Mercurial > hg > orthanc-wsi
diff ViewerPlugin/Plugin.cpp @ 0:4a7a53257c7d
initial commit
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 22 Oct 2016 21:48:33 +0200 |
parents | |
children | 77b76c1a213f |
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--- /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; + } +}