Mercurial > hg > orthanc
view OrthancServer/OrthancFindRequestHandler.cpp @ 3414:b9cba6a91780
simplification
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 11 Jun 2019 19:44:10 +0200 |
parents | 63f59ad9381a |
children | 94f4a18a79cc |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2019 Osimis S.A., Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * In addition, as a special exception, the copyright holders of this * program give permission to link the code of its release with the * OpenSSL project's "OpenSSL" library (or with modified versions of it * that use the same license as the "OpenSSL" library), and distribute * the linked executables. You must obey the GNU General Public License * in all respects for all of the code used other than "OpenSSL". If you * modify file(s) with this exception, you may extend this exception to * your version of the file(s), but you are not obligated to do so. If * you do not wish to do so, delete this exception statement from your * version. If you delete this exception statement from all source files * in the program, then also delete it here. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "PrecompiledHeadersServer.h" #include "OrthancFindRequestHandler.h" #include "../Core/DicomFormat/DicomArray.h" #include "../Core/DicomParsing/FromDcmtkBridge.h" #include "../Core/Logging.h" #include "../Core/Lua/LuaFunctionCall.h" #include "../Core/MetricsRegistry.h" #include "OrthancConfiguration.h" #include "Search/DatabaseLookup.h" #include "ServerContext.h" #include "ServerToolbox.h" #include <boost/regex.hpp> namespace Orthanc { static void GetChildren(std::list<std::string>& target, ServerIndex& index, const std::list<std::string>& source) { target.clear(); for (std::list<std::string>::const_iterator it = source.begin(); it != source.end(); ++it) { std::list<std::string> tmp; index.GetChildren(tmp, *it); target.splice(target.end(), tmp); } } static void StoreSetOfStrings(DicomMap& result, const DicomTag& tag, const std::set<std::string>& values) { bool isFirst = true; std::string s; for (std::set<std::string>::const_iterator it = values.begin(); it != values.end(); ++it) { if (isFirst) { isFirst = false; } else { s += "\\"; } s += *it; } result.SetValue(tag, s, false); } static void ComputePatientCounters(DicomMap& result, ServerIndex& index, const std::string& patient, const DicomMap& query) { std::list<std::string> studies; index.GetChildren(studies, patient); if (query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES)) { result.SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES, boost::lexical_cast<std::string>(studies.size()), false); } if (!query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES) && !query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES)) { return; } std::list<std::string> series; GetChildren(series, index, studies); studies.clear(); // This information is useless below if (query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES)) { result.SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES, boost::lexical_cast<std::string>(series.size()), false); } if (!query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES)) { return; } std::list<std::string> instances; GetChildren(instances, index, series); if (query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES)) { result.SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES, boost::lexical_cast<std::string>(instances.size()), false); } } static void ComputeStudyCounters(DicomMap& result, ServerContext& context, const std::string& study, const DicomMap& query) { ServerIndex& index = context.GetIndex(); std::list<std::string> series; index.GetChildren(series, study); if (query.HasTag(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES)) { result.SetValue(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES, boost::lexical_cast<std::string>(series.size()), false); } if (query.HasTag(DICOM_TAG_MODALITIES_IN_STUDY)) { std::set<std::string> values; for (std::list<std::string>::const_iterator it = series.begin(); it != series.end(); ++it) { DicomMap tags; if (index.GetMainDicomTags(tags, *it, ResourceType_Series, ResourceType_Series)) { const