Mercurial > hg > orthanc
view OrthancServer/ServerJobs/ResourceModificationJob.cpp @ 3982:adc6f1fa7417 Orthanc-1.7.1
Orthanc-1.7.1
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 27 May 2020 08:12:33 +0200 |
parents | 5fe8c6d3212e |
children |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * 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 General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * In addition, as a special exception, the copyright holders of this * program give permission to link the code of its release with the * OpenSSL project's "OpenSSL" library (or with modified versions of it * that use the same license as the "OpenSSL" library), and distribute * the linked executables. You must obey the GNU General Public License * in all respects for all of the code used other than "OpenSSL". If you * modify file(s) with this exception, you may extend this exception to * your version of the file(s), but you are not obligated to do so. If * you do not wish to do so, delete this exception statement from your * version. If you delete this exception statement from all source files * in the program, then also delete it here. * * 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 * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "../PrecompiledHeadersServer.h" #include "ResourceModificationJob.h" #include "../../Core/Logging.h" #include "../../Core/SerializationToolbox.h" #include "../ServerContext.h" #include <dcmtk/dcmdata/dcfilefo.h> #include <dcmtk/dcmdata/dcdeftag.h> #include <cassert> namespace Orthanc { class ResourceModificationJob::Output : public boost::noncopyable { private: ResourceType level_; bool isFirst_; std::string id_; std::string patientId_; public: Output(ResourceType level) : level_(level), isFirst_(true) { if (level_ != ResourceType_Patient && level_ != ResourceType_Study && level_ != ResourceType_Series) { throw OrthancException(ErrorCode_ParameterOutOfRange); } } ResourceType GetLevel() const { return level_; } void Update(DicomInstanceHasher& hasher) { if (isFirst_) { switch (level_) { case ResourceType_Series: id_ = hasher.HashSeries(); break; case ResourceType_Study: id_ = hasher.HashStudy(); break; case ResourceType_Patient: id_ = hasher.HashPatient(); break; default: throw OrthancException(ErrorCode_InternalError); } patientId_ = hasher.HashPatient(); isFirst_ = false; } } bool Format(Json::Value& target) { if (isFirst_) { return false; } else { target = Json::objectValue; target["Type"] = EnumerationToString(level_); target["ID"] = id_; target["Path"] = GetBasePath(level_, id_); target["PatientID"] = patientId_; return true; } } bool GetIdentifier(std::string& id) { if (isFirst_) { return false; } else { id = id_; return true; } } }; bool ResourceModificationJob::HandleInstance(const std::string& instance) { if (modification_.get() == NULL || output_.get() == NULL) { throw OrthancException(ErrorCode_BadSequenceOfCalls, "No modification was provided for this job"); } LOG(INFO) << "Modifying instance in a job: " << instance; /** * Retrieve the original instance from the DICOM cache. **/ std::unique_ptr<DicomInstanceHasher> originalHasher; std::unique_ptr<ParsedDicomFile> modified; try { ServerContext::DicomCacheLocker locker(GetContext(), instance); ParsedDicomFile& original = locker.GetDicom(); originalHasher.reset(new DicomInstanceHasher(original.GetHasher())); modified.reset(original.Clone(true)); } catch (OrthancException& e) { LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails(); return false; } /** * Compute the resulting DICOM instance. **/ modification_->Apply(*modified); const std::string modifiedUid = IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject()); if (transcode_) { std::set<DicomTransferSyntax> syntaxes; syntaxes.insert(transferSyntax_); IDicomTranscoder::DicomImage source; source.AcquireParsed(*modified); // "modified" is invalid below this point IDicomTranscoder::DicomImage transcoded; if (GetContext().Transcode(transcoded, source, syntaxes, true)) { modified.reset(transcoded.ReleaseAsParsedDicomFile()); // Fix the SOP instance UID in order the preserve the // references between instance UIDs in the DICOM hierarchy // (the UID might have changed in the case of lossy transcoding) if (modified.get() == NULL || modified->GetDcmtkObject().getDataset() == NULL || !modified->GetDcmtkObject().getDataset()->putAndInsertString( DCM_SOPInstanceUID, modifiedUid.c_str(), OFTrue /* replace */).good()) { throw OrthancException(ErrorCode_InternalError); } } else { LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance; modified.reset(source.ReleaseAsParsedDicomFile()); } } assert(modifiedUid == IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject())); DicomInstanceToStore