetPyramid(const std::string& seriesId)
+    {
+      // Mutex is assumed to be locked
+
+      if (pyramid_.get() == NULL ||
+          pyramid_->GetSeriesId() != seriesId)
+      {
+        pyramid_.reset(new DicomPyramid(orthanc_, seriesId));
+      }
+
+      if (pyramid_.get() == NULL)
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+      }
+
+      return *pyramid_;
+    }
+
+  public:
+    DicomPyramidCache(IOrthancConnection& orthanc) :
+      orthanc_(orthanc)
+    {
+    }
+
+    void Invalidate(const std::string& seriesId)
+    {
+      boost::mutex::scoped_lock  lock(mutex_);
+
+      if (pyramid_.get() != NULL &&
+          pyramid_->GetSeriesId() == seriesId)
+      {
+        pyramid_.reset(NULL);
+      }
+    }
+
+    class Locker : public boost::noncopyable
+    {
+    private:
+      boost::mutex::scoped_lock  lock_;
+      DicomPyramid&              pyramid_;
+
+    public:
+      Locker(DicomPyramidCache& cache,
+             const std::string& seriesId) :
+        lock_(cache.mutex_),
+        pyramid_(cache.GetPyramid(seriesId))
+      {
+      }
+
+      DicomPyramid& GetPyramid() const
+      {
+        return pyramid_;
+      }
+    };
+  };
+}
+
+
+OrthancPluginContext* context_ = NULL;
+
+std::auto_ptr<OrthancWSI::PluginOrthancConnection>  orthanc_;
+std::auto_ptr<OrthancWSI::DicomPyramidCache>        cache_;
+std::auto_ptr<Orthanc::Semaphore>                   transcoderSemaphore_;
+
+
+static bool DisplayPerformanceWarning()
+{
+  (void) DisplayPerformanceWarning;   // Disable warning about unused function
+  OrthancPluginLogWarning(context_, "Performance warning in whole-slide imaging: "
+                          "Non-release build, runtime debug assertions are turned on");
+  return true;
+}
+
+
+void ServePyramid(OrthancPluginRestOutput* output,
+                  const char* url,
+                  const OrthancPluginHttpRequest* request)
+{
+  std::string seriesId(request->groups[0]);
+
+  char tmp[1024];
+  sprintf(tmp, "Accessing whole-slide pyramid of series %s", seriesId.c_str());
+  OrthancPluginLogInfo(context_, tmp);
+  
+
+  OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
+
+  unsigned int totalWidth = locker.GetPyramid().GetLevelWidth(0);
+  unsigned int totalHeight = locker.GetPyramid().GetLevelHeight(0);
+
+  Json::Value resolutions = Json::arrayValue;
+  for (unsigned int i = 0; i < locker.GetPyramid().GetLevelCount(); i++)
+  {
+    resolutions.append(static_cast<float>(totalWidth) /
+                       static_cast<float>(locker.GetPyramid().GetLevelWidth(i)));
+  }
+
+  Json::Value result;
+  result["ID"] = seriesId;
+  result["TotalWidth"] = totalWidth;
+  result["TotalHeight"] = totalHeight;
+  result["TileWidth"] = locker.GetPyramid().GetTileWidth();
+  result["TileHeight"] = locker.GetPyramid().GetTileHeight();
+  result["Resolutions"] = resolutions;
+
+  std::string s = result.toStyledString();
+  OrthancPluginAnswerBuffer(context_, output, s.c_str(), s.size(), "application/json");
+}
+
+
+void ServeTile(OrthancPluginRestOutput* output,
+               const char* url,
+               const OrthancPluginHttpRequest* request)
+{
+  std::string seriesId(request->groups[0]);
+  int level = boost::lexical_cast<int>(request->groups[1]);
+  int tileY = boost::lexical_cast<int>(request->groups[3]);
+  int tileX = boost::lexical_cast<int>(request->groups[2]);
+
+  char tmp[1024];
+  sprintf(tmp, "Accessing tile in series %s: (%d,%d) at level %d", seriesId.c_str(), tileX, tileY, level);
+  OrthancPluginLogInfo(context_, tmp);
+  
+  if (level < 0 ||
+      tileX < 0 ||
+      tileY < 0)
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+  }
+
+  // Retrieve the raw tile from the WSI pyramid
+  OrthancWSI::ImageCompression compression;
+  Orthanc::PixelFormat format;
+  std::string tile;
+  unsigned int tileWidth, tileHeight;
+
+  {
+    OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
+
+    compression = locker.GetPyramid().GetImageCompression();
+    format = locker.GetPyramid().GetPixelFormat();
+    tileWidth = locker.GetPyramid().GetTileWidth();
+    tileHeight = locker.GetPyramid().GetTileHeight();
+
+    if (!locker.GetPyramid().ReadRawTile(tile, 
+                                         static_cast<unsigned int>(level),
+                                         static_cast<unsigned int>(tileX),
+                                         static_cast<unsigned int>(tileY)))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+    }
+  }
+
+  
+  // Test whether the tile is a JPEG image. In such a case, we can
+  // serve it as such, because any Web browser can handle JPEG
+
+  if (compression == OrthancWSI::ImageCompression_Jpeg)
+  {
+    OrthancPluginAnswerBuffer(context_, output, tile.c_str(), tile.size(), "image/jpeg");
+    return;   // We're done
+  }
+
+
+  // The tile does not come from a DICOM-JPEG instance, we need to
+  // decompress the raw tile
+  std::auto_ptr<Orthanc::ImageAccessor> decoded;
+
+  Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
+
+  switch (compression)
+  {
+    case OrthancWSI::ImageCompression_Jpeg2000:
+      decoded.reset(new OrthancWSI::Jpeg2000Reader);
+      dynamic_cast<OrthancWSI::Jpeg2000Reader&>(*decoded).ReadFromMemory(tile);
