Mercurial > hg > orthanc
view OrthancServer/OrthancRestApi.cpp @ 353:61e4c62b8c35
samples of anonymization
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 28 Jan 2013 16:58:07 +0100 |
parents | 64625960af22 |
children | 8d3a0db39967 |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012 Medical Physics Department, CHU of Liege, * 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 "OrthancRestApi.h" #include "../Core/HttpServer/FilesystemHttpSender.h" #include "../Core/Uuid.h" #include "../Core/Compression/HierarchicalZipWriter.h" #include "DicomProtocol/DicomUserConnection.h" #include "FromDcmtkBridge.h" #include "OrthancInitialization.h" #include "ServerToolbox.h" #include <dcmtk/dcmdata/dcistrmb.h> #include <dcmtk/dcmdata/dcfilefo.h> #include <boost/lexical_cast.hpp> #include <glog/logging.h> #define RETRIEVE_CONTEXT(call) \ OrthancRestApi& contextApi = \ dynamic_cast<OrthancRestApi&>(call.GetContext()); \ ServerContext& context = contextApi.GetContext() #define RETRIEVE_MODALITIES(call) \ const OrthancRestApi::Modalities& modalities = \ dynamic_cast<OrthancRestApi&>(call.GetContext()).GetModalities(); namespace Orthanc { // TODO IMPROVE MULTITHREADING // Every call to "ParsedDicomFile" must lock this mutex!!! static boost::mutex cacheMutex_; // DICOM SCU ---------------------------------------------------------------- static void ConnectToModality(DicomUserConnection& connection, const std::string& name) { std::string aet, address; int port; GetDicomModality(name, aet, address, port); connection.SetLocalApplicationEntityTitle(GetGlobalStringParameter("DicomAet", "ORTHANC")); connection.SetDistantApplicationEntityTitle(aet); connection.SetDistantHost(address); connection.SetDistantPort(port); connection.Open(); } static bool MergeQueryAndTemplate(DicomMap& result, const std::string& postData) { Json::Value query; Json::Reader reader; if (!reader.parse(postData, query) || query.type() != Json::objectValue) { return false; } Json::Value::Members members = query.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { DicomTag t = FromDcmtkBridge::ParseTag(members[i]); result.SetValue(t, query[members[i]].asString()); } return true; } static void DicomFindPatient(RestApi::PostCall& call) { DicomMap m; DicomMap::SetupFindPatientTemplate(m); if (!MergeQueryAndTemplate(m, call.GetPostBody())) { return; } DicomUserConnection connection; ConnectToModality(connection, call.GetUriComponent("id", "")); DicomFindAnswers answers; connection.FindPatient(answers, m); Json::Value result; answers.ToJson(result); call.GetOutput().AnswerJson(result); } static void DicomFindStudy(RestApi::PostCall& call) { DicomMap m; DicomMap::SetupFindStudyTemplate(m); if (!MergeQueryAndTemplate(m, call.GetPostBody())) { return; } if (m.GetValue(DICOM_TAG_ACCESSION_NUMBER).AsString().size() <= 2 && m.GetValue(DICOM_TAG_PATIENT_ID).AsString().size() <= 2) { return; } DicomUserConnection connection; ConnectToModality(connection, call.GetUriComponent("id", "")); DicomFindAnswers answers; connection.FindStudy(answers, m); Json::Value result; answers.ToJson(result); call.GetOutput().AnswerJson(result); } static void DicomFindSeries(RestApi::PostCall& call) { DicomMap m; DicomMap::SetupFindSeriesTemplate(m); if (!MergeQueryAndTemplate(m, call.GetPostBody())) { return; } if ((m.GetValue(DICOM_TAG_ACCESSION_NUMBER).AsString().size() <= 2 && m.GetValue(DICOM_TAG_PATIENT_ID).AsString().size() <= 2) || m.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString().size() <= 2) { return; } DicomUserConnection connection; ConnectToModality(connection, call.GetUriComponent("id", "")); DicomFindAnswers answers; connection.FindSeries(answers, m); Json::Value result; answers.ToJson(result); call.GetOutput().AnswerJson(result); } static void DicomFind(RestApi::PostCall& call) { DicomMap m; DicomMap::SetupFindPatientTemplate(m); if (!MergeQueryAndTemplate(m, call.GetPostBody())) { return; } DicomUserConnection connection; ConnectToModality(connection, call.GetUriComponent("id", "")); DicomFindAnswers patients; connection.FindPatient(patients, m); // Loop over the found patients Json::Value result = Json::arrayValue; for (size_t i = 0; i < patients.GetSize(); i++) { Json::Value patient(Json::objectValue); FromDcmtkBridge::ToJson(patient, patients.GetAnswer(i)); DicomMap::SetupFindStudyTemplate(m); if (!MergeQueryAndTemplate(m, call.GetPostBody())) { return; } m.CopyTagIfExists(patients.GetAnswer(i), DICOM_TAG_PATIENT_ID); DicomFindAnswers studies; connection.FindStudy(studies, m); patient["Studies"] = Json::arrayValue; // Loop over the found studies for (size_t j = 0; j < studies.GetSize(); j++) { Json::Value