Mercurial > hg > orthanc
view OrthancServer/Sources/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 5569:738f80622e91 find-refactoring
merge default -> find-refactoring
author | Alain Mazy <am@orthanc.team> |
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date | Thu, 25 Apr 2024 17:07:33 +0200 |
parents | 4b3f5986eca1 |
children | f7adfb22e20e |
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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) 2017-2024 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 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 "OrthancRestApi.h" #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" #include "../../../OrthancFramework/Sources/Logging.h" #include "../../../OrthancFramework/Sources/SerializationToolbox.h" #include "../OrthancConfiguration.h" #include "../ServerContext.h" #include "../ServerJobs/MergeStudyJob.h" #include "../ServerJobs/ResourceModificationJob.h" #include "../ServerJobs/SplitStudyJob.h" #include <boost/lexical_cast.hpp> #include <boost/algorithm/string/predicate.hpp> #define INFO_SUBSEQUENCES \ "Starting with Orthanc 1.9.4, paths to subsequences can be provided using the "\ "same syntax as the `dcmodify` command-line tool (wildcards are supported as well)." static const char* const CONTENT = "Content"; static const char* const FORCE = "Force"; static const char* const INSTANCES = "Instances"; static const char* const INTERPRET_BINARY_TAGS = "InterpretBinaryTags"; static const char* const KEEP = "Keep"; static const char* const KEEP_PRIVATE_TAGS = "KeepPrivateTags"; static const char* const KEEP_LABELS = "KeepLabels"; static const char* const KEEP_SOURCE = "KeepSource"; static const char* const LEVEL = "Level"; static const char* const PARENT = "Parent"; static const char* const PRIVATE_CREATOR = "PrivateCreator"; static const char* const REMOVE = "Remove"; static const char* const REPLACE = "Replace"; static const char* const RESOURCES = "Resources"; static const char* const SERIES = "Series"; static const char* const TAGS = "Tags"; static const char* const TRANSCODE = "Transcode"; namespace Orthanc { // Modification of DICOM instances ------------------------------------------ static std::string GeneratePatientName(ServerContext& context) { uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence, true /* shared */); return "Anonymized" + boost::lexical_cast<std::string>(seq); } static void DocumentKeepSource(RestApiPostCall& call) { call.GetDocumentation() .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, "If set to `false`, instructs Orthanc to the remove original resources. " "By default, the original resources are kept in Orthanc.", false); } static void DocumentModifyOptions(RestApiPostCall& call) { // Check out "DicomModification::ParseModifyRequest()" call.GetDocumentation() .SetRequestField(TRANSCODE, RestApiCallDocumentation::Type_String, "Transcode the DICOM instances to the provided DICOM transfer syntax: " "https://orthanc.uclouvain.be/book/faq/transcoding.html", false) .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, "Allow the modification of tags related to DICOM identifiers, at the risk of " "breaking the DICOM model of the real world", false) .SetRequestField("RemovePrivateTags", RestApiCallDocumentation::Type_Boolean, "Remove the private tags from the DICOM instances (defaults to `false`)", false) .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, "Associative array to change the value of some DICOM tags in the DICOM instances. " INFO_SUBSEQUENCES, false) .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, "List of tags that must be removed from the DICOM instances. " INFO_SUBSEQUENCES, false) .SetRequestField(KEEP, RestApiCallDocumentation::Type_JsonListOfStrings, "Keep the original value of the specified tags, to be chosen among the `StudyInstanceUID`, " "`SeriesInstanceUID` and `SOPInstanceUID` tags. Avoid this feature as much as possible, " "as this breaks the DICOM model of the real world.", false) .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, "The private creator to be used for private tags in `Replace`", false); // This was existing, but undocumented in Orthanc <= 1.9.6 DocumentKeepSource(call); } static void DocumentAnonymizationOptions(RestApiPostCall& call) { // Check out "DicomModification::ParseAnonymizationRequest()" call.GetDocumentation() .SetRequestField(TRANSCODE, RestApiCallDocumentation::Type_String, "Transcode the DICOM instances to the provided DICOM transfer syntax: " "https://orthanc.uclouvain.be/book/faq/transcoding.html", false) .