Mercurial > hg > orthanc-stone
view OrthancStone/Sources/Loaders/SeriesThumbnailsLoader.cpp @ 2174:2410a171ebfb
refactoring using DicomWebDataset and OrthancNativeDataset
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 22 Oct 2024 21:52:34 +0200 |
parents | 16c01cc201e7 |
children |
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/** * Stone of Orthanc * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2023 Osimis S.A., 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 "SeriesThumbnailsLoader.h" #include "LoadedDicomResources.h" #include "../Oracle/ParseDicomFromWadoCommand.h" #include "../Toolbox/ImageToolbox.h" #include <DicomFormat/DicomMap.h> #include <DicomFormat/DicomInstanceHasher.h> #include <Images/Image.h> #include <Images/ImageProcessing.h> #include <Images/JpegReader.h> #include <Images/JpegWriter.h> #include <OrthancException.h> #include <Toolbox.h> #include <boost/algorithm/string/predicate.hpp> #if ORTHANC_ENABLE_DCMTK == 1 # include <DicomParsing/ParsedDicomFile.h> #endif static const unsigned int JPEG_QUALITY = 70; // Only used for Orthanc source namespace OrthancStone { SeriesThumbnailsLoader::Thumbnail::Thumbnail(const std::string& image, const std::string& mime) : type_(SeriesThumbnailType_Image), image_(image), mime_(mime) { } SeriesThumbnailsLoader::Thumbnail::Thumbnail(SeriesThumbnailType type) : type_(type) { if (type == SeriesThumbnailType_Image) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } } Orthanc::ImageAccessor* SeriesThumbnailsLoader::SuccessMessage::DecodeImage() const { if (GetType() != SeriesThumbnailType_Image) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } Orthanc::MimeType mime; if (!Orthanc::LookupMimeType(mime, GetMime())) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported MIME type for thumbnail: " + GetMime()); } switch (mime) { case Orthanc::MimeType_Jpeg: { std::unique_ptr<Orthanc::JpegReader> reader(new Orthanc::JpegReader); reader->ReadFromMemory(GetEncodedImage()); return reader.release(); } default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Cannot decode MIME type for thumbnail: " + GetMime()); } } void SeriesThumbnailsLoader::AcquireThumbnail(const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid, SeriesThumbnailsLoader::Thumbnail* thumbnail) { assert(thumbnail != NULL); std::unique_ptr<Thumbnail> protection(thumbnail); Thumbnails::iterator found = thumbnails_.find(seriesInstanceUid); if (found == thumbnails_.end()) { thumbnails_[seriesInstanceUid] = protection.release(); } else { assert(found->second != NULL); if (protection->GetType() == SeriesThumbnailType_NotLoaded || protection->GetType() == SeriesThumbnailType_Unsupported) { // Don't replace an old entry if the current one is worse return; } else { delete found->second; found->second = protection.release(); } } LOG(INFO) << "Thumbnail updated for series: " << seriesInstanceUid << ": " << thumbnail->GetType(); SuccessMessage message(*this, source, studyInstanceUid, seriesInstanceUid, *thumbnail); BroadcastMessage(message); } class SeriesThumbnailsLoader::Handler : public Orthanc::IDynamicObject { private: boost::shared_ptr<SeriesThumbnailsLoader> loader_; DicomSource source_; std::string studyInstanceUid_; std::string seriesInstanceUid_; public: Handler(boost::shared_ptr<SeriesThumbnailsLoader> loader, const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) : loader_(loader), source_(source), studyInstanceUid_(studyInstanceUid), seriesInstanceUid_(seriesInstanceUid) { if (!loader) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } } boost::shared_ptr<SeriesThumbnailsLoader> GetLoader() { return loader_; } const DicomSource& GetSource() const { return source_; } const std::string& GetStudyInstanceUid() const { return studyInstanceUid_; } const std::string& GetSeriesInstanceUid() const { return seriesInstanceUid_; } virtual void HandleSuccess(const std::string& body, const std::map<std::string, std::string>& headers) = 0; virtual void HandleError() { LOG(INFO) << "Cannot