Mercurial > hg > orthanc
view OrthancServer/OrthancFindRequestHandler.cpp @ 2277:c6defdc4c611 issue-46-anonymization
updated list of fields to remove during anonymization following PS 3.15-2011 Table E.1-1
author | amazy |
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date | Wed, 10 May 2017 22:40:59 +0200 |
parents | de1ba22fd28a |
children | 5b7556568fa4 |
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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 Osimis, 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/Lua/LuaFunctionCall.h" #include "../Core/Logging.h" #include "FromDcmtkBridge.h" #include "OrthancInitialization.h" #include "Search/LookupResource.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 ExtractTagFromMainDicomTags(std::set<std::string>& target, ServerIndex& index, const DicomTag& tag, const std::list<std::string>& resources, ResourceType level) { for (std::list<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) { DicomMap tags; if (index.GetMainDicomTags(tags, *it, level, level) && tags.HasTag(tag)) { target.insert(tags.GetValue(tag).GetContent()); } } } static bool ExtractMetadata(std::set<std::string>& target, ServerIndex& index, MetadataType metadata, const std::list<std::string>& resources) { for (std::list<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) { std::string value; if (index.LookupMetadata(value, *it, metadata)) { target.insert(value); } else { // This metadata is unavailable for some resource, give up return false; } } return true; } static void ExtractTagFromInstancesOnDisk(std::set<std::string>& target, ServerContext& context, const DicomTag& tag, const std::list<std::string>& instances) { // WARNING: This function is slow, as it reads the JSON file // summarizing each instance of interest from the hard drive. std::string formatted = tag.Format(); for (std::list<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { Json::Value dicom; context.ReadDicomAsJson(dicom, *it); if (dicom.isMember(formatted)) { const Json::Value& source = dicom[formatted]; if (source.type() == Json::objectValue && source.isMember("Type") && source.isMember("Value") && source["Type"].asString() == "String" && source["Value"].type() == Json::stringValue) { target.insert(source["Value"].asString()); } } } } 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; ExtractTagFromMainDicomTags(values, index, DICOM_TAG_MODALITY, series, ResourceType_Series); 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; if (ExtractMetadata(values, index, MetadataType_Instance_SopClassUid, instances)) { // The metadata "SopClassUid" is available for each of these instances StoreSetOfStrings(result, DICOM_TAG_SOP_CLASSES_IN_STUDY, values); } else if (Configuration::GetGlobalBoolParameter("AllowFindSopClassesInStudy", false)) { ExtractTagFromInstancesOnDisk(values, context, DICOM_TAG_SOP_CLASS_UID, instances); StoreSetOfStrings(result, DICOM_TAG_SOP_CLASSES_IN_STUDY, values); } else { result.SetValue(DICOM_TAG_SOP_CLASSES_IN_STUDY, "", false); LOG(WARNING) << "The handling of \"SOP Classes in Study\" (0008,0062) " << "in C-FIND requests is disabled"; } } } 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 Json::Value& resource, const DicomArray& query, const std::list<DicomTag>& sequencesToReturn, const DicomMap* counters) { 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 { std::string tag = query.GetElement(i).GetTag().Format(); std::string value; if (resource.isMember(tag)) { value = resource.get(tag, Json::arrayValue).get("Value", "").asString(); result.SetValue(query.GetElement(i).GetTag(), value, false); } else { result.SetValue(query.GetElement(i).GetTag(), "", 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 { ParsedDicomFile dicom(result); for (std::list<DicomTag>::const_iterator tag = sequencesToReturn.begin(); tag != sequencesToReturn.end(); ++tag) { const Json::Value& source = resource[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) { switch (manufacturer) { case ModalityManufacturer_EFilm2: // Following Denis Nesterov's mail on 2015-11-30 if (tag == DicomTag(0x0008, 0x0000) || // "GenericGroupLength" tag == DicomTag(0x0010, 0x0000) || // "GenericGroupLength" tag == DicomTag(0x0020, 0x0000)) // "GenericGroupLength" { return false; } break; 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) { static const char* LUA_CALLBACK = "IncomingFindRequestFilter"; LuaScripting::Locker locker(context_.GetLua()); if (!locker.GetLua().IsExistingFunction(LUA_CALLBACK)) { return false; } else { Json::Value origin = Json::objectValue; origin["RemoteIp"] = remoteIp; origin["RemoteAet"] = remoteAet; origin["CalledAet"] = calledAet; LuaFunctionCall call(locker.GetLua(), LUA_CALLBACK); call.PushDicom(source); call.PushJson(origin); FromDcmtkBridge::ExecuteToDicom(target, call); return true; } } 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) { /** * Possibly apply the user-supplied Lua filter. **/ DicomMap lua; const DicomMap* filteredInput = &input; if (ApplyLuaFilter(lua, input, remoteIp, remoteAet, calledAet)) { 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()) { LOG(ERROR) << "C-FIND request without the tag 0008,0052 (QueryRetrieveLevel)"; throw OrthancException(ErrorCode_BadRequest); } 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. **/ LookupResource finder(level); const bool caseSensitivePN = Configuration::GetGlobalBoolParameter("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 a "*" wildcard 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; } finder.AddDicomConstraint(tag, value, sensitive); } 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 maxResults = (level == ResourceType_Instance) ? maxInstances_ : maxResults_; std::vector<std::string> resources, instances; context_.GetIndex().FindCandidates(resources, instances, finder); LOG(INFO) << "Number of candidate resources after fast DB filtering: " << resources.size(); assert(resources.size() == instances.size()); bool complete = true; for (size_t i = 0; i < instances.size(); i++) { Json::Value dicom; context_.ReadDicomAsJson(dicom, instances[i]); if (finder.IsMatch(dicom)) { if (maxResults != 0 && answers.GetSize() >= maxResults) { complete = false; break; } else { std::auto_ptr<DicomMap> counters(ComputeCounters(context_, instances[i], level, *filteredInput)); AddAnswer(answers, dicom, query, sequencesToReturn, counters.get()); } } } LOG(INFO) << "Number of matching resources: " << answers.GetSize(); answers.SetComplete(complete); } }