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, "Allow the modification of tags related to DICOM identifiers, at the risk of " "breaking the DICOM model of the real world", false) .SetRequestField("DicomVersion", RestApiCallDocumentation::Type_String, "Version of the DICOM standard to be used for anonymization. Check out " "configuration option `DeidentifyLogsDicomVersion` for possible values.", false) .SetRequestField(KEEP_PRIVATE_TAGS, RestApiCallDocumentation::Type_Boolean, "Keep the private tags from the DICOM instances (defaults to `false`)", false) .SetRequestField(KEEP_LABELS, RestApiCallDocumentation::Type_Boolean, "Keep the labels of all resources level (defaults to `false`)", false) .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, "Associative array to change the value of some DICOM tags in the DICOM instances. " INFO_SUBSEQUENCES, false) .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, "List of additional tags to be removed from the DICOM instances. " INFO_SUBSEQUENCES, false) .SetRequestField(KEEP, RestApiCallDocumentation::Type_JsonListOfStrings, "List of DICOM tags whose value must not be destroyed by the anonymization. " INFO_SUBSEQUENCES, false) .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, "The private creator to be used for private tags in `Replace`", false); // This was existing, but undocumented in Orthanc <= 1.9.6 DocumentKeepSource(call); } static void ParseModifyRequest(Json::Value& request, DicomModification& target, const RestApiPostCall& call) { // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"},"Priority":9}' { OrthancConfiguration::ReaderLock lock; target.SetPrivateCreator(lock.GetConfiguration().GetDefaultPrivateCreator()); } if (call.ParseJsonRequest(request)) { target.ParseModifyRequest(request); } else { throw OrthancException(ErrorCode_BadFileFormat); } } static void ParseAnonymizationRequest(Json::Value& request, DicomModification& target, RestApiPostCall& call) { // curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{"Replace":{"PatientName":"hello","0010-0020":"world"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": true,"Remove":["Modality"]}' > Anonymized.dcm { OrthancConfiguration::ReaderLock lock; target.SetPrivateCreator(lock.GetConfiguration().GetDefaultPrivateCreator()); } if (call.ParseJsonRequest(request) && request.isObject()) { bool patientNameOverridden; target.ParseAnonymizationRequest(patientNameOverridden, request); if (!patientNameOverridden) { // Override the random Patient's Name by one that is more // user-friendly (provided none was specified by the user) target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)), true); } } else { throw OrthancException(ErrorCode_BadFileFormat); } } static void AnonymizeOrModifyInstance(DicomModification& modification, RestApiPostCall& call, bool transcode, DicomTransferSyntax targetSyntax) { ServerContext& context = OrthancRestApi::GetContext(call); std::string id = call.GetUriComponent("id", ""); std::unique_ptr<ParsedDicomFile> modified; { ServerContext::DicomCacheLocker locker(context, id); modified.reset(locker.GetDicom().Clone(true)); } modification.Apply(*modified); if (transcode) { IDicomTranscoder::DicomImage source; source.AcquireParsed(*modified); // "modified" is invalid below this point IDicomTranscoder::DicomImage transcoded; std::set<DicomTransferSyntax> s; s.insert(targetSyntax); if (context.Transcode(transcoded, source, s, true)) { call.GetOutput().AnswerBuffer(transcoded.GetBufferData(), transcoded.GetBufferSize(), MimeType_Dicom); } else { throw OrthancException(ErrorCode_InternalError, "Cannot transcode to transfer syntax: " + std::string(GetTransferSyntaxUid(targetSyntax))); } } else { modified->Answer(call.GetOutput()); } } static ResourceType DetectModifyLevel(const DicomModification& modification) { if (modification.IsReplaced(DICOM_TAG_PATIENT_ID)) { return ResourceType_Patient; } else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) { return ResourceType_Study; } else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) { return ResourceType_Series; } else { return ResourceType_Instance; } } static void ModifyInstance(RestApiPostCall& call) { if (call.IsDocumentation()) { DocumentModifyOptions(call); call.GetDocumentation() .SetTag("Instances") .SetSummary("Modify instance") .SetDescription("Download a modified version of the DICOM instance whose Orthanc identifier is provided in the URL: " "https://orthanc.uclouvain.be/book/users/anonymization.html#modification-of-a-single-instance") .SetUriArgument("id", "Orthanc identifier of the instance of interest") .AddAnswerType(MimeType_Dicom, "The modified DICOM instance"); return; } DicomModification modification; modification.SetAllowManualIdentifiers(true); Json::Value request; ParseModifyRequest(request, modification, call); modification.SetLevel(DetectModifyLevel(modification)); if (request.isMember(TRANSCODE)) { std::string s = SerializationToolbox::ReadString(request, TRANSCODE); DicomTransferSyntax syntax; if (LookupTransferSyntax(syntax, s)) { AnonymizeOrModifyInstance(modification, call, true, syntax); } else { throw OrthancException(ErrorCode_ParameterOutOfRange, "Unknown transfer syntax: " + s); } } else { AnonymizeOrModifyInstance(modification, call, false /* no transcoding */, DicomTransferSyntax_LittleEndianImplicit /* unused */); } } static void AnonymizeInstance(RestApiPostCall& call) { if (call.IsDocumentation()) { DocumentAnonymizationOptions(call); call.GetDocumentation() .SetTag("Instances") .SetSummary("Anonymize instance") .SetDescription("Download an anonymized version of the DICOM instance whose Orthanc identifier is provided in the URL: " "https://orthanc.uclouvain.be/book/users/anonymization.html#anonymization-of-a-single-instance") .SetUriArgument("id", "Orthanc identifier of the instance of interest") .AddAnswerType(MimeType_Dicom, "The anonymized DICOM instance"); return; } DicomModification modification; modification.SetAllowManualIdentifiers(true); Json::Value request; ParseAnonymizationRequest(request, modification, call); AnonymizeOrModifyInstance(modification, call, false /* no transcoding */, DicomTransferSyntax_LittleEndianImplicit /* unused */); } static void SetKeepSource(CleaningInstancesJob& job, const Json::Value& body) { if (body.isMember(KEEP_SOURCE)) { job.SetKeepSource(SerializationToolbox::ReadBoolean(body, KEEP_SOURCE)); } } static void SetKeepSource(ThreadedSetOfInstancesJob& job, const Json::Value& body) { if (body.isMember(KEEP_SOURCE)) { job.SetKeepSource(SerializationToolbox::ReadBoolean(body, KEEP_SOURCE)); } } static void SubmitModificationJob(std::unique_ptr<DicomModification>& modification, bool isAnonymization, RestApiPostCall& call, const Json::Value& body, ResourceType outputLevel /* unused for multiple resources */, bool isSingleResource, const std::set<std::string>& resources) { ServerContext& context = OrthancRestApi::GetContext(call); unsigned int workersCount = 0; { OrthancConfiguration::ReaderLock lock; workersCount = lock.GetConfiguration().GetJobsEngineWorkersThread("ResourceModification"); } std::unique_ptr<ResourceModificationJob> job(new ResourceModificationJob(context, workersCount)); if (isSingleResource) // This notably configures the output format { job->SetSingleResourceModification(modification.release(), outputLevel, isAnonymization); } else { job->SetMultipleResourcesModification(modification.release(), isAnonymization); } job->SetOrigin(call); SetKeepSource(*job, body); if (body.isMember(TRANSCODE)) { job->SetTranscode(SerializationToolbox::ReadString(body, TRANSCODE)); } for (std::set<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) { std::list<std::string> instances; context.GetIndex().GetChildInstances(instances, *it); job->AddInstances(instances); job->AddParentResource(*it); } job->PerformSanityChecks(); OrthancRestApi::GetApi(call).SubmitThreadedInstancesJob (call, job.release(), true /* synchronous by default */, body); } static void SubmitModificationJob(std::unique_ptr<DicomModification>& modification, bool isAnonymization, RestApiPostCall& call, const Json::Value& body, ResourceType outputLevel) { // This was the only flavor in Orthanc <= 1.9.3 std::set<std::string> resources; resources.insert(call.GetUriComponent("id", "")); SubmitModificationJob(modification, isAnonymization, call, body, outputLevel, true /* single resource */, resources); } static void SubmitBulkJob(std::unique_ptr<DicomModification>& modification, bool isAnonymization, RestApiPostCall& call, const Json::Value& body) { std::set<std::string> resources; SerializationToolbox::ReadSetOfStrings(resources, body, RESOURCES); SubmitModificationJob(modification, isAnonymization, call, body, ResourceType_Instance /* arbitrary value, unused */, false /* multiple resources */, resources); } template <enum ResourceType resourceType> static void ModifyResource(RestApiPostCall& call) { if (call.IsDocumentation()) { OrthancRestApi::DocumentSubmitCommandsJob(call); DocumentModifyOptions(call); const std::string r = GetResourceTypeText(resourceType, false /* plural */, false /* lower case */); call.GetDocumentation() .SetTag(GetResourceTypeText(resourceType, true /* plural */, true /* upper case */)) .SetSummary("Modify " + r) .SetDescription("Start a job that will modify all the DICOM instances within the " + r + " whose identifier is provided in the URL. The modified DICOM instances will be " "stored into a brand new " + r + ", whose Orthanc identifiers will be returned by the job. " "https://orthanc.uclouvain.be/book/users/anonymization.html#modification-of-studies-or-series") .