Mercurial > hg > orthanc
view OrthancServer/Sources/ResourceFinder.cpp @ 5684:9b3816c21008 find-refactoring
integration mainline->find-refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 09 Jul 2024 11:39:07 +0200 |
parents | fd4c5e064cbe |
children | 11575590e493 |
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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) 2017-2023 Osimis S.A., Belgium * Copyright (C) 2024-2024 Orthanc Team SRL, 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 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 * 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 "ResourceFinder.h" #include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" #include "../../OrthancFramework/Sources/Logging.h" #include "../../OrthancFramework/Sources/OrthancException.h" #include "../../OrthancFramework/Sources/SerializationToolbox.h" #include "OrthancConfiguration.h" #include "Search/DatabaseLookup.h" #include "ServerContext.h" #include "ServerIndex.h" namespace Orthanc { void ResourceFinder::ConfigureChildrenCountComputedTag(DicomTag tag, ResourceType parentLevel, ResourceType childLevel) { if (request_.GetLevel() == parentLevel) { requestedComputedTags_.insert(tag); hasRequestedTags_ = true; request_.GetChildrenSpecification(childLevel).SetRetrieveIdentifiers(true); } } void ResourceFinder::InjectChildrenCountComputedTag(DicomMap& requestedTags, DicomTag tag, const FindResponse::Resource& resource, ResourceType level) const { if (IsRequestedComputedTag(tag)) { const std::set<std::string>& children = resource.GetChildrenIdentifiers(level); requestedTags.SetValue(tag, boost::lexical_cast<std::string>(children.size()), false); } } void ResourceFinder::InjectComputedTags(DicomMap& requestedTags, const FindResponse::Resource& resource) const { switch (resource.GetLevel()) { case ResourceType_Patient: InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES, resource, ResourceType_Study); InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES, resource, ResourceType_Series); InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES, resource, ResourceType_Instance); break; case ResourceType_Study: InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES, resource, ResourceType_Series); InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES, resource, ResourceType_Instance); if (IsRequestedComputedTag(DICOM_TAG_MODALITIES_IN_STUDY)) { std::set<std::string> modalities; resource.GetChildrenMainDicomTagValues(modalities, ResourceType_Series, DICOM_TAG_MODALITY); std::string s; Toolbox::JoinStrings(s, modalities, "\\"); requestedTags.SetValue(DICOM_TAG_MODALITIES_IN_STUDY, s, false); } if (IsRequestedComputedTag(DICOM_TAG_SOP_CLASSES_IN_STUDY)) { std::set<std::string> classes; resource.GetChildrenMetadataValues(classes, ResourceType_Instance, MetadataType_Instance_SopClassUid); std::string s; Toolbox::JoinStrings(s, classes, "\\"); requestedTags.SetValue(DICOM_TAG_SOP_CLASSES_IN_STUDY, s, false); } break; case ResourceType_Series: InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES, resource, ResourceType_Instance); break; case ResourceType_Instance: if (IsRequestedComputedTag(DICOM_TAG_INSTANCE_AVAILABILITY)) { requestedTags.SetValue(DICOM_TAG_INSTANCE_AVAILABILITY, "ONLINE", false); } break; default: throw OrthancException(ErrorCode_InternalError); } } SeriesStatus ResourceFinder::GetSeriesStatus(uint32_t& expectedNumberOfInstances, const FindResponse::Resource& resource) const { if (request_.GetLevel() != ResourceType_Series) { throw OrthancException(ErrorCode_BadParameterType); } std::string s; if (!resource.LookupMetadata(s, ResourceType_Series, MetadataType_Series_ExpectedNumberOfInstances) || !SerializationToolbox::ParseUnsignedInteger32(expectedNumberOfInstances, s)) { return SeriesStatus_Unknown; } std::set<std::string> values; resource.GetChildrenMetadataValues(values, ResourceType_Instance, MetadataType_Instance_IndexInSeries); std::set<int64_t> instances; for (std::set<std::string>::const_iterator it = values.begin(); it != values.end(); ++it) { int64_t index; if (!SerializationToolbox::ParseInteger64(index, *it)) { return SeriesStatus_Unknown; } if (index <= 0 || index > static_cast<int64_t>(expectedNumberOfInstances)) { // Out-of-range instance index return SeriesStatus_Inconsistent; } if (instances.find(index) != instances.end()) { // Twice the same instance index return SeriesStatus_Inconsistent; } instances.insert(index); } if (instances.size() == static_cast<size_t>(expectedNumberOfInstances)) { return SeriesStatus_Complete; } else { return SeriesStatus_Missing; } } void ResourceFinder::Expand(Json::Value& target, const FindResponse::Resource& resource, ServerIndex& index) const { /** * This method closely follows "SerializeExpandedResource()" in * "ServerContext.cpp" from Orthanc 1.12.3. **/ if (resource.GetLevel() != request_.GetLevel()) { throw OrthancException(ErrorCode_InternalError); } target = Json::objectValue; target["Type"] = GetResourceTypeText(resource.GetLevel(), false, true); target["ID"] = resource.GetIdentifier(); switch (resource.GetLevel()) { case ResourceType_Patient: break; case ResourceType_Study: target["ParentPatient"] = resource.GetParentIdentifier(); break; case ResourceType_Series: target["ParentStudy"] = resource.GetParentIdentifier(); break; case ResourceType_Instance: target["ParentSeries"] = resource.GetParentIdentifier(); break; default: throw OrthancException(ErrorCode_InternalError); } if (resource.GetLevel() != ResourceType_Instance) { const std::set<std::string>& children = resource.GetChildrenIdentifiers(GetChildResourceType(resource.GetLevel())); Json::Value c = Json::arrayValue; for (std::set<std::string>::const_iterator it = children.begin(); it != children.end(); ++it) { c.append(*it); } switch (resource.GetLevel()) { case ResourceType_Patient: target["Studies"] = c; break; case ResourceType_Study: target["Series"] = c; break; case ResourceType_Series: target["Instances"] = c; break; default: throw OrthancException(ErrorCode_InternalError); } } switch (resource.GetLevel()) { case ResourceType_Patient: case ResourceType_Study: break; case ResourceType_Series: { uint32_t expectedNumberOfInstances; SeriesStatus status = GetSeriesStatus(expectedNumberOfInstances, resource); target["Status"] = EnumerationToString(status); static const char* const EXPECTED_NUMBER_OF_INSTANCES = "ExpectedNumberOfInstances"; if (status == SeriesStatus_Unknown) { target[EXPECTED_NUMBER_OF_INSTANCES] = Json::nullValue; } else { target[EXPECTED_NUMBER_OF_INSTANCES] = expectedNumberOfInstances; } break; } case ResourceType_Instance: { FileInfo info; if (resource.LookupAttachment(info, FileContentType_Dicom)) { target["FileSize"] = static_cast<Json::UInt64>(info.GetUncompressedSize()); target["FileUuid"] = info.GetUuid(); } else { throw OrthancException(ErrorCode_InternalError); } static const char* const INDEX_IN_SERIES = "IndexInSeries"; std::string s; uint32_t index; if (resource.LookupMetadata(s, ResourceType_Instance, MetadataType_Instance_IndexInSeries) && SerializationToolbox::ParseUnsignedInteger32(index, s)) { target[INDEX_IN_SERIES] = index; } else { target[INDEX_IN_SERIES] = Json::nullValue; } break; } default: throw OrthancException(ErrorCode_InternalError); } std::string s; if (resource.LookupMetadata(s, resource.GetLevel(), MetadataType_AnonymizedFrom)) { target["AnonymizedFrom"] = s; } if (resource.LookupMetadata(s, resource.GetLevel(), MetadataType_ModifiedFrom)) { target["ModifiedFrom"] = s; } if (resource.GetLevel() == ResourceType_Patient || resource.GetLevel() == ResourceType_Study || resource.GetLevel() == ResourceType_Series) { target["IsStable"] = !index.IsUnstableResource(resource.GetLevel(), resource.GetInternalId()); if (resource.LookupMetadata(s, resource.GetLevel(), MetadataType_LastUpdate)) { target["LastUpdate"] = s; } } { DicomMap allMainDicomTags; resource.GetMainDicomTags(allMainDicomTags, resource.GetLevel()); /** * This section was part of "StatelessDatabaseOperations::ExpandResource()" * in Orthanc <= 1.12.3 **/ // read all main sequences from DB std::string serializedSequences; if (resource.LookupMetadata(serializedSequences, resource.GetLevel(), MetadataType_MainDicomSequences)) { Json::Value