Mercurial > hg > orthanc
view OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 2956:bfee0b9f3209
cont
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 03 Dec 2018 15:11:42 +0100 |
parents | bbfd95a0c429 |
children | 750de70b3603 |
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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) 2017-2018 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 "OrthancRestApi.h" #include "../../Core/DicomParsing/FromDcmtkBridge.h" #include "../../Core/Logging.h" #include "../../Core/SerializationToolbox.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> namespace Orthanc { // Modification of DICOM instances ------------------------------------------ static std::string GeneratePatientName(ServerContext& context) { uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence); return "Anonymized" + boost::lexical_cast<std::string>(seq); } 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}' 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 if (call.ParseJsonRequest(request) && request.isObject()) { bool patientNameReplaced; target.ParseAnonymizationRequest(patientNameReplaced, request); if (patientNameReplaced) { // Overwrite 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) { std::string id = call.GetUriComponent("id", ""); std::auto_ptr<ParsedDicomFile> modified; { ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id); modified.reset(locker.GetDicom().Clone(true)); } modification.Apply(*modified); modified->Answer(call.GetOutput()); } static void ModifyInstance(RestApiPostCall& call) { DicomModification modification; modification.SetAllowManualIdentifiers(true); Json::Value request; ParseModifyRequest(request, modification, call); if (modification.IsReplaced(DICOM_TAG_PATIENT_ID)) { modification.SetLevel(ResourceType_Patient); } else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) { modification.SetLevel(ResourceType_Study); } else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) { modification.SetLevel(ResourceType_Series); } else { modification.SetLevel(ResourceType_Instance); } AnonymizeOrModifyInstance(modification, call); } static void AnonymizeInstance(RestApiPostCall& call) { DicomModification modification; modification.SetAllowManualIdentifiers(true); Json::Value request; ParseAnonymizationRequest(request, modification, call); AnonymizeOrModifyInstance(modification, call); } static void SubmitModificationJob(std::auto_ptr<DicomModification>& modification, bool isAnonymization, RestApiPostCall& call, const Json::Value& body, ResourceType level) { ServerContext& context = OrthancRestApi::GetContext(call); std::auto_ptr<ResourceModificationJob> job(new ResourceModificationJob(context)); job->SetModification(modification.release(), level, isAnonymization); job->SetOrigin(call); context.AddChildInstances(*job, call.GetUriComponent("id", "")); OrthancRestApi::GetApi(call).SubmitCommandsJob (call, job.release(), true /* synchronous by default */, body); } template <enum ResourceType resourceType> static void ModifyResource(RestApiPostCall& call) { std::auto_ptr<DicomModification> modification(new DicomModification); Json::Value body; ParseModifyRequest(body, *modification, call); modification->SetLevel(resourceType); SubmitModificationJob(modification, false /* not an anonymization */, call, body, resourceType); } template <enum ResourceType resourceType> static void AnonymizeResource(RestApiPostCall& call) { std::auto_ptr<DicomModification> modification(new DicomModification); Json::Value body; ParseAnonymizationRequest(body, *modification, call); SubmitModificationJob(modification, true /* anonymization */, call, body, resourceType); } static void StoreCreatedInstance(std::string& id /* out */, RestApiPostCall& call, ParsedDicomFile& dicom, bool sendAnswer) { DicomInstanceToStore toStore; toStore.SetOrigin(DicomInstanceOrigin::FromRest(call)); toStore.SetParsedDicomFile(dicom); ServerContext& context = OrthancRestApi::GetContext(call); StoreStatus status = context.Store(id, toStore); if (status == StoreStatus_Failure) { throw OrthancException(ErrorCode_CannotStoreInstance); } if (sendAnswer) { OrthancRestApi::GetApi(call).AnswerStoredInstance(call, toStore, status); } } 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) { 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 (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); } } } } static void CreateSeries(RestApiPostCall& call, ParsedDicomFile& base /* in */, const Json::Value& content, bool decodeBinaryTags) { 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::auto_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); } } 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) { 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("SpecificCharacterSet")) { const char* tmp = request["Tags"]["SpecificCharacterSet"].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; { // 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); } context.ReadDicomAsJson(siblingTags, siblingInstances.front()); } // Choose the same encoding as the parent resource { static const char* 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())) { throw OrthancException(ErrorCode_CreateDicomParentEncoding); } 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(); dicom.ReplacePlainString(*it, Toolbox::ConvertFromUtf8(value, dicom.GetEncoding())); } } } } bool decodeBinaryTags = true; if (request.isMember("InterpretBinaryTags")) { const Json::Value& v = request["InterpretBinaryTags"]; if (v.type() != Json::booleanValue) { throw OrthancException(ErrorCode_BadRequest); } decodeBinaryTags = 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); // Inject the content (either an image, or a PDF 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); return; } } else { throw OrthancException(ErrorCode_CreateDicomUseDataUriScheme); } } std::string id; StoreCreatedInstance(id, call, dicom, true); } static void CreateDicom(RestApiPostCall& call) { 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) { 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::auto_ptr<SplitStudyJob> job(new SplitStudyJob(context, study)); job->SetOrigin(call); std::vector<std::string> series; SerializationToolbox::ReadArrayOfStrings(series, request, "Series"); for (size_t i = 0; i < series.size(); i++) { job->AddSourceSeries(series[i]); } job->AddTrailingStep(); static const char* KEEP_SOURCE = "KeepSource"; if (request.isMember(KEEP_SOURCE)) { job->SetKeepSource(SerializationToolbox::ReadBoolean(request, KEEP_SOURCE)); } static const char* REMOVE = "Remove"; 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())); } } } static const char* REPLACE = "Replace"; 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) { 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::auto_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(); static const char* KEEP_SOURCE = "KeepSource"; if (request.isMember(KEEP_SOURCE)) { job->SetKeepSource(SerializationToolbox::ReadBoolean(request, KEEP_SOURCE)); } 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("/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/create-dicom", CreateDicom); Register("/studies/{id}/split", SplitStudy); Register("/studies/{id}/merge", MergeStudy); } }