study(Json::objectValue); FromDcmtkBridge::ToJson(study, studies.GetAnswer(j)); DicomMap::SetupFindSeriesTemplate(m); if (!MergeQueryAndTemplate(m, call.GetPostBody())) { return; } m.CopyTagIfExists(studies.GetAnswer(j), DICOM_TAG_PATIENT_ID); m.CopyTagIfExists(studies.GetAnswer(j), DICOM_TAG_STUDY_INSTANCE_UID); DicomFindAnswers series; connection.FindSeries(series, m); // Loop over the found series study["Series"] = Json::arrayValue; for (size_t k = 0; k < series.GetSize(); k++) { Json::Value series2(Json::objectValue); FromDcmtkBridge::ToJson(series2, series.GetAnswer(k)); study["Series"].append(series2); } patient["Studies"].append(study); } result.append(patient); } call.GetOutput().AnswerJson(result); } static void DicomStore(RestApi::PostCall& call) { RETRIEVE_CONTEXT(call); std::string remote = call.GetUriComponent("id", ""); DicomUserConnection connection; ConnectToModality(connection, remote); const std::string& resourceId = call.GetPostBody(); Json::Value found; if (context.GetIndex().LookupResource(found, resourceId, ResourceType_Series)) { // The UUID corresponds to a series context.GetIndex().LogExportedResource(resourceId, remote); for (Json::Value::ArrayIndex i = 0; i < found["Instances"].size(); i++) { std::string instanceId = found["Instances"][i].asString(); std::string dicom; context.ReadFile(dicom, instanceId, FileContentType_Dicom); connection.Store(dicom); } call.GetOutput().AnswerBuffer("{}", "application/json"); } else if (context.GetIndex().LookupResource(found, resourceId, ResourceType_Instance)) { // The UUID corresponds to an instance context.GetIndex().LogExportedResource(resourceId, remote); std::string dicom; context.ReadFile(dicom, resourceId, FileContentType_Dicom); connection.Store(dicom); call.GetOutput().AnswerBuffer("{}", "application/json"); } else { // The POST body is not a known resource, assume that it // contains a raw DICOM instance connection.Store(resourceId); call.GetOutput().AnswerBuffer("{}", "application/json"); } } // System information ------------------------------------------------------- static void ServeRoot(RestApi::GetCall& call) { call.GetOutput().Redirect("app/explorer.html"); } static void GetSystemInformation(RestApi::GetCall& call) { Json::Value result = Json::objectValue; result["Version"] = ORTHANC_VERSION; result["Name"] = GetGlobalStringParameter("Name", ""); call.GetOutput().AnswerJson(result); } static void GetStatistics(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); Json::Value result = Json::objectValue; context.GetIndex().ComputeStatistics(result); call.GetOutput().AnswerJson(result); } static void GenerateUid(RestApi::GetCall& call) { std::string level = call.GetArgument("level", ""); if (level == "patient") { call.GetOutput().AnswerBuffer(FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Patient), "text/plain"); } else if (level == "study") { call.GetOutput().AnswerBuffer(FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Study), "text/plain"); } else if (level == "series") { call.GetOutput().AnswerBuffer(FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Series), "text/plain"); } else if (level == "instance") { call.GetOutput().AnswerBuffer(FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Instance), "text/plain"); } } // List all the patients, studies, series or instances ---------------------- template <enum ResourceType resourceType> static void ListResources(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); Json::Value result; context.GetIndex().GetAllUuids(result, resourceType); call.GetOutput().AnswerJson(result); } template <enum ResourceType resourceType> static void GetSingleResource(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); Json::Value result; if (context.GetIndex().LookupResource(result, call.GetUriComponent("id", ""), resourceType)) { call.GetOutput().AnswerJson(result); } } template <enum ResourceType resourceType> static void DeleteSingleResource(RestApi::DeleteCall& call) { RETRIEVE_CONTEXT(call); Json::Value result; if (context.GetIndex().DeleteResource(result, call.GetUriComponent("id", ""), resourceType)) { call.GetOutput().AnswerJson(result); } } // Download of ZIP files ---------------------------------------------------- static std::string GetDirectoryNameInArchive(const Json::Value& resource, ResourceType resourceType) { switch (resourceType) { case ResourceType_Patient: { std::string p = resource["MainDicomTags"]["PatientID"].asString(); std::string n = resource["MainDicomTags"]["PatientName"].asString(); return p + " " + n; } case ResourceType_Study: { return resource["MainDicomTags"]["StudyDescription"].asString(); } case ResourceType_Series: { std::string d = resource["MainDicomTags"]["SeriesDescription"].asString(); std::string m = resource["MainDicomTags"]["Modality"].asString(); return m + " " + d; } default: throw OrthancException(ErrorCode_InternalError); } } static bool CreateRootDirectoryInArchive(HierarchicalZipWriter& writer, ServerContext& context, const Json::Value& resource, ResourceType resourceType) { if (resourceType == ResourceType_Patient) { return true; } ResourceType parentType = GetParentResourceType(resourceType); Json::Value parent; switch (resourceType) { case ResourceType_Study: { if (!context.GetIndex().LookupResource(parent, resource["ParentPatient"].asString(), parentType)) { return false; } break; } case ResourceType_Series: if (!context.GetIndex().LookupResource(parent, resource["ParentStudy"].asString(), parentType) || !CreateRootDirectoryInArchive(writer, context, parent, parentType)) { return false; } break; default: throw OrthancException(ErrorCode_NotImplemented); } writer.OpenDirectory(GetDirectoryNameInArchive(parent, parentType).c_str()); return true; } static bool ArchiveInstance(HierarchicalZipWriter& writer, ServerContext& context, const std::string& instancePublicId) { Json::Value instance; if (!context.GetIndex().LookupResource(instance, instancePublicId, ResourceType_Instance)) { return false; } std::string filename = instance["MainDicomTags"]["SOPInstanceUID"].asString() + ".dcm"; writer.OpenFile(filename.c_str()); std::string dicom; context.ReadFile(dicom, instancePublicId, FileContentType_Dicom); writer.Write(dicom); return true; } static bool ArchiveInternal(HierarchicalZipWriter& writer, ServerContext& context, const std::string& publicId, ResourceType resourceType, bool isFirstLevel) { Json::Value resource; if (!context.GetIndex().LookupResource(resource, publicId, resourceType)) { return false; } if (isFirstLevel && !CreateRootDirectoryInArchive(writer, context, resource, resourceType)) { return false; } writer.OpenDirectory(GetDirectoryNameInArchive(resource, resourceType).c_str()); switch (resourceType) { case ResourceType_Patient: for (Json::Value::ArrayIndex i = 0; i < resource["Studies"].size(); i++) { std::string studyId = resource["Studies"][i].asString(); if (!ArchiveInternal(writer, context, studyId, ResourceType_Study, false)) { return false; } } break; case ResourceType_Study: for (Json::Value::ArrayIndex i = 0; i < resource["Series"].size(); i++) { std::string seriesId = resource["Series"][i].asString(); if (!ArchiveInternal(writer, context, seriesId, ResourceType_Series, false)) { return false; } } break; case ResourceType_Series: for (Json::Value::ArrayIndex i = 0; i < resource["Instances"].size(); i++) { if (!ArchiveInstance(writer, context, resource["Instances"][i].asString())) { return false; } } break; default: throw OrthancException(ErrorCode_InternalError); } writer.CloseDirectory(); return true; } template <enum ResourceType resourceType> static void GetArchive(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); // Create a RAII for the temporary file to manage the ZIP file Toolbox::TemporaryFile tmp; std::string id = call.GetUriComponent("id", ""); { // Create a ZIP writer HierarchicalZipWriter writer(tmp.GetPath().c_str()); // Store the requested resource into the ZIP if (!ArchiveInternal(writer, context, id, resourceType, true)) { return; } } // Prepare the sending of the ZIP file FilesystemHttpSender sender(tmp.GetPath().c_str()); sender.SetContentType("application/zip"); sender.SetDownloadFilename(id + ".zip"); // Send the ZIP call.GetOutput().AnswerFile(sender); // The temporary file is automatically removed thanks to the RAII } // Changes API -------------------------------------------------------------- static void GetSinceAndLimit(int64_t& since, unsigned int& limit, bool& last, const RestApi::GetCall& call) { static const unsigned int MAX_RESULTS = 100; if (call.HasArgument("last")) { last = true; return; } last = false; try { since = boost::lexical_cast<int64_t>(call.GetArgument("since", "0")); limit = boost::lexical_cast<unsigned int>(call.GetArgument("limit", "0")); } catch (boost::bad_lexical_cast) { return; } if (limit == 0 || limit > MAX_RESULTS) { limit = MAX_RESULTS; } } static void GetChanges(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); //std::string filter = GetArgument(getArguments, "filter", ""); int64_t since; unsigned int limit; bool last; GetSinceAndLimit(since, limit, last, call); Json::Value result; if ((!last && context.GetIndex().GetChanges(result, since, limit)) || ( last && context.GetIndex().GetLastChange(result))) { call.GetOutput().AnswerJson(result); } } static void GetExports(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); int64_t