jsonMetadata; Toolbox::ReadJson(jsonMetadata, serializedSequences); if (jsonMetadata["Version"].asInt() == 1) { allMainDicomTags.FromDicomAsJson(jsonMetadata["Sequences"], true /* append */, true /* parseSequences */); } else { throw OrthancException(ErrorCode_NotImplemented); } } /** * End of section from StatelessDatabaseOperations **/ static const char* const MAIN_DICOM_TAGS = "MainDicomTags"; static const char* const PATIENT_MAIN_DICOM_TAGS = "PatientMainDicomTags"; // TODO-FIND : Ignore "null" values DicomMap levelMainDicomTags; allMainDicomTags.ExtractResourceInformation(levelMainDicomTags, resource.GetLevel()); target[MAIN_DICOM_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], levelMainDicomTags, format_); if (resource.GetLevel() == ResourceType_Study) { DicomMap patientMainDicomTags; allMainDicomTags.ExtractPatientInformation(patientMainDicomTags); target[PATIENT_MAIN_DICOM_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[PATIENT_MAIN_DICOM_TAGS], patientMainDicomTags, format_); } } { Json::Value labels = Json::arrayValue; for (std::set<std::string>::const_iterator it = resource.GetLabels().begin(); it != resource.GetLabels().end(); ++it) { labels.append(*it); } target["Labels"] = labels; } if (includeAllMetadata_) // new in Orthanc 1.12.4 { const std::map<MetadataType, std::string>& m = resource.GetMetadata(resource.GetLevel()); Json::Value metadata = Json::objectValue; for (std::map<MetadataType, std::string>::const_iterator it = m.begin(); it != m.end(); ++it) { metadata[EnumerationToString(it->first)] = it->second; } target["Metadata"] = metadata; } } ResourceFinder::ResourceFinder(ResourceType level, bool expand) : request_(level), expand_(expand), format_(DicomToJsonFormat_Human), allowStorageAccess_(true), hasRequestedTags_(false), includeAllMetadata_(false) { if (expand) { request_.SetRetrieveMainDicomTags(true); request_.SetRetrieveMetadata(true); request_.SetRetrieveLabels(true); switch (level) { case ResourceType_Patient: request_.GetChildrenSpecification(ResourceType_Study).SetRetrieveIdentifiers(true); break; case ResourceType_Study: request_.GetChildrenSpecification(ResourceType_Series).SetRetrieveIdentifiers(true); request_.SetRetrieveParentIdentifier(true); break; case ResourceType_Series: request_.GetChildrenSpecification(ResourceType_Instance).AddMetadata(MetadataType_Instance_IndexInSeries); // required for the SeriesStatus request_.GetChildrenSpecification(ResourceType_Instance).SetRetrieveIdentifiers(true); request_.SetRetrieveParentIdentifier(true); break; case ResourceType_Instance: request_.SetRetrieveAttachments(true); // for FileSize & FileUuid request_.SetRetrieveParentIdentifier(true); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } } void ResourceFinder::SetDatabaseLookup(const DatabaseLookup& lookup) { MainDicomTagsRegistry registry; registry.NormalizeLookup(request_.GetDicomTagConstraints(), lookup, request_.GetLevel()); } void ResourceFinder::AddRequestedTags(const DicomTag& tag) { if (DicomMap::IsMainDicomTag(tag, ResourceType_Patient)) { if (request_.GetLevel() == ResourceType_Patient) { request_.GetParentSpecification(ResourceType_Patient).SetRetrieveMainDicomTags(true); request_.GetParentSpecification(ResourceType_Patient).SetRetrieveMetadata(true); requestedPatientTags_.insert(tag); } else { /** * This comes from the fact that patient-level tags are copied * at the study level, as implemented by "ResourcesContent::AddResource()". **/ request_.GetParentSpecification(ResourceType_Study).SetRetrieveMainDicomTags(true); request_.GetParentSpecification(ResourceType_Study).SetRetrieveMetadata(true); requestedStudyTags_.insert(tag); } hasRequestedTags_ = true; } else if (DicomMap::IsMainDicomTag(tag, ResourceType_Study)) { if (request_.GetLevel() == ResourceType_Patient) { LOG(WARNING) << "Requested tag " << tag.Format() << " should only be read at the study, series, or instance level"; requestedTagsFromFileStorage_.insert(tag); request_.SetRetrieveOneInstanceIdentifier(true); } else { request_.GetParentSpecification(ResourceType_Study).SetRetrieveMainDicomTags(true); request_.GetParentSpecification(ResourceType_Study).SetRetrieveMetadata(true); requestedStudyTags_.insert(tag); } hasRequestedTags_ = true; } else if (DicomMap::IsMainDicomTag(tag, ResourceType_Series)) { if (request_.GetLevel() == ResourceType_Patient || request_.GetLevel() == ResourceType_Study) { LOG(WARNING) << "Requested tag " << tag.Format() << " should only be read at the series or instance level"; requestedTagsFromFileStorage_.insert(tag); request_.SetRetrieveOneInstanceIdentifier(true); } else { request_.GetParentSpecification(ResourceType_Series).SetRetrieveMainDicomTags(true); request_.GetParentSpecification(ResourceType_Series).SetRetrieveMetadata(true); requestedSeriesTags_.insert(tag); } hasRequestedTags_ = true; } else if (DicomMap::IsMainDicomTag(tag, ResourceType_Instance)) { if (request_.GetLevel() == ResourceType_Patient || request_.GetLevel() == ResourceType_Study || request_.GetLevel() == ResourceType_Series) { LOG(WARNING) << "Requested tag " << tag.Format() << " should only be read at the instance level"; requestedTagsFromFileStorage_.insert(tag); request_.SetRetrieveOneInstanceIdentifier(true); } else { // Main DICOM tags from the instance level will be retrieved anyway assert(request_.IsRetrieveMainDicomTags()); assert(request_.IsRetrieveMetadata()); requestedInstanceTags_.insert(tag); } hasRequestedTags_ = true; } else if (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES) { ConfigureChildrenCountComputedTag(tag, ResourceType_Patient, ResourceType_Study); } else if (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES) { ConfigureChildrenCountComputedTag(tag, ResourceType_Patient, ResourceType_Series); } else if (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES) { ConfigureChildrenCountComputedTag(tag, ResourceType_Patient, ResourceType_Instance); } else if (tag == DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES) { ConfigureChildrenCountComputedTag(tag, ResourceType_Study, ResourceType_Series); } else if (tag == DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES) { ConfigureChildrenCountComputedTag(tag, ResourceType_Study, ResourceType_Instance); } else if (tag == DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES) { ConfigureChildrenCountComputedTag(tag, ResourceType_Series, ResourceType_Instance); } else if (tag == DICOM_TAG_SOP_CLASSES_IN_STUDY) { requestedComputedTags_.insert(tag); hasRequestedTags_ = true; request_.GetChildrenSpecification(ResourceType_Instance).AddMetadata(MetadataType_Instance_SopClassUid); } else if (tag == DICOM_TAG_MODALITIES_IN_STUDY) { requestedComputedTags_.insert(tag); hasRequestedTags_ = true; request_.GetChildrenSpecification(ResourceType_Series).AddMainDicomTag(DICOM_TAG_MODALITY); } else if (tag == DICOM_TAG_INSTANCE_AVAILABILITY) { requestedComputedTags_.insert(tag); hasRequestedTags_ = true; } else { // This is neither a main DICOM tag, nor a computed DICOM tag: // We will be forced to access the DICOM file anyway requestedTagsFromFileStorage_.insert(tag); if (request_.GetLevel() != ResourceType_Instance) { request_.SetRetrieveOneInstanceIdentifier(true); } hasRequestedTags_ = true; } } void ResourceFinder::AddRequestedTags(const std::set<DicomTag>& tags) { for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) { AddRequestedTags(*it); } } static void InjectRequestedTags(DicomMap& requestedTags, std::set<DicomTag>& missingTags /* out */, const FindResponse::Resource& resource, ResourceType level, const std::set<DicomTag>& tags) { if (!tags.empty()) { DicomMap m; resource.GetMainDicomTags(m, level); for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) { std::string value; if (m.LookupStringValue(value, *it, false /* not binary */)) { requestedTags.SetValue(*it, value, false /* not binary */); } else { // This is the case where the Housekeeper should be run missingTags.insert(*it); } } } } static void ReadMissingTagsFromStorageArea(DicomMap& requestedTags, ServerContext& context, const FindRequest& request, const FindResponse::Resource& resource, const