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest"); return; } std::unique_ptr<DicomModification> modification(new DicomModification); Json::Value body; ParseModifyRequest(body, *modification, call); modification->SetLevel(resourceType); SubmitModificationJob(modification, false /* not an anonymization */, call, body, resourceType); } // New in Orthanc 1.9.4 static void BulkModify(RestApiPostCall& call) { if (call.IsDocumentation()) { OrthancRestApi::DocumentSubmitCommandsJob(call); DocumentModifyOptions(call); call.GetDocumentation() .SetTag("System") .SetSummary("Modify a set of resources") .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, "List of the Orthanc identifiers of the patients/studies/series/instances of interest.", true) .SetRequestField(LEVEL, RestApiCallDocumentation::Type_String, "Level of the modification (`Patient`, `Study`, `Series` or `Instance`). If absent, " "the level defaults to `Instance`, but is set to `Patient` if `PatientID` is modified, " "to `Study` if `StudyInstanceUID` is modified, or to `Series` if `SeriesInstancesUID` " "is modified. (new in Orthanc 1.9.7)", false) .SetDescription("Start a job that will modify all the DICOM patients, studies, series or instances " "whose identifiers are provided in the `Resources` field.") .AddAnswerType(MimeType_Json, "The list of all the resources that have been altered by this modification"); return; } std::unique_ptr<DicomModification> modification(new DicomModification); Json::Value body; ParseModifyRequest(body, *modification, call); if (body.isMember(LEVEL)) { // This case was introduced in Orthanc 1.9.7 modification->SetLevel(StringToResourceType(body[LEVEL].asCString())); } else { modification->SetLevel(DetectModifyLevel(*modification)); } SubmitBulkJob(modification, false /* not an anonymization */, call, body); } template <enum ResourceType resourceType> static void AnonymizeResource(RestApiPostCall& call) { if (call.IsDocumentation()) { OrthancRestApi::DocumentSubmitCommandsJob(call); DocumentAnonymizationOptions(call); const std::string r = GetResourceTypeText(resourceType, false /* plural */, false /* lower case */); call.GetDocumentation() .SetTag(GetResourceTypeText(resourceType, true /* plural */, true /* upper case */)) .SetSummary("Anonymize " + r) .SetDescription("Start a job that will anonymize all the DICOM instances within the " + r + " whose identifier is provided in the URL. The modified DICOM instances will be " "stored into a brand new " + r + ", whose Orthanc identifiers will be returned by the job. " "https://orthanc.uclouvain.be/book/users/anonymization.html#anonymization-of-patients-studies-or-series") .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest"); return; } std::unique_ptr<DicomModification> modification(new DicomModification); Json::Value body; ParseAnonymizationRequest(body, *modification, call); SubmitModificationJob(modification, true /* anonymization */, call, body, resourceType); } // New in Orthanc 1.9.4 static void BulkAnonymize(RestApiPostCall& call) { if (call.IsDocumentation()) { OrthancRestApi::DocumentSubmitCommandsJob(call); DocumentAnonymizationOptions(call); call.GetDocumentation() .SetTag("System") .SetSummary("Anonymize a set of resources") .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, "List of the Orthanc identifiers of the patients/studies/series/instances of interest.", true) .SetDescription("Start a job that will anonymize all the DICOM patients, studies, series or instances " "whose identifiers are provided in the `Resources` field.") .AddAnswerType(MimeType_Json, "The list of all the resources that have been created by this anonymization"); return; } std::unique_ptr<DicomModification> modification(new DicomModification); Json::Value body; ParseAnonymizationRequest(body, *modification, call); SubmitBulkJob(modification, true /* anonymization */, call, body); } static void StoreCreatedInstance(std::string& id /* out */, RestApiPostCall& call, ParsedDicomFile& dicom, bool sendAnswer) { std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(dicom)); toStore->SetOrigin(DicomInstanceOrigin::FromRest(call)); ServerContext& context = OrthancRestApi::GetContext(call); ServerContext::StoreResult result = context.Store(id, *toStore, StoreInstanceMode_Default); if (result.GetStatus() == StoreStatus_Failure) { throw OrthancException(ErrorCode_CannotStoreInstance); } if (sendAnswer) { OrthancRestApi::GetApi(call).AnswerStoredInstance(call, *toStore, result.GetStatus(), id); } } static void CreateDicomV1(ParsedDicomFile& dicom, RestApiPostCall& call, const Json::Value& request) { // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}' // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World","PixelData":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAAAAAA6mKC9AAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH3gUGDDcB53FulQAAAElJREFUGNNtj0sSAEEEQ1+U+185s1CtmRkblQ9CZldsKHJDk6DLGLJa6chjh0ooQmpjXMM86zPwydGEj6Ed/UGykkEM8X+p3u8/8LcOJIWLGeMAAAAASUVORK5CYII="}' assert(request.isObject()); LOG(WARNING) << "Using a deprecated call to /tools/create-dicom"; Json::Value::Members members = request.