generate thumbnail for SeriesInstanceUID: " << seriesInstanceUid_; } }; class SeriesThumbnailsLoader::DicomWebSopClassHandler : public SeriesThumbnailsLoader::Handler { private: static bool GetSopClassUid(std::string& sopClassUid, const Json::Value& json) { Orthanc::DicomMap dicom; dicom.FromDicomWeb(json); return dicom.LookupStringValue(sopClassUid, Orthanc::DICOM_TAG_SOP_CLASS_UID, false); } public: DicomWebSopClassHandler(boost::shared_ptr<SeriesThumbnailsLoader> loader, const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) : Handler(loader, source, studyInstanceUid, seriesInstanceUid) { } virtual void HandleSuccess(const std::string& body, const std::map<std::string, std::string>& headers) ORTHANC_OVERRIDE { Json::Value value; if (!Orthanc::Toolbox::ReadJson(value, body) || value.type() != Json::arrayValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } else { SeriesThumbnailType type = SeriesThumbnailType_Unsupported; std::string sopClassUid; if (value.size() > 0 && GetSopClassUid(sopClassUid, value[0])) { bool ok = true; for (Json::Value::ArrayIndex i = 1; i < value.size() && ok; i++) { std::string s; if (!GetSopClassUid(s, value[i]) || s != sopClassUid) { ok = false; } } if (ok) { type = GetSeriesThumbnailType(StringToSopClassUid(sopClassUid)); } } GetLoader()->AcquireThumbnail(GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid(), new Thumbnail(type)); } } }; class SeriesThumbnailsLoader::DicomWebThumbnailHandler : public SeriesThumbnailsLoader::Handler { public: DicomWebThumbnailHandler(boost::shared_ptr<SeriesThumbnailsLoader> loader, const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) : Handler(loader, source, studyInstanceUid, seriesInstanceUid) { } virtual void HandleSuccess(const std::string& body, const std::map<std::string, std::string>& headers) ORTHANC_OVERRIDE { std::string mime = Orthanc::MIME_JPEG; for (std::map<std::string, std::string>::const_iterator it = headers.begin(); it != headers.end(); ++it) { if (boost::iequals(it->first, "content-type")) { mime = it->second; } } GetLoader()->AcquireThumbnail(GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid(), new Thumbnail(body, mime)); } virtual void HandleError() ORTHANC_OVERRIDE { // The DICOMweb wasn't able to generate a thumbnail, try to // retrieve the SopClassUID tag using QIDO-RS std::map<std::string, std::string> arguments, headers; arguments["0020000D"] = GetStudyInstanceUid(); arguments["0020000E"] = GetSeriesInstanceUid(); arguments["includefield"] = "00080016"; // SOP Class UID std::unique_ptr<IOracleCommand> command( GetSource().CreateDicomWebCommand( "/instances", arguments, headers, new DicomWebSopClassHandler( GetLoader(), GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid()))); GetLoader()->Schedule(command.release()); } }; class SeriesThumbnailsLoader::ThumbnailInformation : public Orthanc::IDynamicObject { private: DicomSource source_; std::string studyInstanceUid_; std::string seriesInstanceUid_; public: ThumbnailInformation(const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) : source_(source), studyInstanceUid_(studyInstanceUid), seriesInstanceUid_(seriesInstanceUid) { } const DicomSource& GetDicomSource() const { return source_; } const std::string& GetStudyInstanceUid() const { return studyInstanceUid_; } const std::string& GetSeriesInstanceUid() const { return seriesInstanceUid_; } }; class SeriesThumbnailsLoader::OrthancSopClassHandler : public SeriesThumbnailsLoader::Handler { private: std::string instanceId_; public: OrthancSopClassHandler(boost::shared_ptr<SeriesThumbnailsLoader> loader, const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid, const std::string& instanceId) : Handler(loader, source, studyInstanceUid, seriesInstanceUid), instanceId_(instanceId) { } virtual void HandleSuccess(const std::string& body, const std::map<std::string, std::string>& headers) ORTHANC_OVERRIDE { SeriesThumbnailType type = GetSeriesThumbnailType(StringToSopClassUid(body)); if (type == SeriesThumbnailType_Pdf || type == SeriesThumbnailType_Video) { GetLoader()->AcquireThumbnail(GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid(), new Thumbnail(type)); } else { std::unique_ptr<GetOrthancImageCommand> command(new GetOrthancImageCommand); command->SetUri("/instances/" + instanceId_ + "/preview"); command->SetHttpHeader("Accept", Orthanc::MIME_JPEG); command->AcquirePayload(new ThumbnailInformation( GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid())); GetLoader()->Schedule(command.release()); } } }; class SeriesThumbnailsLoader::SelectOrthancInstanceHandler : public SeriesThumbnailsLoader::Handler { public: SelectOrthancInstanceHandler(boost::shared_ptr<SeriesThumbnailsLoader> loader, const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) : Handler(loader, source, studyInstanceUid, seriesInstanceUid) { } virtual void HandleSuccess(const std::string& body, const std::map<std::string, std::string>& headers) ORTHANC_OVERRIDE { static const char* const INSTANCES = "Instances"; Json::Value json; if (!Orthanc::Toolbox::ReadJson(json, body) || json.type() != Json::objectValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } if (json.isMember(INSTANCES) && json[INSTANCES].type() == Json::arrayValue && json[INSTANCES].size() > 0) { // Select one instance of the series to generate the thumbnail Json::Value::ArrayIndex index = json[INSTANCES].size() / 2; if (json[INSTANCES][index].type() == Json::stringValue) { const std::string instance = json[INSTANCES][index].asString(); std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); command->SetUri("/instances/" + instance + "/metadata/SopClassUid"); command->AcquirePayload( new OrthancSopClassHandler( GetLoader(), GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid(), instance)); GetLoader()->Schedule(command.release()); } } } }; #if ORTHANC_ENABLE_DCMTK == 1 class SeriesThumbnailsLoader::SelectDicomWebInstanceHandler : public SeriesThumbnailsLoader::Handler { public: SelectDicomWebInstanceHandler(boost::shared_ptr<SeriesThumbnailsLoader> loader, const DicomSource& source, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) : Handler(loader, source, studyInstanceUid, seriesInstanceUid) { } virtual void HandleSuccess(const std::string& body, const std::map<std::string, std::string>& headers) ORTHANC_OVERRIDE { Json::Value json; if (!Orthanc::Toolbox::ReadJson(json, body) || json.type() != Json::arrayValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } LoadedDicomResources instances(Orthanc::DICOM_TAG_SOP_INSTANCE_UID); instances.AddFromDicomWeb(json); std::string sopInstanceUid; if (instances.GetSize() == 0 || !instances.GetResource(0).LookupStringValue(sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) { LOG(ERROR) << "Series without an instance: " << GetSeriesInstanceUid(); } else { GetLoader()->Schedule( ParseDicomFromWadoCommand::Create( GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid(), sopInstanceUid, false, Orthanc::DicomTransferSyntax_LittleEndianExplicit /* useless, as no transcoding */, new ThumbnailInformation( GetSource(), GetStudyInstanceUid(), GetSeriesInstanceUid()))); } } }; #endif void SeriesThumbnailsLoader::Schedule(IOracleCommand* command) { std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock()); lock->Schedule(GetSharedObserver(), priority_, command); } void SeriesThumbnailsLoader::Handle(const HttpCommand::SuccessMessage& message) { assert(message.GetOrigin().HasPayload()); dynamic_cast<Handler&>(message.GetOrigin().GetPayload()).HandleSuccess(message.GetAnswer(), message.GetAnswerHeaders()); } void SeriesThumbnailsLoader::Handle(const OrthancRestApiCommand::SuccessMessage& message) { assert(message.GetOrigin().HasPayload()); dynamic_cast<Handler&>(message.GetOrigin().GetPayload()).HandleSuccess(message.GetAnswer(), message.GetAnswerHeaders()); } void SeriesThumbnailsLoader::Handle(const GetOrthancImageCommand::SuccessMessage& message) { assert(message.GetOrigin().HasPayload()); const