toStore; toStore.SetOrigin(origin_); toStore.SetParsedDicomFile(*modified); /** * Prepare the metadata information to associate with the * resulting DICOM instance (AnonymizedFrom/ModifiedFrom). **/ DicomInstanceHasher modifiedHasher = modified->GetHasher(); MetadataType metadataType = (isAnonymization_ ? MetadataType_AnonymizedFrom : MetadataType_ModifiedFrom); if (originalHasher->HashSeries() != modifiedHasher.HashSeries()) { toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries()); } if (originalHasher->HashStudy() != modifiedHasher.HashStudy()) { toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy()); } if (originalHasher->HashPatient() != modifiedHasher.HashPatient()) { toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient()); } assert(instance == originalHasher->HashInstance()); toStore.AddMetadata(ResourceType_Instance, metadataType, instance); /** * Store the resulting DICOM instance into the Orthanc store. **/ std::string modifiedInstance; if (GetContext().Store(modifiedInstance, toStore, StoreInstanceMode_Default) != StoreStatus_Success) { throw OrthancException(ErrorCode_CannotStoreInstance, "Error while storing a modified instance " + instance); } /** * The assertion below will fail if automated transcoding to a * lossy transfer syntax is enabled in the Orthanc core, and if * the source instance is not in this transfer syntax. **/ // assert(modifiedInstance == modifiedHasher.HashInstance()); output_->Update(modifiedHasher); return true; } ResourceModificationJob::ResourceModificationJob(ServerContext& context) : CleaningInstancesJob(context, true /* by default, keep source */), modification_(new DicomModification), isAnonymization_(false), transcode_(false) { } void ResourceModificationJob::SetModification(DicomModification* modification, ResourceType level, bool isAnonymization) { if (modification == NULL) { throw OrthancException(ErrorCode_NullPointer); } else if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { modification_.reset(modification); output_.reset(new Output(level)); isAnonymization_ = isAnonymization; } } void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin) { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { origin_ = origin; } } void ResourceModificationJob::SetOrigin(const RestApiCall& call) { SetOrigin(DicomInstanceOrigin::FromRest(call)); } const DicomModification& ResourceModificationJob::GetModification() const { if (modification_.get() == NULL) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { return *modification_; } } DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const { if (transcode_) { return transferSyntax_; } else { throw OrthancException(ErrorCode_BadSequenceOfCalls); } } void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax) { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { transcode_ = true; transferSyntax_ = syntax; } } void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid) { DicomTransferSyntax s; if (LookupTransferSyntax(s, transferSyntaxUid)) { SetTranscode(s); } else { throw OrthancException(ErrorCode_BadFileFormat, "Unknown transfer syntax UID: " + transferSyntaxUid); } } void ResourceModificationJob::ClearTranscode() { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { transcode_ = false; } } void ResourceModificationJob::GetPublicContent(Json::Value& value) { CleaningInstancesJob::GetPublicContent(value); value["IsAnonymization"] = isAnonymization_; if (output_.get() != NULL) { output_->Format(value); } if (transcode_) { value["Transcode"] = GetTransferSyntaxUid(transferSyntax_); } } static const char* MODIFICATION = "Modification"; static const char* ORIGIN = "Origin"; static const char* IS_ANONYMIZATION = "IsAnonymization"; static const char* TRANSCODE = "Transcode"; ResourceModificationJob::ResourceModificationJob(ServerContext& context, const Json::Value& serialized) : CleaningInstancesJob(context, serialized, true /* by default, keep source */) { assert(serialized.type() == Json::objectValue); isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION); origin_ = DicomInstanceOrigin(serialized[ORIGIN]); modification_.reset(new DicomModification(serialized[MODIFICATION])); if (serialized.isMember(TRANSCODE)) { SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE)); } else { transcode_ = false; } } bool ResourceModificationJob::Serialize(Json::Value& value) { if (!CleaningInstancesJob::Serialize(value)) { return false; } else { assert(value.type() == Json::objectValue); value[IS_ANONYMIZATION] = isAnonymization_; if (transcode_) { value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); } origin_.Serialize(value[ORIGIN]); Json::Value tmp; modification_->Serialize(tmp); value[MODIFICATION] = tmp; return true; } } }