std::set<DicomTag>& missingTags) { OrthancConfiguration::ReaderLock lock; if (lock.GetConfiguration().IsWarningEnabled(Warnings_001_TagsBeingReadFromStorage)) { std::string missings; FromDcmtkBridge::FormatListOfTags(missings, missingTags); LOG(WARNING) << "W001: Accessing Dicom tags from storage when accessing " << Orthanc::GetResourceTypeText(resource.GetLevel(), false, false) << ": " << missings; } std::string instancePublicId; if (request.IsRetrieveOneInstanceIdentifier()) { instancePublicId = resource.GetOneInstanceIdentifier(); } else if (request.GetLevel() == ResourceType_Instance) { instancePublicId = resource.GetIdentifier(); } else { FindRequest requestDicomAttachment(request.GetLevel()); requestDicomAttachment.SetOrthancId(request.GetLevel(), resource.GetIdentifier()); requestDicomAttachment.SetRetrieveOneInstanceIdentifier(true); FindResponse responseDicomAttachment; context.GetIndex().ExecuteFind(responseDicomAttachment, requestDicomAttachment); if (responseDicomAttachment.GetSize() != 1 || !responseDicomAttachment.GetResourceByIndex(0).HasOneInstanceIdentifier()) { throw OrthancException(ErrorCode_InexistentFile); } else { instancePublicId = responseDicomAttachment.GetResourceByIndex(0).GetOneInstanceIdentifier(); } } LOG(INFO) << "Will retrieve missing DICOM tags from instance: " << instancePublicId; // TODO-FIND: What do we do if the DICOM has been removed since the request? // Do we fail, or do we skip the resource? Json::Value tmpDicomAsJson; context.ReadDicomAsJson(tmpDicomAsJson, instancePublicId, missingTags /* ignoreTagLength */); DicomMap tmpDicomMap; tmpDicomMap.FromDicomAsJson(tmpDicomAsJson, false /* append */, true /* parseSequences*/); for (std::set<DicomTag>::const_iterator it = missingTags.begin(); it != missingTags.end(); ++it) { assert(!requestedTags.HasTag(*it)); if (tmpDicomMap.HasTag(*it)) { requestedTags.SetValue(*it, tmpDicomMap.GetValue(*it)); } else { requestedTags.SetNullValue(*it); // TODO-FIND: Is this compatible with Orthanc <= 1.12.3? } } } void ResourceFinder::Execute(FindResponse& response, ServerIndex& index) const { if (hasRequestedTags_) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { index.ExecuteFind(response, request_); } } void ResourceFinder::Execute(Json::Value& target, ServerContext& context) const { FindResponse response; context.GetIndex().ExecuteFind(response, request_); target = Json::arrayValue; for (size_t i = 0; i < response.GetSize(); i++) { const FindResponse::Resource& resource = response.GetResourceByIndex(i); if (expand_) { Json::Value item; Expand(item, resource, context.GetIndex()); if (hasRequestedTags_) { DicomMap requestedTags; InjectComputedTags(requestedTags, resource); std::set<DicomTag> missingTags = requestedTagsFromFileStorage_; InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Patient, requestedPatientTags_); InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Study, requestedStudyTags_); InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Series, requestedSeriesTags_); InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Instance, requestedInstanceTags_); if (!missingTags.empty()) { if (!allowStorageAccess_) { throw OrthancException(ErrorCode_BadSequenceOfCalls, "Cannot add missing requested tags, as access to file storage is disallowed"); } else { ReadMissingTagsFromStorageArea(requestedTags, context, request_, resource, missingTags); } } static const char* const REQUESTED_TAGS = "RequestedTags"; item[REQUESTED_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(item[REQUESTED_TAGS], requestedTags, format_); } target.append(item); } else { target.append(resource.GetIdentifier()); } } } bool ResourceFinder::ExecuteOneResource(Json::Value& target, ServerContext& context) const { Json::Value answer; Execute(answer, context); if (answer.type() != Json::arrayValue) { throw OrthancException(ErrorCode_InternalError); } else if (answer.size() > 1) { throw OrthancException(ErrorCode_DatabasePlugin); } else if (answer.empty()) { // Inexistent resource (or was deleted between the first and second phases) return false; } else { target = answer[0]; return true; } } }