ThumbnailInformation& info = dynamic_cast<ThumbnailInformation&>(message.GetOrigin().GetPayload()); std::unique_ptr<Orthanc::ImageAccessor> resized(Orthanc::ImageProcessing::FitSize(message.GetImage(), width_, height_)); std::string jpeg; Orthanc::JpegWriter writer; writer.SetQuality(JPEG_QUALITY); Orthanc::IImageWriter::WriteToMemory(writer, jpeg, *resized); AcquireThumbnail(info.GetDicomSource(), info.GetStudyInstanceUid(), info.GetSeriesInstanceUid(), new Thumbnail(jpeg, Orthanc::MIME_JPEG)); } #if ORTHANC_ENABLE_DCMTK == 1 void SeriesThumbnailsLoader::Handle(const ParseDicomSuccessMessage& message) { assert(message.GetOrigin().HasPayload()); const ParseDicomFromWadoCommand& origin = dynamic_cast<const ParseDicomFromWadoCommand&>(message.GetOrigin()); const ThumbnailInformation& info = dynamic_cast<ThumbnailInformation&>(origin.GetPayload()); Orthanc::DicomTransferSyntax transferSyntax; if (!message.GetDicom().LookupTransferSyntax(transferSyntax)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "DICOM instance without a transfer syntax: " + origin.GetSopInstanceUid()); } else if (!ImageToolbox::IsDecodingSupported(transferSyntax)) { LOG(INFO) << "Asking the DICOMweb server to transcode, " << "as I don't support this transfer syntax: " << Orthanc::GetTransferSyntaxUid(transferSyntax); Schedule(ParseDicomFromWadoCommand::Create( origin.GetSource(), info.GetStudyInstanceUid(), info.GetSeriesInstanceUid(), origin.GetSopInstanceUid(), true, Orthanc::DicomTransferSyntax_LittleEndianExplicit, new ThumbnailInformation( origin.GetSource(), info.GetStudyInstanceUid(), info.GetSeriesInstanceUid()))); } else { std::unique_ptr<Orthanc::ImageAccessor> frame(message.GetDicom().DecodeFrame(0)); std::unique_ptr<Orthanc::ImageAccessor> thumbnail; if (frame->GetFormat() == Orthanc::PixelFormat_RGB24) { thumbnail.reset(Orthanc::ImageProcessing::FitSizeKeepAspectRatio(*frame, width_, height_)); } else { std::unique_ptr<Orthanc::ImageAccessor> converted( new Orthanc::Image(Orthanc::PixelFormat_Float32, frame->GetWidth(), frame->GetHeight(), false)); Orthanc::ImageProcessing::Convert(*converted, *frame); std::unique_ptr<Orthanc::ImageAccessor> resized( Orthanc::ImageProcessing::FitSizeKeepAspectRatio(*converted, width_, height_)); float minValue, maxValue; Orthanc::ImageProcessing::GetMinMaxFloatValue(minValue, maxValue, *resized); if (minValue + 0.01f < maxValue) { Orthanc::ImageProcessing::ShiftScale(*resized, -minValue, 255.0f / (maxValue - minValue), false); } else { Orthanc::ImageProcessing::Set(*resized, 0); } converted.reset(NULL); thumbnail.reset(new Orthanc::Image(Orthanc::PixelFormat_Grayscale8, width_, height_, false)); Orthanc::ImageProcessing::Convert(*thumbnail, *resized); } std::string jpeg; Orthanc::JpegWriter writer; writer.SetQuality(JPEG_QUALITY); Orthanc::IImageWriter::WriteToMemory(writer, jpeg, *thumbnail); AcquireThumbnail(info.GetDicomSource(), info.GetStudyInstanceUid(), info.GetSeriesInstanceUid(), new Thumbnail(jpeg, Orthanc::MIME_JPEG)); } } #endif void SeriesThumbnailsLoader::Handle(const OracleCommandExceptionMessage& message) { const OracleCommandBase& command = dynamic_cast<const OracleCommandBase&>(message.GetOrigin()); assert(command.HasPayload()); if (command.GetType() == IOracleCommand::Type_GetOrthancImage) { // This is presumably a HTTP status 301 (Moved permanently) // because of an unsupported DICOM file in "/preview" const ThumbnailInformation& info = dynamic_cast<const ThumbnailInformation&>(command.GetPayload()); AcquireThumbnail(info.GetDicomSource(), info.GetStudyInstanceUid(), info.GetSeriesInstanceUid(), new Thumbnail(SeriesThumbnailType_Unsupported)); } else { dynamic_cast<Handler&>(command.GetPayload()).HandleError(); } } SeriesThumbnailsLoader::SeriesThumbnailsLoader(ILoadersContext& context, int priority) : context_(context), priority_(priority), width_(128), height_(128) { } boost::shared_ptr<SeriesThumbnailsLoader> SeriesThumbnailsLoader::Create( const ILoadersContext::ILock& stone, int