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { const std::string& name = members[i]; if (request[name].type() != Json::stringValue) { throw OrthancException(ErrorCode_CreateDicomNotString); } std::string value = request[name].asString(); DicomTag tag = FromDcmtkBridge::ParseTag(name); if (tag == DICOM_TAG_PIXEL_DATA) { dicom.EmbedContent(value); } else { // This is V1, don't try and decode data URI scheme dicom.ReplacePlainString(tag, value); } } } static void InjectTags(ParsedDicomFile& dicom, const Json::Value& tags, bool decodeBinaryTags, const std::string& privateCreator, bool force) { if (tags.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadRequest, "Tags field is not an array"); } // Inject the user-specified tags Json::Value::Members members = tags.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { const std::string& name = members[i]; DicomTag tag = FromDcmtkBridge::ParseTag(name); if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) { if (!force && tag != DICOM_TAG_PATIENT_ID && tag != DICOM_TAG_ACQUISITION_DATE && tag != DICOM_TAG_ACQUISITION_TIME && tag != DICOM_TAG_CONTENT_DATE && tag != DICOM_TAG_CONTENT_TIME && tag != DICOM_TAG_INSTANCE_CREATION_DATE && tag != DICOM_TAG_INSTANCE_CREATION_TIME && tag != DICOM_TAG_SERIES_DATE && tag != DICOM_TAG_SERIES_TIME && tag != DICOM_TAG_STUDY_DATE && tag != DICOM_TAG_STUDY_TIME && dicom.HasTag(tag)) { throw OrthancException(ErrorCode_CreateDicomOverrideTag, name); } if (tag == DICOM_TAG_PIXEL_DATA) { throw OrthancException(ErrorCode_CreateDicomUseContent); } else { dicom.Replace(tag, tags[name], decodeBinaryTags, DicomReplaceMode_InsertIfAbsent, privateCreator); } } } } static void CreateSeries(RestApiPostCall& call, ParsedDicomFile& base /* in */, const Json::Value& content, bool decodeBinaryTags, const std::string& privateCreator, bool force) { assert(content.isArray()); assert(content.size() > 0); ServerContext& context = OrthancRestApi::GetContext(call); base.ReplacePlainString(DICOM_TAG_IMAGES_IN_ACQUISITION, boost::lexical_cast<std::string>(content.size())); base.ReplacePlainString(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS, "1"); std::string someInstance; try { for (Json::ArrayIndex i = 0; i < content.size(); i++) { std::unique_ptr<ParsedDicomFile> dicom(base.Clone(false)); const Json::Value* payload = NULL; if (content[i].type() == Json::stringValue) { payload = &content[i]; } else if (content[i].type() == Json::objectValue) { if (!content[i].isMember(CONTENT)) { throw OrthancException(ErrorCode_CreateDicomNoPayload); } payload = &content[i][CONTENT]; if (content[i].isMember(TAGS)) { InjectTags(*dicom, content[i][TAGS], decodeBinaryTags, privateCreator, force); } } if (payload == NULL || payload->type() != Json::stringValue) { throw OrthancException(ErrorCode_CreateDicomUseDataUriScheme); } dicom->EmbedContent(payload->asString()); dicom->ReplacePlainString(DICOM_TAG_INSTANCE_NUMBER, boost::lexical_cast<std::string>(i + 1)); dicom->ReplacePlainString(DICOM_TAG_IMAGE_INDEX, boost::lexical_cast<std::string>(i + 1)); StoreCreatedInstance(someInstance, call, *dicom, false); } } catch (OrthancException&) { // Error: Remove the newly-created series std::string series; if (context.GetIndex().LookupParent(series, someInstance)) { Json::Value dummy; context.GetIndex().DeleteResource(dummy, series, ResourceType_Series); } throw; } std::string series; if (context.GetIndex().LookupParent(series, someInstance)) { OrthancRestApi::GetApi(call).AnswerStoredResource(call, series, ResourceType_Series, StoreStatus_Success); } } static void CreateDicomV2(RestApiPostCall& call, const Json::Value& request) { static const char* const SPECIFIC_CHARACTER_SET_2 = "SpecificCharacterSet"; static const char* const TYPE = "Type"; static const char* const VALUE = "Value"; assert(request.isObject()); ServerContext& context = OrthancRestApi::GetContext(call); if (!request.isMember(TAGS) || request[TAGS].type() != Json::objectValue) { throw OrthancException(ErrorCode_BadRequest); } ParsedDicomFile dicom(true); { Encoding encoding; if (request[TAGS].isMember(SPECIFIC_CHARACTER_SET_2)) { const char* tmp = request[TAGS][SPECIFIC_CHARACTER_SET_2].asCString(); if (!GetDicomEncoding(encoding, tmp)) { throw OrthancException(ErrorCode_ParameterOutOfRange, "Unknown