since; unsigned int limit; bool last; GetSinceAndLimit(since, limit, last, call); Json::Value result; if ((!last && context.GetIndex().GetExportedResources(result, since, limit)) || ( last && context.GetIndex().GetLastExportedResource(result))) { call.GetOutput().AnswerJson(result); } } // Get information about a single patient ----------------------------------- static void IsProtectedPatient(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); std::string publicId = call.GetUriComponent("id", ""); bool isProtected = context.GetIndex().IsProtectedPatient(publicId); call.GetOutput().AnswerBuffer(isProtected ? "1" : "0", "text/plain"); } static void SetPatientProtection(RestApi::PutCall& call) { RETRIEVE_CONTEXT(call); std::string publicId = call.GetUriComponent("id", ""); std::string s = Toolbox::StripSpaces(call.GetPutBody()); if (s == "0") { context.GetIndex().SetProtectedPatient(publicId, false); call.GetOutput().AnswerBuffer("", "text/plain"); } else if (s == "1") { context.GetIndex().SetProtectedPatient(publicId, true); call.GetOutput().AnswerBuffer("", "text/plain"); } else { // Bad request } } // Get information about a single instance ---------------------------------- static void GetInstanceFile(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); std::string publicId = call.GetUriComponent("id", ""); context.AnswerFile(call.GetOutput(), publicId, FileContentType_Dicom); } template <bool simplify> static void GetInstanceTags(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); std::string publicId = call.GetUriComponent("id", ""); Json::Value full; context.ReadJson(full, publicId); if (simplify) { Json::Value simplified; SimplifyTags(simplified, full); call.GetOutput().AnswerJson(simplified); } else { call.GetOutput().AnswerJson(full); } } static void ListFrames(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); Json::Value instance; if (context.GetIndex().LookupResource(instance, call.GetUriComponent("id", ""), ResourceType_Instance)) { unsigned int numberOfFrames = 1; try { Json::Value tmp = instance["MainDicomTags"]["NumberOfFrames"]; numberOfFrames = boost::lexical_cast<unsigned int>(tmp.asString()); } catch (...) { } Json::Value result = Json::arrayValue; for (unsigned int i = 0; i < numberOfFrames; i++) { result.append(i); } call.GetOutput().AnswerJson(result); } } template <enum ImageExtractionMode mode> static void GetImage(RestApi::GetCall& call) { RETRIEVE_CONTEXT(call); std::string frameId = call.GetUriComponent("frame", "0"); unsigned int frame; try { frame = boost::lexical_cast<unsigned int>(frameId); } catch (boost::bad_lexical_cast) { return; } std::string publicId = call.GetUriComponent("id", ""); std::string dicomContent, png; context.ReadFile(dicomContent, publicId, FileContentType_Dicom); try { FromDcmtkBridge::ExtractPngImage(png, dicomContent, frame, mode); call.GetOutput().AnswerBuffer(png, "image/png"); } catch (OrthancException& e) { if (e.GetErrorCode() == ErrorCode_ParameterOutOfRange) { // The frame number is out of the range for this DICOM // instance, the resource is not existent } else { std::string root = ""; for (size_t i = 1; i < call.GetFullUri().size(); i++) { root += "../"; } call.GetOutput().Redirect(root + "app/images/unsupported.png"); } } } // Upload of DICOM files through HTTP --------------------------------------- static void UploadDicomFile(RestApi::PostCall& call) { RETRIEVE_CONTEXT(call); const std::string& postData = call.GetPostBody(); if (postData.size() == 0) { return; } LOG(INFO) << "Receiving a DICOM file of " << postData.size() << " bytes through HTTP"; std::string publicId; StoreStatus status = context.Store(publicId, postData); Json::Value result = Json::objectValue; if (status != StoreStatus_Failure) { result["ID"] = publicId; result["Path"] = GetBasePath(ResourceType_Instance, publicId); } result["Status"] = ToString(status); call.GetOutput().AnswerJson(result); } // DICOM bridge ------------------------------------------------------------- static bool IsExistingModality(const OrthancRestApi::Modalities& modalities, const std::string& id) { return modalities.find(id) != modalities.end(); } static void ListModalities(RestApi::GetCall& call) { RETRIEVE_MODALITIES(call); Json::Value result = Json::arrayValue; for (OrthancRestApi::Modalities::const_iterator it = modalities.begin(); it != modalities.end(); it++) { result.append(*it); } call.GetOutput().AnswerJson(result); } static void ListModalityOperations(RestApi::GetCall& call) { RETRIEVE_MODALITIES(call); std::string id = call.GetUriComponent("id", ""); if (IsExistingModality(modalities, id)) { Json::Value result = Json::arrayValue; result.append("find-patient"); result.append("find-study"); result.append("find-series"); result.append("find"); result.append("store"); call.GetOutput().AnswerJson(result); } } // Raw access to the DICOM tags of an instance ------------------------------ static void GetRawContent(RestApi::GetCall& call) { boost::mutex::scoped_lock lock(cacheMutex_); RETRIEVE_CONTEXT(call); std::string id = call.GetUriComponent("id", ""); ParsedDicomFile& dicom = context.GetDicomFile(id); dicom.SendPathValue(call.GetOutput(), call.GetTrailingUri()); } // Modification of DICOM instances ------------------------------------------ namespace { typedef std::set<DicomTag> Removals; typedef std::map<DicomTag, std::string> Replacements; typedef std::map< std::pair<DicomRootLevel, std::string>, std::string> UidMap; } static void ReplaceInstanceInternal(ParsedDicomFile& toModify, const Removals& removals, const Replacements& replacements, DicomReplaceMode mode, bool removePrivateTags) { if (removePrivateTags) { toModify.RemovePrivateTags(); } for (Removals::const_iterator it = removals.begin(); it != removals.end(); it++) { toModify.Remove(*it); } for (Replacements::const_iterator it = replacements.begin(); it != replacements.end(); it++) { toModify.Replace(it->first, it->second, mode); } // A new SOP instance UID is automatically generated std::string instanceUid = FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Instance); toModify.Replace(DICOM_TAG_SOP_INSTANCE_UID, instanceUid, DicomReplaceMode_InsertIfAbsent); } static void ParseRemovals(Removals& target, const Json::Value& removals) { if (!removals.isArray()) { throw OrthancException(ErrorCode_BadRequest); } target.clear(); for (Json::Value::ArrayIndex i = 0; i < removals.size(); i++) { DicomTag tag = FromDcmtkBridge::ParseTag(removals[i].asString()); target.insert(tag); } } static void ParseReplacements(Replacements& target, const Json::Value& replacements) { if (!replacements.isObject()) { throw OrthancException(ErrorCode_BadRequest); } target.clear(); Json::Value::Members members = replacements.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { const std::string& name = members[i]; std::string value = replacements[name].asString(); DicomTag tag = FromDcmtkBridge::ParseTag(name); target[tag] = value; } } static std::string GeneratePatientName(ServerContext& context) { uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence); return "Anonymized" + boost::lexical_cast<std::string>(seq); } static void SetupAnonymization(Removals& removals, Replacements& replacements) { // This is Table E.1-1 from PS 3.15-2008 - DICOM Part 15: Security and System Management Profiles removals.insert(DicomTag(0x0008, 0x0014)); // Instance Creator UID //removals.insert(DicomTag(0x0008, 0x0018)); // SOP Instance UID => set by ReplaceInstanceInternal() removals.insert(DicomTag(0x0008, 0x0050)); // Accession Number removals.insert(DicomTag(0x0008, 0x0080)); // Institution Name removals.insert(DicomTag(0x0008, 0x0081)); // Institution Address removals.insert(DicomTag(0x0008, 0x0090)); // Referring Physician's Name removals.insert(DicomTag(0x0008, 0x0092)); // Referring Physician's Address removals.insert(DicomTag(0x0008, 0x0094)); // Referring Physician's Telephone Numbers removals.insert(DicomTag(0x0008, 0x1010)); // Station Name removals.insert(DicomTag(0x0008, 0x1030)); // Study Description removals.insert(DicomTag(0x0008, 0x103e)); // Series Description removals.insert(DicomTag(0x0008, 0x1040)); // Institutional Department Name removals.insert(DicomTag(0x0008, 0x1048)); // Physician(s) of Record removals.insert(DicomTag(0x0008, 0x1050)); // Performing Physicians' Name removals.insert(DicomTag(0x0008, 0x1060)); // Name of Physician(s) Reading Study removals.insert(DicomTag(0x0008, 0x1070)); // Operators' Name removals.insert(DicomTag(0x0008, 0x1080)); // Admitting Diagnoses Description removals.insert(DicomTag(0x0008, 0x1155)); // Referenced SOP Instance UID removals.insert(DicomTag(0x0008, 0x2111)); // Derivation Description removals.insert(DicomTag(0x0010, 0x0010)); // Patient's Name removals.insert(DicomTag(0x0010, 0x0020)); // Patient ID removals.insert(DicomTag(0x0010, 0x0030)); // Patient's Birth Date removals.insert(DicomTag(0x0010, 0x0032)); // Patient's Birth Time removals.insert(DicomTag(0x0010, 0x0040)); // Patient's Sex removals.insert(DicomTag(0x0010, 0x1000)); // Other Patient Ids removals.insert(DicomTag(0x0010, 0x1001)); // Other Patient Names removals.insert(DicomTag(0x0010, 0x1010)); // Patient's Age removals.insert(DicomTag(0x0010, 0x1020)); // Patient's Size removals.insert(DicomTag(0x0010, 0x1030)); // Patient's Weight removals.insert(DicomTag(0x0010, 