DicomValue* value = tags.TestAndGetValue(DICOM_TAG_MODALITY); if (value != NULL && !value->IsNull() && !value->IsBinary()) { values.insert(value->GetContent()); } } } StoreSetOfStrings(result, DICOM_TAG_MODALITIES_IN_STUDY, values); } if (!query.HasTag(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES) && !query.HasTag(DICOM_TAG_SOP_CLASSES_IN_STUDY)) { return; } std::list<std::string> instances; GetChildren(instances, index, series); if (query.HasTag(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES)) { result.SetValue(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES, boost::lexical_cast<std::string>(instances.size()), false); } if (query.HasTag(DICOM_TAG_SOP_CLASSES_IN_STUDY)) { std::set<std::string> values; for (std::list<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { std::string value; if (context.LookupOrReconstructMetadata(value, *it, MetadataType_Instance_SopClassUid)) { values.insert(value); } } StoreSetOfStrings(result, DICOM_TAG_SOP_CLASSES_IN_STUDY, values); } } static void ComputeSeriesCounters(DicomMap& result, ServerIndex& index, const std::string& series, const DicomMap& query) { std::list<std::string> instances; index.GetChildren(instances, series); if (query.HasTag(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES)) { result.SetValue(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES, boost::lexical_cast<std::string>(instances.size()), false); } } static DicomMap* ComputeCounters(ServerContext& context, const std::string& instanceId, ResourceType level, const DicomMap& query) { switch (level) { case ResourceType_Patient: if (!query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES) && !query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES) && !query.HasTag(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES)) { return NULL; } break; case ResourceType_Study: if (!query.HasTag(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES) && !query.HasTag(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES) && !query.HasTag(DICOM_TAG_SOP_CLASSES_IN_STUDY) && !query.HasTag(DICOM_TAG_MODALITIES_IN_STUDY)) { return NULL; } break; case ResourceType_Series: if (!query.HasTag(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES)) { return NULL; } break; default: return NULL; } std::string parent; if (!context.GetIndex().LookupParent(parent, instanceId, level)) { throw OrthancException(ErrorCode_UnknownResource); // The resource was deleted in between } std::auto_ptr<DicomMap> result(new DicomMap); switch (level) { case ResourceType_Patient: ComputePatientCounters(*result, context.GetIndex(), parent, query); break; case ResourceType_Study: ComputeStudyCounters(*result, context, parent, query); break; case ResourceType_Series: ComputeSeriesCounters(*result, context.GetIndex(), parent, query); break; default: throw OrthancException(ErrorCode_InternalError); } return result.release(); } static void AddAnswer(DicomFindAnswers& answers, const DicomMap& mainDicomTags, const Json::Value* dicomAsJson, const DicomArray& query, const std::list<DicomTag>& sequencesToReturn, const DicomMap* counters) { DicomMap match; if (dicomAsJson != NULL) { match.FromDicomAsJson(*dicomAsJson); } else { match.Assign(mainDicomTags); } DicomMap result; for (size_t i = 0; i < query.GetSize(); i++) { if (query.GetElement(i).GetTag() == DICOM_TAG_QUERY_RETRIEVE_LEVEL) { // Fix issue 30 on Google Code (QR response missing "Query/Retrieve Level" (008,0052)) result.SetValue(query.GetElement(i).GetTag(), query.GetElement(i).GetValue()); } else if (query.GetElement(i).GetTag() == DICOM_TAG_SPECIFIC_CHARACTER_SET) { // Do not include the encoding, this is handled by class ParsedDicomFile } else { const DicomTag& tag = query.GetElement(i).GetTag(); const DicomValue* value = match.TestAndGetValue(tag); if (value != NULL && !value->IsNull() && !value->IsBinary()) { result.SetValue(tag, value->GetContent(), false); } else { result.SetValue(tag, "", false); } } } if (counters != NULL) { DicomArray tmp(*counters); for (size_t i = 0; i < tmp.GetSize(); i++) { result.SetValue(tmp.GetElement(i).GetTag(), tmp.GetElement(i).GetValue().GetContent(), false); } } if (result.GetSize() == 0 && sequencesToReturn.empty()) { LOG(WARNING) << "The C-FIND request does not return any DICOM tag"; } else if (sequencesToReturn.empty()) { answers.Add(result); } else if (dicomAsJson == NULL) { LOG(WARNING) << "C-FIND query requesting a sequence, but reading JSON from disk is disabled"; answers.Add(result); } else { ParsedDicomFile dicom(result, GetDefaultDicomEncoding(), true /* be permissive, cf. issue #136 */); for (std::list<DicomTag>::const_iterator tag = sequencesToReturn.begin(); tag != sequencesToReturn.end(); ++tag) { assert(dicomAsJson != NULL); const Json::Value& source = (*dicomAsJson) [tag->Format()]; if (source.type() == Json::objectValue && source.isMember("Type") && source.isMember("Value") && source["Type"].asString() == "Sequence" && source["Value"].type() == Json::arrayValue) { Json::Value content = Json::arrayValue; for (Json::Value::ArrayIndex i = 0; i < source["Value"].size(); i++) { Json::Value item; ServerToolbox::SimplifyTags(item, source["Value"][i], DicomToJsonFormat_Short); content.append(item); } dicom.Replace(*tag, content, false, DicomReplaceMode_InsertIfAbsent); } } answers.Add(dicom); } } bool OrthancFindRequestHandler::FilterQueryTag(std::string& value /* can be modified */, ResourceType level, const DicomTag& tag, ModalityManufacturer manufacturer) { // Whatever the manufacturer, remove the GenericGroupLength tags // http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.2.html // https://bitbucket.org/sjodogne/orthanc/issues/31/ if (tag.GetElement() == 0x0000) { return false; } switch (manufacturer) { case ModalityManufacturer_Vitrea: // Following Denis Nesterov's mail on 2015-11-30 if (tag == DicomTag(0x5653, 0x0010)) // "PrivateCreator = Vital Images SW 3.4" { return false; } break; default: break; } return true; } bool OrthancFindRequestHandler::ApplyLuaFilter(DicomMap& target, const DicomMap& source, const std::string& remoteIp, const std::string& remoteAet, const std::string& calledAet, ModalityManufacturer manufacturer) { static const char* LUA_CALLBACK = "IncomingFindRequestFilter"; LuaScripting::Lock lock(context_.GetLuaScripting()); if (!lock.GetLua().IsExistingFunction(LUA_CALLBACK)) { return false; } else { Json::Value origin; FormatOrigin(origin, remoteIp, remoteAet, calledAet, manufacturer); LuaFunctionCall call(lock.GetLua(), LUA_CALLBACK); call.PushDicom(source); call.PushJson(origin); FromDcmtkBridge::ExecuteToDicom(target, call); return true; } } OrthancFindRequestHandler::OrthancFindRequestHandler(ServerContext& context) : context_(context), maxResults_(0), maxInstances_(0) { } class OrthancFindRequestHandler::LookupVisitor : public ServerContext::ILookupVisitor { private: DicomFindAnswers& answers_; ServerContext& context_; ResourceType level_; const DicomMap& query_; DicomArray queryAsArray_; const std::list<DicomTag>& sequencesToReturn_; public: LookupVisitor(DicomFindAnswers& answers, ServerContext& context, ResourceType level, const DicomMap& query, const std::list<DicomTag>& sequencesToReturn) : answers_(answers), context_(context), level_(level), query_(query), queryAsArray_(query), sequencesToReturn_(sequencesToReturn) { answers_.SetComplete(false); } virtual bool IsDicomAsJsonNeeded() const { // Ask the "DICOM-as-JSON" attachment only if sequences are to // be returned OR if "query_" contains non-main DICOM tags! DicomMap withoutSpecialTags; withoutSpecialTags.Assign(query_); // Check out "ComputeCounters()" withoutSpecialTags.Remove(DICOM_TAG_MODALITIES_IN_STUDY); withoutSpecialTags.Remove(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES); withoutSpecialTags.Remove(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES); withoutSpecialTags.Remove(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES); withoutSpecialTags.Remove(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES); withoutSpecialTags.Remove(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES); withoutSpecialTags.Remove(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES); withoutSpecialTags.Remove(DICOM_TAG_SOP_CLASSES_IN_STUDY); // Check out "AddAnswer()" withoutSpecialTags.Remove(DICOM_TAG_SPECIFIC_CHARACTER_SET); withoutSpecialTags.Remove(DICOM_TAG_QUERY_RETRIEVE_LEVEL); return (!sequencesToReturn_.empty() || !withoutSpecialTags.HasOnlyMainDicomTags()); } virtual void MarkAsComplete() { answers_.SetComplete(true); } virtual void Visit(const std::string& publicId, const std::string& instanceId, const DicomMap& mainDicomTags, const Json::Value* dicomAsJson) { std::auto_ptr<DicomMap> counters(ComputeCounters(context_, instanceId, level_, query_)); AddAnswer(answers_, mainDicomTags, dicomAsJson, queryAsArray_, sequencesToReturn_, counters.get()); } }; void OrthancFindRequestHandler::Handle(DicomFindAnswers& answers, const DicomMap& input, const std::list<DicomTag>& sequencesToReturn, const std::string& remoteIp, const std::string& remoteAet, const std::string& calledAet, ModalityManufacturer manufacturer) { MetricsRegistry::Timer timer(context_.GetMetricsRegistry(), "orthanc_find_scp_duration_ms"); /** * Possibly apply the user-supplied Lua filter. **/ DicomMap lua; const DicomMap* filteredInput = &input; if (ApplyLuaFilter(lua, input, remoteIp, remoteAet, calledAet, manufacturer)) { filteredInput = &lua; } /** * Retrieve the query level. **/ assert(filteredInput != NULL); const DicomValue* levelTmp = filteredInput->TestAndGetValue(DICOM_TAG_QUERY_RETRIEVE_LEVEL); if (levelTmp == NULL || levelTmp->IsNull() || levelTmp->IsBinary()) { throw OrthancException(ErrorCode_BadRequest, "C-FIND request without the tag 0008,0052 (QueryRetrieveLevel)"); } ResourceType level = StringToResourceType(levelTmp->GetContent().c_str()); if (level != ResourceType_Patient && level != ResourceType_Study && level != ResourceType_Series && level != ResourceType_Instance) { throw OrthancException(ErrorCode_NotImplemented); } DicomArray query(*filteredInput); LOG(INFO) << "DICOM C-Find request at level: " << EnumerationToString(level); for (size_t i = 0; i < query.GetSize(); i++) { if (!query.GetElement(i).GetValue().IsNull()) { LOG(INFO) << " " << query.GetElement(i).GetTag() << " " << FromDcmtkBridge::GetTagName(query.GetElement(i)) << " = " << query.GetElement(i).GetValue().GetContent(); } } for (std::list<DicomTag>::const_iterator it = sequencesToReturn.begin(); it != sequencesToReturn.end(); ++it) { LOG(INFO) << " (" << it->Format() << ") " << FromDcmtkBridge::GetTagName(*it, "") << " : sequence tag whose content will be copied"; } /** * Build up the query object. **/ DatabaseLookup lookup; bool caseSensitivePN; { OrthancConfiguration::ReaderLock lock; caseSensitivePN = lock.GetConfiguration().GetBooleanParameter("CaseSensitivePN", false); } for (size_t i = 0; i < query.GetSize(); i++) { const DicomElement& element = query.GetElement(i); const DicomTag tag = element.GetTag(); if (element.GetValue().IsNull() || tag == DICOM_TAG_QUERY_RETRIEVE_LEVEL || tag == DICOM_TAG_SPECIFIC_CHARACTER_SET) { continue; } std::string value = element.GetValue().GetContent(); if (value.size() == 0) { // An empty string corresponds to an universal constraint, so we ignore it continue; } if (FilterQueryTag(value, level, tag, manufacturer)) { ValueRepresentation vr = FromDcmtkBridge::LookupValueRepresentation(tag); // DICOM specifies that searches must be case sensitive, except // for tags with a PN value representation bool sensitive = true; if (vr == ValueRepresentation_PersonName) { sensitive = caseSensitivePN; } lookup.AddDicomConstraint(tag, value, sensitive, true /* mandatory */); } else { LOG(INFO) << "Because of a patch for the manufacturer of the remote modality, " << "ignoring constraint on tag (" << tag.Format() << ") " << FromDcmtkBridge::GetTagName(element); } } /** * Run the query. **/ size_t limit = (level == ResourceType_Instance) ? maxInstances_ : maxResults_; LookupVisitor visitor(answers, context_, level, *filteredInput, sequencesToReturn); context_.Apply(visitor, lookup, level, 0 /* "since" is not relevant to C-FIND */, limit); } void OrthancFindRequestHandler::FormatOrigin(Json::Value& origin, const std::string& remoteIp, const std::string& remoteAet, const std::string& calledAet, ModalityManufacturer manufacturer) { origin = Json::objectValue; origin["RemoteIp"] = remoteIp; origin["RemoteAet"] = remoteAet; origin["CalledAet"] = calledAet; origin["Manufacturer"] = EnumerationToString(manufacturer); } }