specific character set: " + std::string(tmp)); } } else { encoding = GetDefaultDicomEncoding(); } dicom.SetEncoding(encoding); } ResourceType parentType = ResourceType_Instance; if (request.isMember(PARENT)) { // Locate the parent tags std::string parent = request[PARENT].asString(); if (!context.GetIndex().LookupResourceType(parentType, parent)) { throw OrthancException(ErrorCode_CreateDicomBadParent); } if (parentType == ResourceType_Instance) { throw OrthancException(ErrorCode_CreateDicomParentIsInstance); } // Select one existing child instance of the parent resource, to // retrieve all its tags Json::Value siblingTags; std::string siblingInstanceId; { // Retrieve all the instances of the parent resource std::list<std::string> siblingInstances; context.GetIndex().GetChildInstances(siblingInstances, parent); if (siblingInstances.empty()) { // Error: No instance (should never happen) throw OrthancException(ErrorCode_InternalError); } siblingInstanceId = siblingInstances.front(); context.ReadDicomAsJson(siblingTags, siblingInstanceId); } // Choose the same encoding as the parent resource { static const char* const SPECIFIC_CHARACTER_SET = "0008,0005"; if (siblingTags.isMember(SPECIFIC_CHARACTER_SET)) { Encoding encoding; if (!siblingTags[SPECIFIC_CHARACTER_SET].isMember(VALUE) || siblingTags[SPECIFIC_CHARACTER_SET][VALUE].type() != Json::stringValue || !GetDicomEncoding(encoding, siblingTags[SPECIFIC_CHARACTER_SET][VALUE].asCString())) { LOG(WARNING) << "Instance with an incorrect Specific Character Set, " << "using the default Orthanc encoding: " << siblingInstanceId; encoding = GetDefaultDicomEncoding(); } dicom.SetEncoding(encoding); } } // Retrieve the tags for all the parent modules typedef std::set<DicomTag> ModuleTags; ModuleTags moduleTags; ResourceType type = parentType; for (;;) { DicomTag::AddTagsForModule(moduleTags, GetModule(type)); if (type == ResourceType_Patient) { break; // We're done } // Go up std::string tmp; if (!context.GetIndex().LookupParent(tmp, parent)) { throw OrthancException(ErrorCode_InternalError); } parent = tmp; type = GetParentResourceType(type); } for (ModuleTags::const_iterator it = moduleTags.begin(); it != moduleTags.end(); ++it) { std::string t = it->Format(); if (siblingTags.isMember(t)) { const Json::Value& tag = siblingTags[t]; if (tag[TYPE] == "Null") { dicom.ReplacePlainString(*it, ""); } else if (tag[TYPE] == "String") { std::string value = tag[VALUE].asString(); // This is an UTF-8 value (as it comes from JSON) dicom.ReplacePlainString(*it, value); } } } } bool decodeBinaryTags = true; if (request.isMember(INTERPRET_BINARY_TAGS)) { const Json::Value& v = request[INTERPRET_BINARY_TAGS]; if (v.type() != Json::booleanValue) { throw OrthancException(ErrorCode_BadRequest); } decodeBinaryTags = v.asBool(); } // New argument in Orthanc 1.6.0 std::string privateCreator; if (request.isMember(PRIVATE_CREATOR)) { const Json::Value& v = request[PRIVATE_CREATOR]; if (v.type() != Json::stringValue) { throw OrthancException(ErrorCode_BadRequest); } privateCreator = v.asString(); } else { OrthancConfiguration::ReaderLock lock; privateCreator = lock.GetConfiguration().GetDefaultPrivateCreator(); } // New in Orthanc 1.9.0 bool force = false; if (request.isMember(FORCE)) { const Json::Value& v = request[FORCE]; if (v.type() != Json::booleanValue) { throw OrthancException(ErrorCode_BadRequest); } force = v.asBool(); } // Inject time-related information std::string date, time; SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); dicom.ReplacePlainString(DICOM_TAG_ACQUISITION_DATE, date); dicom.ReplacePlainString(DICOM_TAG_ACQUISITION_TIME, time); dicom.ReplacePlainString(DICOM_TAG_CONTENT_DATE, date); dicom.ReplacePlainString(DICOM_TAG_CONTENT_TIME, time); dicom.ReplacePlainString(DICOM_TAG_INSTANCE_CREATION_DATE, date); dicom.ReplacePlainString(DICOM_TAG_INSTANCE_CREATION_TIME, time); if (parentType == ResourceType_Patient || parentType == ResourceType_Study || parentType == ResourceType_Instance /* no parent */) { dicom.ReplacePlainString(DICOM_TAG_SERIES_DATE, date); dicom.ReplacePlainString(DICOM_TAG_SERIES_TIME, time); } if (parentType == ResourceType_Patient || parentType == ResourceType_Instance /* no parent */) { dicom.ReplacePlainString(DICOM_TAG_STUDY_DATE, date); dicom.ReplacePlainString(DICOM_TAG_STUDY_TIME, time); } InjectTags(dicom, request[TAGS], decodeBinaryTags, privateCreator, force); // Inject the content (either an image, a PDF file, or a STL/OBJ/MTL file) if (request.isMember(CONTENT)) { const Json::Value& content = request[CONTENT]; if (content.type() == Json::stringValue) { dicom.EmbedContent(request[CONTENT].asString()); } else if (content.type() == Json::arrayValue) { if (content.size() > 