0x1090)); // Medical Record Locator removals.insert(DicomTag(0x0010, 0x2160)); // Ethnic Group removals.insert(DicomTag(0x0010, 0x2180)); // Occupation removals.insert(DicomTag(0x0010, 0x21b0)); // Additional Patient's History removals.insert(DicomTag(0x0010, 0x4000)); // Patient Comments removals.insert(DicomTag(0x0018, 0x1000)); // Device Serial Number removals.insert(DicomTag(0x0018, 0x1030)); // Protocol Name //removals.insert(DicomTag(0x0020, 0x000d)); // Study Instance UID => generated below //removals.insert(DicomTag(0x0020, 0x000e)); // Series Instance UID => generated below removals.insert(DicomTag(0x0020, 0x0010)); // Study ID removals.insert(DicomTag(0x0020, 0x0052)); // Frame of Reference UID removals.insert(DicomTag(0x0020, 0x0200)); // Synchronization Frame of Reference UID removals.insert(DicomTag(0x0020, 0x4000)); // Image Comments removals.insert(DicomTag(0x0040, 0x0275)); // Request Attributes Sequence removals.insert(DicomTag(0x0040, 0xa124)); // UID removals.insert(DicomTag(0x0040, 0xa730)); // Content Sequence removals.insert(DicomTag(0x0088, 0x0140)); // Storage Media File-set UID removals.insert(DicomTag(0x3006, 0x0024)); // Referenced Frame of Reference UID removals.insert(DicomTag(0x3006, 0x00c2)); // Related Frame of Reference UID // Some more removals (from the experience of DICOM files at the CHU of Liege) removals.insert(DicomTag(0x0010, 0x1040)); // Patient's Address removals.insert(DicomTag(0x0032, 0x1032)); // Requesting Physician // Set the DeidentificationMethod tag replacements.insert(std::make_pair(DicomTag(0x0012, 0x0063), "Orthanc " ORTHANC_VERSION " - PS 3.15-2008 Table E.1-1")); // Set the PatientIdentityRemoved replacements.insert(std::make_pair(DicomTag(0x0012, 0x0062), "YES")); // Generate random study UID if not specified if (replacements.find(DICOM_TAG_STUDY_INSTANCE_UID) == replacements.end()) { replacements.insert(std::make_pair(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Study))); } // Generate random series UID if not specified if (replacements.find(DICOM_TAG_SERIES_INSTANCE_UID) == replacements.end()) { replacements.insert(std::make_pair(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Series))); } } static bool ParseModifyRequest(Removals& removals, Replacements& replacements, bool& removePrivateTags, const RestApi::PostCall& call) { removePrivateTags = false; Json::Value request; if (call.ParseJsonRequest(request) && request.isObject()) { Json::Value removalsPart = Json::arrayValue; Json::Value replacementsPart = Json::objectValue; if (request.isMember("Remove")) { removalsPart = request["Remove"]; } if (request.isMember("Replace")) { replacementsPart = request["Replace"]; } if (request.isMember("RemovePrivateTags")) { removePrivateTags = true; } ParseRemovals(removals, removalsPart); ParseReplacements(replacements, replacementsPart); return true; } else { return false; } } static bool ParseAnonymizationRequest(Removals& removals, Replacements& replacements, bool& removePrivateTags, RestApi::PostCall& call) { RETRIEVE_CONTEXT(call); removePrivateTags = true; Json::Value request; if (call.ParseJsonRequest(request) && request.isObject()) { Json::Value keepPart = Json::arrayValue; Json::Value removalsPart = Json::arrayValue; Json::Value replacementsPart = Json::objectValue; if (request.isMember("Keep")) { keepPart = request["Keep"]; } if (request.isMember("KeepPrivateTags")) { removePrivateTags = false; } if (request.isMember("Replace")) { replacementsPart = request["Replace"]; } Removals toKeep; ParseRemovals(toKeep, keepPart); SetupAnonymization(removals, replacements); for (Removals::iterator it = toKeep.begin(); it != toKeep.end(); it++) { removals.erase(*it); } Removals additionalRemovals; ParseRemovals(additionalRemovals, removalsPart); for (Removals::iterator it = additionalRemovals.begin(); it != additionalRemovals.end(); it++) { removals.insert(*it); } ParseReplacements(replacements, replacementsPart); // Generate random Patient's Name if none is specified if (replacements.find(DicomTag(0x0010, 0x0010)) == replacements.end()) { replacements.insert(std::make_pair(DicomTag(0x0010, 0x0010), GeneratePatientName(context))); } // Generate random Patient's ID if none is specified if (replacements.find(DICOM_TAG_PATIENT_ID) == replacements.end()) { replacements.insert(std::make_pair(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Patient))); } return true; } else { return false; } } static void AnonymizeOrModifyInstance(Removals& removals, Replacements& replacements, bool removePrivateTags, RestApi::PostCall& call) { boost::mutex::scoped_lock lock(cacheMutex_); RETRIEVE_CONTEXT(call); std::string id = call.GetUriComponent("id", ""); ParsedDicomFile& dicom = context.GetDicomFile(id); std::auto_ptr<ParsedDicomFile> modified(dicom.Clone()); ReplaceInstanceInternal(*modified, removals, replacements, DicomReplaceMode_InsertIfAbsent, removePrivateTags); modified->Answer(call.GetOutput()); } static bool RetrieveMappedUid(ParsedDicomFile& dicom, DicomRootLevel level, Replacements& replacements, UidMap& uidMap) { std::auto_ptr<DicomTag> tag; if (level == DicomRootLevel_Series) { tag.reset(new DicomTag(DICOM_TAG_SERIES_INSTANCE_UID)); } else { assert(level == DicomRootLevel_Study); tag.reset(new DicomTag(DICOM_TAG_STUDY_INSTANCE_UID)); } std::string original; if (!dicom.GetTagValue(original, *tag)) { throw OrthancException(ErrorCode_InternalError); } std::string mapped; bool isNew; UidMap::const_iterator previous = uidMap.find(std::make_pair(level, original)); if (previous == uidMap.end()) { mapped = FromDcmtkBridge::GenerateUniqueIdentifier(level); uidMap.insert(std::make_pair(std::make_pair(level, original), mapped)); isNew = true; } else { mapped = previous->second; isNew = false; } replacements[*tag] = mapped; return isNew; } static void AnonymizeOrModifyResource(Removals& removals, Replacements& replacements, bool removePrivateTags, MetadataType metadataType, ChangeType changeType, ResourceType resourceType, RestApi::PostCall& call) { typedef std::list<std::string> Instances; bool isFirst = true; Json::Value result(Json::objectValue); boost::mutex::scoped_lock lock(cacheMutex_); RETRIEVE_CONTEXT(call); Instances instances; std::string id = call.GetUriComponent("id", ""); context.GetIndex().GetChildInstances(instances, id); if (instances.size() == 0) { return; } /** * Loop over all the instances of the resource. **/ UidMap uidMap; for (Instances::const_iterator it = instances.begin(); it != instances.end(); it++) { LOG(INFO) << "Modifying instance " << *it; ParsedDicomFile& original = context.GetDicomFile(*it); bool isNewSeries = RetrieveMappedUid(original, DicomRootLevel_Series, replacements, uidMap); bool isNewStudy = false; if (resourceType == ResourceType_Study || resourceType == ResourceType_Patient) { isNewStudy = RetrieveMappedUid(original, DicomRootLevel_Study, replacements, uidMap); } /** * Compute the resulting DICOM instance and store it into the Orthanc store. **/ std::auto_ptr<ParsedDicomFile> modified(original.Clone()); ReplaceInstanceInternal(*modified, removals, replacements, DicomReplaceMode_InsertIfAbsent, removePrivateTags); std::string modifiedInstance; if (context.Store(modifiedInstance, modified->GetDicom()) != StoreStatus_Success) { LOG(ERROR) << "Error while storing a modified instance " << *it; return; } /** * Record metadata information (AnonimizedFrom/ModifiedFrom). **/ DicomInstanceHasher modifiedHasher = modified->GetHasher(); DicomInstanceHasher originalHasher = original.GetHasher(); if (isNewSeries) { context.GetIndex().SetMetadata(modifiedHasher.HashSeries(), metadataType, originalHasher.HashSeries()); } if (isNewStudy) { context.GetIndex().SetMetadata(modifiedHasher.HashStudy(), metadataType, originalHasher.HashStudy()); } assert(*it == originalHasher.HashInstance()); assert(modifiedInstance == modifiedHasher.HashInstance()); context.GetIndex().SetMetadata(modifiedInstance, metadataType, *it); /** * Compute the JSON object that is returned by the REST call. **/ if (isFirst) { std::string newId; switch (resourceType) { case ResourceType_Series: newId = modifiedHasher.HashSeries(); break; case ResourceType_Study: newId = modifiedHasher.HashStudy(); break; case ResourceType_Patient: newId = modifiedHasher.HashPatient(); break; default: throw OrthancException(ErrorCode_InternalError); } result["Type"] = ToString(resourceType); result["ID"] = newId; result["Path"] = GetBasePath(resourceType, newId); result["PatientID"] = modifiedHasher.HashPatient(); isFirst = false; } } call.GetOutput().AnswerJson(result); } static void ModifyInstance(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseModifyRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyInstance(removals, replacements, removePrivateTags, call); } } static void AnonymizeInstance(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseAnonymizationRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyInstance(removals, replacements, removePrivateTags, call); } } static void ModifySeriesInplace(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseModifyRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyResource(removals, replacements, removePrivateTags, MetadataType_ModifiedFrom, ChangeType_ModifiedSeries, ResourceType_Series, call); } } static void