priority) { boost::shared_ptr<SeriesThumbnailsLoader> result(new SeriesThumbnailsLoader(stone.GetContext(), priority)); result->Register<GetOrthancImageCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesThumbnailsLoader::Handle); result->Register<HttpCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesThumbnailsLoader::Handle); result->Register<OracleCommandExceptionMessage>(stone.GetOracleObservable(), &SeriesThumbnailsLoader::Handle); result->Register<OrthancRestApiCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesThumbnailsLoader::Handle); #if ORTHANC_ENABLE_DCMTK == 1 result->Register<ParseDicomSuccessMessage>(stone.GetOracleObservable(), &SeriesThumbnailsLoader::Handle); #endif return result; } void SeriesThumbnailsLoader::SetThumbnailSize(unsigned int width, unsigned int height) { if (width == 0 || height == 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } else { width_ = width; height_ = height; } } void SeriesThumbnailsLoader::Clear() { for (Thumbnails::iterator it = thumbnails_.begin(); it != thumbnails_.end(); ++it) { assert(it->second != NULL); delete it->second; } thumbnails_.clear(); } SeriesThumbnailType SeriesThumbnailsLoader::GetSeriesThumbnail(std::string& image, std::string& mime, const std::string& seriesInstanceUid) const { Thumbnails::const_iterator found = thumbnails_.find(seriesInstanceUid); if (found == thumbnails_.end()) { return SeriesThumbnailType_NotLoaded; } else { assert(found->second != NULL); image.assign(found->second->GetImage()); mime.assign(found->second->GetMime()); return found->second->GetType(); } } void SeriesThumbnailsLoader::ScheduleLoadThumbnail(const DicomSource& source, const std::string& patientId, const std::string& studyInstanceUid, const std::string& seriesInstanceUid) { if (IsScheduledSeries(seriesInstanceUid)) { return; } if (source.IsDicomWeb()) { if (!source.HasDicomWebRendered()) { #if ORTHANC_ENABLE_DCMTK == 1 // Issue a QIDO-RS request to select one of the instances in the series std::map<std::string, std::string> arguments, headers; arguments["0020000D"] = studyInstanceUid; arguments["0020000E"] = seriesInstanceUid; arguments["includefield"] = "00080018"; // SOP Instance UID is mandatory std::unique_ptr<IOracleCommand> command( source.CreateDicomWebCommand( "/instances", arguments, headers, new SelectDicomWebInstanceHandler( GetSharedObserver(), source, studyInstanceUid, seriesInstanceUid))); Schedule(command.release()); #else throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Stone of Orthanc was built without support to decode DICOM images"); #endif } else { const std::string uri = ("/studies/" + studyInstanceUid + "/series/" + seriesInstanceUid + "/rendered"); std::map<std::string, std::string> arguments, headers; arguments["viewport"] = (boost::lexical_cast<std::string>(width_) + "," + boost::lexical_cast<std::string>(height_)); // Needed to set this header explicitly, as long as emscripten // does not include macro "EMSCRIPTEN_FETCH_RESPONSE_HEADERS" // https://github.com/emscripten-core/emscripten/pull/8486 headers["Accept"] = Orthanc::MIME_JPEG; std::unique_ptr<IOracleCommand> command( source.CreateDicomWebCommand( uri, arguments, headers, new DicomWebThumbnailHandler( GetSharedObserver(), source, studyInstanceUid, seriesInstanceUid))); Schedule(command.release()); } scheduledSeries_.insert(seriesInstanceUid); } else if (source.IsOrthanc()) { // Dummy SOP Instance UID, as we are working at the "series" level Orthanc::DicomInstanceHasher hasher(patientId, studyInstanceUid, seriesInstanceUid, "dummy"); std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); command->SetUri("/series/" + hasher.HashSeries()); command->AcquirePayload(new SelectOrthancInstanceHandler( GetSharedObserver(), source, studyInstanceUid, seriesInstanceUid)); Schedule(command.release()); scheduledSeries_.insert(seriesInstanceUid); } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Can only load thumbnails from Orthanc or DICOMweb"); } } }