0) { // Let's create a series instead of a single instance CreateSeries(call, dicom, content, decodeBinaryTags, privateCreator, force); return; } } else { throw OrthancException(ErrorCode_CreateDicomUseDataUriScheme); } } std::string id; StoreCreatedInstance(id, call, dicom, true); } static void CreateDicom(RestApiPostCall& call) { if (call.IsDocumentation()) { call.GetDocumentation() .SetTag("System") .SetSummary("Create one DICOM instance") .SetDescription("Create one DICOM instance, and store it into Orthanc") .SetRequestField(TAGS, RestApiCallDocumentation::Type_JsonObject, "Associative array containing the tags of the new instance to be created", true) .SetRequestField(CONTENT, RestApiCallDocumentation::Type_String, "This field can be used to embed an image (pixel data encoded as PNG or JPEG), a PDF, or a " "3D manufactoring model (MTL/OBJ/STL) inside the created DICOM instance. " "The file to be encapsulated must be provided using its " "[data URI scheme encoding](https://en.wikipedia.org/wiki/Data_URI_scheme). " "This field can possibly contain a JSON array, in which case a DICOM series is created " "containing one DICOM instance for each item in the `Content` field.", false) .SetRequestField(PARENT, RestApiCallDocumentation::Type_String, "If present, the newly created instance will be attached to the parent DICOM resource " "whose Orthanc identifier is contained in this field. The DICOM tags of the parent " "modules in the DICOM hierarchy will be automatically copied to the newly created instance.", false) .SetRequestField(INTERPRET_BINARY_TAGS, RestApiCallDocumentation::Type_Boolean, "If some value in the `Tags` associative array is formatted according to some " "[data URI scheme encoding](https://en.wikipedia.org/wiki/Data_URI_scheme), " "whether this value is decoded to a binary value or kept as such (`true` by default)", false) .SetRequestField(PRIVATE_CREATOR, RestApiCallDocumentation::Type_String, "The private creator to be used for private tags in `Tags`", false) .SetRequestField(FORCE, RestApiCallDocumentation::Type_Boolean, "Avoid the consistency checks for the DICOM tags that enforce the DICOM model of the real-world. " "You can notably use this flag if you need to manually set the tags `StudyInstanceUID`, " "`SeriesInstanceUID`, or `SOPInstanceUID`. Be careful with this feature.", false) .SetAnswerField("ID", RestApiCallDocumentation::Type_String, "Orthanc identifier of the newly created instance") .SetAnswerField("Path", RestApiCallDocumentation::Type_String, "Path to access the instance in the REST API"); return; } Json::Value request; if (!call.ParseJsonRequest(request) || !request.isObject()) { throw OrthancException(ErrorCode_BadRequest); } if (request.isMember(TAGS)) { CreateDicomV2(call, request); } else { // Compatibility with Orthanc <= 0.9.3 ParsedDicomFile dicom(true); CreateDicomV1(dicom, call, request); std::string id; StoreCreatedInstance(id, call, dicom, true); } } static void SplitStudy(RestApiPostCall& call) { if (call.IsDocumentation()) { OrthancRestApi::DocumentSubmitCommandsJob(call); call.GetDocumentation() .SetTag("Studies") .SetSummary("Split study") .SetDescription("Start a new job so as to split the DICOM study whose Orthanc identifier is provided in the URL, " "by taking some of its children series or instances out of it and putting them into a brand new study " "(this new study is created by setting the `StudyInstanceUID` tag to a random identifier): " "https://orthanc.uclouvain.be/book/users/anonymization.html#splitting") .SetUriArgument("id", "Orthanc identifier of the study of interest") .SetRequestField(SERIES, RestApiCallDocumentation::Type_JsonListOfStrings, "The list of series to be separated from the parent study. " "These series must all be children of the same source study, that is specified in the URI.", false) .SetRequestField(REPLACE, RestApiCallDocumentation::Type_JsonObject, "Associative array to change the value of some DICOM tags in the new study. " "These tags must be part of the \"Patient Module Attributes\" or the \"General Study " "Module Attributes\", as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3.", false) .SetRequestField(KEEP_LABELS, RestApiCallDocumentation::Type_Boolean, "Keep the labels of all resources level (defaults to `false`)", false) .SetRequestField(REMOVE, RestApiCallDocumentation::Type_JsonListOfStrings, "List of tags that must be removed in the new study (from the same modules as in the `Replace` option)", false) .