Mercurial > hg > orthanc
view OrthancServer/ServerJobs/SplitStudyJob.cpp @ 3520:77bede920d22
merge
author | amazy |
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date | Thu, 19 Sep 2019 13:11:11 +0200 |
parents | 69e49fc044f8 |
children | 94f4a18a79cc |
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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) 2017-2019 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 "SplitStudyJob.h" #include "../../Core/DicomParsing/FromDcmtkBridge.h" #include "../../Core/Logging.h" #include "../../Core/SerializationToolbox.h" #include "../ServerContext.h" namespace Orthanc { void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const { if (allowedTags_.find(tag) == allowedTags_.end()) { throw OrthancException(ErrorCode_ParameterOutOfRange, "Cannot modify the following tag while splitting a study " "(not in the patient/study modules): " + FromDcmtkBridge::GetTagName(tag, "") + " (" + tag.Format() + ")"); } } void SplitStudyJob::Setup() { SetPermissive(false); DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient); DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study); allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID); allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID); } bool SplitStudyJob::HandleInstance(const std::string& instance) { /** * Retrieve the DICOM instance to be modified **/ std::auto_ptr<ParsedDicomFile> modified; try { ServerContext::DicomCacheLocker locker(context_, instance); modified.reset(locker.GetDicom().Clone(true)); } catch (OrthancException&) { LOG(WARNING) << "An instance was removed after the job was issued: " << instance; return false; } /** * Chose the target UIDs **/ assert(modified->GetHasher().HashStudy() == sourceStudy_); std::string series = modified->GetHasher().HashSeries(); SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series); if (targetSeriesUid == seriesUidMap_.end()) { throw OrthancException(ErrorCode_BadFileFormat); // Should never happen } /** * Apply user-specified modifications **/ for (std::set<DicomTag>::const_iterator it = removals_.begin(); it != removals_.end(); ++it) { modified->Remove(*it); } for (Replacements::const_iterator it = replacements_.begin(); it != replacements_.end(); ++it) { modified->ReplacePlainString(it->first, it->second); } /** * Store the new instance into Orthanc **/ modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_); modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second); // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); if (targetStudy_.empty()) { targetStudy_ = modified->GetHasher().HashStudy(); } DicomInstanceToStore toStore; toStore.SetOrigin(origin_); toStore.SetParsedDicomFile(*modified); std::string modifiedInstance; if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success) { LOG(ERROR) << "Error while storing a modified instance " << instance; return false; } return true; } bool SplitStudyJob::HandleTrailingStep() { if (!keepSource_) { const size_t n = GetInstancesCount(); for (size_t i = 0; i < n; i++) { Json::Value tmp; context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance); } } return true; } SplitStudyJob::SplitStudyJob(ServerContext& context, const std::string& sourceStudy) : context_(context), keepSource_(false), sourceStudy_(sourceStudy), targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)) { Setup(); ResourceType type; if (!context_.GetIndex().LookupResourceType(type, sourceStudy) || type != ResourceType_Study) { throw OrthancException(ErrorCode_UnknownResource, "Cannot split unknown study " + sourceStudy); } } void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin) { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { origin_ = origin; } } void SplitStudyJob::SetOrigin(const RestApiCall& call) { SetOrigin(DicomInstanceOrigin::FromRest(call)); } void SplitStudyJob::AddSourceSeries(const std::string& series) { std::string parent; if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study) || parent != sourceStudy_) { throw OrthancException(ErrorCode_UnknownResource, "This series does not belong to the study to be split: " + series); } else { // Generate a target SeriesInstanceUID for this series seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); // Add all the instances of the series as to be processed std::list<std::string> instances; context_.GetIndex().GetChildren(instances, series); for (std::list<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { AddInstance(*it); } } } void SplitStudyJob::SetKeepSource(bool keep) { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } keepSource_ = keep; } bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid, const std::string& series) const { SeriesUidMap::const_iterator found = seriesUidMap_.find(series); if (found == seriesUidMap_.end()) { return false; } else { uid = found->second; return true; } } void SplitStudyJob::Remove(const DicomTag& tag) { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } CheckAllowedTag(tag); removals_.insert(tag); } void SplitStudyJob::Replace(const DicomTag& tag, const std::string& value) { if (IsStarted()) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } CheckAllowedTag(tag); replacements_[tag] = value; } bool SplitStudyJob::LookupReplacement(std::string& value, const DicomTag& tag) const { Replacements::const_iterator found = replacements_.find(tag); if (found == replacements_.end()) { return false; } else { value = found->second; return true; } } void SplitStudyJob::GetPublicContent(Json::Value& value) { SetOfInstancesJob::GetPublicContent(value); if (!targetStudy_.empty()) { value["TargetStudy"] = targetStudy_; } value["TargetStudyUID"] = targetStudyUid_; } static const char* KEEP_SOURCE = "KeepSource"; static const char* SOURCE_STUDY = "SourceStudy"; static const char* TARGET_STUDY = "TargetStudy"; static const char* TARGET_STUDY_UID = "TargetStudyUID"; static const char* SERIES_UID_MAP = "SeriesUIDMap"; static const char* ORIGIN = "Origin"; static const char* REPLACEMENTS = "Replacements"; static const char* REMOVALS = "Removals"; SplitStudyJob::SplitStudyJob(ServerContext& context, const Json::Value& serialized) : SetOfInstancesJob(serialized), // (*) context_(context) { if (!HasTrailingStep()) { // Should have been set by (*) throw OrthancException(ErrorCode_InternalError); } Setup(); keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE); sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY); targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY); targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID); SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP); origin_ = DicomInstanceOrigin(serialized[ORIGIN]); SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS); SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS); } bool SplitStudyJob::Serialize(Json::Value& target) { if (!SetOfInstancesJob::Serialize(target)) { return false; } else { target[KEEP_SOURCE] = keepSource_; target[SOURCE_STUDY] = sourceStudy_; target[TARGET_STUDY] = targetStudy_; target[TARGET_STUDY_UID] = targetStudyUid_; SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP); origin_.Serialize(target[ORIGIN]); SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS); SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS); return true; } } }