+      break;
+
+    case OrthancWSI::ImageCompression_None:
+    {
+      unsigned int bpp = Orthanc::GetBytesPerPixel(format);
+      if (bpp * tileWidth * tileHeight != tile.size())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+      }
+
+      decoded.reset(new Orthanc::ImageAccessor);
+      decoded->AssignReadOnly(format, tileWidth, tileHeight, bpp * tileWidth, tile.c_str());
+      break;
+    }
+
+    default:
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
+  }
+
+
+  // This is a lossless frame (coming from a JPEG2000 or uncompressed
+  // DICOM instance), serve it as a PNG image so as to prevent lossy
+  // compression
+
+  std::string png;
+  Orthanc::PngWriter writer;
+  writer.WriteToMemory(png, *decoded);
+
+  OrthancPluginAnswerBuffer(context_, output, png.c_str(), png.size(), "image/png");
+}
+
+
+OrthancPluginErrorCode OnChangeCallback(OrthancPluginChangeType changeType, 
+                                        OrthancPluginResourceType resourceType, 
+                                        const char *resourceId)
+{
+  if (resourceType == OrthancPluginResourceType_Series &&
+      changeType == OrthancPluginChangeType_NewChildInstance)
+  { 
+    char tmp[1024];
+    sprintf(tmp, "New instance has been added to series %s, invalidating it", resourceId);
+    OrthancPluginLogInfo(context_, tmp);
+
+    cache_->Invalidate(resourceId);
+  }
+
+  return OrthancPluginErrorCode_Success;
+}
+
+
+
+void ServeFile(OrthancPluginRestOutput* output,
+               const char* url,
+               const OrthancPluginHttpRequest* request)
+{
+  Orthanc::EmbeddedResources::FileResourceId resource;
+
+  std::string f(request->groups[0]);
+  std::string mime;
+
+  if (f == "viewer.html")
+  {
+    resource = Orthanc::EmbeddedResources::VIEWER_HTML;
+    mime = "text/html";
+  }
+  else if (f == "viewer.js")
+  {
+    resource = Orthanc::EmbeddedResources::VIEWER_JS;
+    mime = "application/javascript";
+  }
+  else if (f == "ol.js")
+  {
+    resource = Orthanc::EmbeddedResources::OPENLAYERS_JS;
+    mime = "application/javascript";
+  }
+  else if (f == "ol.css")
+  {
+    resource = Orthanc::EmbeddedResources::OPENLAYERS_CSS;
+    mime = "text/css";
+  }
+  else
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+  }
+
+  std::string content;
+  Orthanc::EmbeddedResources::GetFileResource(content, resource);
+
+  OrthancPluginAnswerBuffer(context_, output, content.c_str(), content.size(), mime.c_str());
+}
+
+
+
+extern "C"
+{
+  ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context)
+  {
+    context_ = context;
+    assert(DisplayPerformanceWarning());
+
+    /* Check the version of the Orthanc core */
+    if (OrthancPluginCheckVersion(context_) == 0)
+    {
+      char info[1024];
+      sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin",
+              context_->orthancVersion,
+              ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER,
+              ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER,
+              ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER);
+      OrthancPluginLogError(context_, info);
+      return -1;
+    }
+
+    // Limit the number of PNG transcoders to the number of available
+    // hardware threads (e.g. number of CPUs or cores or
+    // hyperthreading units)
+    unsigned int threads = boost::thread::hardware_concurrency();
+    
+    if (threads <= 0)
+    {
+      threads = 1;
+    }
+    
+    transcoderSemaphore_.reset(new Orthanc::Semaphore(threads));
+
+    char info[1024];
+    sprintf(info, "The whole-slide imaging plugin will use at most %d threads to transcode the tiles", threads);
+    OrthancPluginLogWarning(context_, info);
+
+    OrthancPluginSetDescription(context, "Plugin to serve whole-slide microscopic images from Orthanc.");
+
+    orthanc_.reset(new OrthancWSI::PluginOrthancConnection(context));
+    cache_.reset(new OrthancWSI::DicomPyramidCache(*orthanc_));
+
+    OrthancPluginRegisterOnChangeCallback(context_, OnChangeCallback);
+
+    OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(ol.css)", true);
+    OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(ol.js)", true);
+    OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(viewer.html)", true);
+    OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(viewer.js)", true);
+    OrthancPlugins::RegisterRestCallback<ServePyramid>(context, "/wsi/pyramids/([0-9a-f-]+)", true);
+    OrthancPlugins::RegisterRestCallback<ServeTile>(context, "/wsi/tiles/([0-9a-f-]+)/([0-9-]+)/([0-9-]+)/([0-9-]+)", true);
+
+    // Extend the default Orthanc Explorer with custom JavaScript for WSI
+    std::string explorer;
+    Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER);
+    OrthancPluginExtendOrthancExplorer(context_, explorer.c_str());
+
+    return 0;
+  }
+
+
+  ORTHANC_PLUGINS_API void OrthancPluginFinalize()
+  {
+    cache_.reset(NULL);
+    orthanc_.reset(NULL);
+    transcoderSemaphore_.reset(NULL);
+  }
+
+
+  ORTHANC_PLUGINS_API const char* OrthancPluginGetName()
+  {
+    return "wsi";
+  }
+
+
+  ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion()
+  {
+    return ORTHANC_WSI_VERSION;
+  }
+}