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, "If set to `true`, instructs Orthanc to keep a copy of the original series/instances in the source study. " "By default, the original series/instances are deleted from Orthanc.", false) .SetRequestField(INSTANCES, RestApiCallDocumentation::Type_JsonListOfStrings, "The list of instances to be separated from the parent study. " "These instances must all be children of the same source study, that is specified in the URI.", false); return; } ServerContext& context = OrthancRestApi::GetContext(call); Json::Value request; if (!call.ParseJsonRequest(request)) { // Bad JSON request throw OrthancException(ErrorCode_BadFileFormat); } const std::string study = call.GetUriComponent("id", ""); std::unique_ptr<SplitStudyJob> job(new SplitStudyJob(context, study)); job->SetOrigin(call); bool ok = false; if (request.isMember(SERIES)) { std::vector<std::string> series; SerializationToolbox::ReadArrayOfStrings(series, request, SERIES); for (size_t i = 0; i < series.size(); i++) { job->AddSourceSeries(series[i]); ok = true; } } if (request.isMember(INSTANCES)) { std::vector<std::string> instances; SerializationToolbox::ReadArrayOfStrings(instances, request, INSTANCES); for (size_t i = 0; i < instances.size(); i++) { job->AddSourceInstance(instances[i]); ok = true; } } if (!ok) { throw OrthancException(ErrorCode_BadRequest, "Both the \"Series\" and the \"Instances\" fields are missing"); } job->AddTrailingStep(); SetKeepSource(*job, request); if (request.isMember(REMOVE)) { if (request[REMOVE].type() != Json::arrayValue) { throw OrthancException(ErrorCode_BadFileFormat); } for (Json::Value::ArrayIndex i = 0; i < request[REMOVE].size(); i++) { if (request[REMOVE][i].type() != Json::stringValue) { throw OrthancException(ErrorCode_BadFileFormat); } else { job->Remove(FromDcmtkBridge::ParseTag(request[REMOVE][i].asCString())); } } } if (request.isMember(REPLACE)) { if (request[REPLACE].type() != Json::objectValue) { throw OrthancException(ErrorCode_BadFileFormat); } Json::Value::Members tags = request[REPLACE].getMemberNames(); for (size_t i = 0; i < tags.size(); i++) { const Json::Value& value = request[REPLACE][tags[i]]; if (value.type() != Json::stringValue) { throw OrthancException(ErrorCode_BadFileFormat); } else { job->Replace(FromDcmtkBridge::ParseTag(tags[i]), value.asString()); } } } OrthancRestApi::GetApi(call).SubmitCommandsJob (call, job.release(), true /* synchronous by default */, request); } static void MergeStudy(RestApiPostCall& call) { if (call.IsDocumentation()) { OrthancRestApi::DocumentSubmitCommandsJob(call); call.GetDocumentation() .SetTag("Studies") .SetSummary("Merge study") .SetDescription("Start a new job so as to move some DICOM resources into the DICOM study whose Orthanc identifier " "is provided in the URL: https://orthanc.uclouvain.be/book/users/anonymization.html#merging") .SetUriArgument("id", "Orthanc identifier of the study of interest") .SetRequestField(RESOURCES, RestApiCallDocumentation::Type_JsonListOfStrings, "The list of DICOM resources (studies, series, and/or instances) to be merged " "into the study of interest (mandatory option)", true) .SetRequestField(KEEP_SOURCE, RestApiCallDocumentation::Type_Boolean, "If set to `true`, instructs Orthanc to keep a copy of the original resources in their source study. " "By default, the original resources are deleted from Orthanc.", false); return; } ServerContext& context = OrthancRestApi::GetContext(call); Json::Value request; if (!call.ParseJsonRequest(request)) { // Bad JSON request throw OrthancException(ErrorCode_BadFileFormat); } const std::string study = call.GetUriComponent("id", ""); std::unique_ptr<MergeStudyJob> job(new MergeStudyJob(context, study)); job->SetOrigin(call); std::vector<std::string> resources; SerializationToolbox::ReadArrayOfStrings(resources, request, RESOURCES); for (size_t i = 0; i < resources.size(); i++) { job->AddSource(resources[i]); } job->AddTrailingStep(); SetKeepSource(*job, request); OrthancRestApi::GetApi(call).SubmitCommandsJob (call, job.release(), true /* synchronous by default */, request); } void OrthancRestApi::RegisterAnonymizeModify() { Register("/instances/{id}/modify", ModifyInstance); Register("/series/{id}/modify", ModifyResource<ResourceType_Series>); Register("/studies/{id}/modify", ModifyResource<ResourceType_Study>); Register("/patients/{id}/modify", ModifyResource<ResourceType_Patient>); Register("/tools/bulk-modify", BulkModify); Register("/instances/{id}/anonymize", AnonymizeInstance); Register("/series/{id}/anonymize", AnonymizeResource<ResourceType_Series>); Register("/studies/{id}/anonymize", AnonymizeResource<ResourceType_Study>); Register("/patients/{id}/anonymize", AnonymizeResource<ResourceType_Patient>); Register("/tools/bulk-anonymize", BulkAnonymize); Register("/tools/create-dicom", CreateDicom); Register("/studies/{id}/split", SplitStudy); Register("/studies/{id}/merge", MergeStudy); } }