AnonymizeSeriesInplace(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseAnonymizationRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyResource(removals, replacements, removePrivateTags, MetadataType_AnonymizedFrom, ChangeType_AnonymizedSeries, ResourceType_Series, call); } } static void ModifyStudyInplace(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseModifyRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyResource(removals, replacements, removePrivateTags, MetadataType_ModifiedFrom, ChangeType_ModifiedStudy, ResourceType_Study, call); } } static void AnonymizeStudyInplace(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseAnonymizationRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyResource(removals, replacements, removePrivateTags, MetadataType_AnonymizedFrom, ChangeType_AnonymizedStudy, ResourceType_Study, call); } } static void ModifyPatientInplace(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseModifyRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyResource(removals, replacements, removePrivateTags, MetadataType_ModifiedFrom, ChangeType_ModifiedPatient, ResourceType_Patient, call); } } static void AnonymizePatientInplace(RestApi::PostCall& call) { Removals removals; Replacements replacements; bool removePrivateTags; if (ParseAnonymizationRequest(removals, replacements, removePrivateTags, call)) { AnonymizeOrModifyResource(removals, replacements, removePrivateTags, MetadataType_AnonymizedFrom, ChangeType_AnonymizedPatient, ResourceType_Patient, call); } } // Registration of the various REST handlers -------------------------------- OrthancRestApi::OrthancRestApi(ServerContext& context) : context_(context) { GetListOfDicomModalities(modalities_); Register("/", ServeRoot); Register("/system", GetSystemInformation); Register("/statistics", GetStatistics); Register("/changes", GetChanges); Register("/exports", GetExports); Register("/instances", UploadDicomFile); Register("/instances", ListResources<ResourceType_Instance>); Register("/patients", ListResources<ResourceType_Patient>); Register("/series", ListResources<ResourceType_Series>); Register("/studies", ListResources<ResourceType_Study>); Register("/instances/{id}", DeleteSingleResource<ResourceType_Instance>); Register("/instances/{id}", GetSingleResource<ResourceType_Instance>); Register("/patients/{id}", DeleteSingleResource<ResourceType_Patient>); Register("/patients/{id}", GetSingleResource<ResourceType_Patient>); Register("/series/{id}", DeleteSingleResource<ResourceType_Series>); Register("/series/{id}", GetSingleResource<ResourceType_Series>); Register("/studies/{id}", DeleteSingleResource<ResourceType_Study>); Register("/studies/{id}", GetSingleResource<ResourceType_Study>); Register("/patients/{id}/archive", GetArchive<ResourceType_Patient>); Register("/studies/{id}/archive", GetArchive<ResourceType_Study>); Register("/series/{id}/archive", GetArchive<ResourceType_Series>); Register("/patients/{id}/protected", IsProtectedPatient); Register("/patients/{id}/protected", SetPatientProtection); Register("/instances/{id}/file", GetInstanceFile); Register("/instances/{id}/tags", GetInstanceTags<false>); Register("/instances/{id}/simplified-tags", GetInstanceTags<true>); Register("/instances/{id}/frames", ListFrames); Register("/instances/{id}/content/*", GetRawContent); Register("/instances/{id}/frames/{frame}/preview", GetImage<ImageExtractionMode_Preview>); Register("/instances/{id}/frames/{frame}/image-uint8", GetImage<ImageExtractionMode_UInt8>); Register("/instances/{id}/frames/{frame}/image-uint16", GetImage<ImageExtractionMode_UInt16>); Register("/instances/{id}/preview", GetImage<ImageExtractionMode_Preview>); Register("/instances/{id}/image-uint8", GetImage<ImageExtractionMode_UInt8>); Register("/instances/{id}/image-uint16", GetImage<ImageExtractionMode_UInt16>); Register("/modalities", ListModalities); Register("/modalities/{id}", ListModalityOperations); Register("/modalities/{id}/find-patient", DicomFindPatient); Register("/modalities/{id}/find-study", DicomFindStudy); Register("/modalities/{id}/find-series", DicomFindSeries); Register("/modalities/{id}/find", DicomFind); Register("/modalities/{id}/store", DicomStore); Register("/instances/{id}/modify", ModifyInstance); Register("/series/{id}/modify", ModifySeriesInplace); Register("/studies/{id}/modify", ModifyStudyInplace); Register("/patients/{id}/modify", ModifyPatientInplace); Register("/instances/{id}/anonymize", AnonymizeInstance); Register("/series/{id}/anonymize", AnonymizeSeriesInplace); Register("/studies/{id}/anonymize", AnonymizeStudyInplace); Register("/patients/{id}/anonymize", AnonymizePatientInplace); Register("/tools/generate-uid", GenerateUid); } }