Mercurial > hg > orthanc-dicomweb
view Plugin/QidoRs.cpp @ 275:0d1815ffe865
cont
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Mon, 03 Jun 2019 14:33:58 +0200 |
parents | 83cb0fdf4bd1 |
children | 0222a9afa866 |
line wrap: on
line source
/** * 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 Affero General Public License * as published by the Free Software Foundation, either version 3 of * the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "QidoRs.h" #include "StowRs.h" // For IsXmlExpected() #include "Configuration.h" #include "DicomWebFormatter.h" #include <Core/DicomFormat/DicomTag.h> #include <Core/Toolbox.h> #include <Plugins/Samples/Common/OrthancPluginCppWrapper.h> #include <list> #include <boost/lexical_cast.hpp> #include <boost/regex.hpp> #include <boost/algorithm/string/replace.hpp> namespace { static std::string GetOrthancTag(const Json::Value& source, const Orthanc::DicomTag& tag, const std::string& defaultValue) { const std::string s = tag.Format(); if (source.isMember(s)) { switch (source[s].type()) { case Json::stringValue: return source[s].asString(); // The conversions below should *not* be necessary case Json::intValue: return boost::lexical_cast<std::string>(source[s].asInt()); case Json::uintValue: return boost::lexical_cast<std::string>(source[s].asUInt()); case Json::realValue: return boost::lexical_cast<std::string>(source[s].asFloat()); default: return defaultValue; } } else { return defaultValue; } } class ModuleMatcher { public: typedef std::map<Orthanc::DicomTag, std::string> Filters; private: bool fuzzy_; unsigned int offset_; unsigned int limit_; std::list<Orthanc::DicomTag> includeFields_; bool includeAllFields_; Filters filters_; static void AddResultAttributesForLevel(std::list<Orthanc::DicomTag>& result, Orthanc::ResourceType level) { switch (level) { case Orthanc::ResourceType_Study: // http://medical.nema.org/medical/dicom/current/output/html/part18.html#table_6.7.1-2 //result.push_back(Orthanc::DicomTag(0x0008, 0x0005)); // Specific Character Set => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0008, 0x0020)); // Study Date result.push_back(Orthanc::DicomTag(0x0008, 0x0030)); // Study Time result.push_back(Orthanc::DicomTag(0x0008, 0x0050)); // Accession Number result.push_back(Orthanc::DicomTag(0x0008, 0x0056)); // Instance Availability //result.push_back(Orthanc::DicomTag(0x0008, 0x0061)); // Modalities in Study => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0008, 0x0090)); // Referring Physician's Name result.push_back(Orthanc::DicomTag(0x0008, 0x0201)); // Timezone Offset From UTC //result.push_back(Orthanc::DicomTag(0x0008, 0x1190)); // Retrieve URL => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0010, 0x0010)); // Patient's Name result.push_back(Orthanc::DicomTag(0x0010, 0x0020)); // Patient ID result.push_back(Orthanc::DicomTag(0x0010, 0x0030)); // Patient's Birth Date result.push_back(Orthanc::DicomTag(0x0010, 0x0040)); // Patient's Sex result.push_back(Orthanc::DicomTag(0x0020, 0x000D)); // Study Instance UID result.push_back(Orthanc::DicomTag(0x0020, 0x0010)); // Study ID //result.push_back(Orthanc::DicomTag(0x0020, 0x1206)); // Number of Study Related Series => SPECIAL CASE //result.push_back(Orthanc::DicomTag(0x0020, 0x1208)); // Number of Study Related Instances => SPECIAL CASE break; case Orthanc::ResourceType_Series: // http://medical.nema.org/medical/dicom/current/output/html/part18.html#table_6.7.1-2a //result.push_back(Orthanc::DicomTag(0x0008, 0x0005)); // Specific Character Set => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0008, 0x0060)); // Modality result.push_back(Orthanc::DicomTag(0x0008, 0x0201)); // Timezone Offset From UTC result.push_back(Orthanc::DicomTag(0x0008, 0x103E)); // Series Description //result.push_back(Orthanc::DicomTag(0x0008, 0x1190)); // Retrieve URL => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0020, 0x000E)); // Series Instance UID result.push_back(Orthanc::DicomTag(0x0020, 0x0011)); // Series Number //result.push_back(Orthanc::DicomTag(0x0020, 0x1209)); // Number of Series Related Instances => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0040, 0x0244)); // Performed Procedure Step Start Date result.push_back(Orthanc::DicomTag(0x0040, 0x0245)); // Performed Procedure Step Start Time result.push_back(Orthanc::DicomTag(0x0040, 0x0275)); // Request Attribute Sequence break; case Orthanc::ResourceType_Instance: // http://medical.nema.org/medical/dicom/current/output/html/part18.html#table_6.7.1-2b //result.push_back(Orthanc::DicomTag(0x0008, 0x0005)); // Specific Character Set => SPECIAL CASE result.push_back(Orthanc::DicomTag(0x0008, 0x0016)); // SOP Class UID result.push_back(Orthanc::DicomTag(0x0008, 0x0018)); // SOP Instance UID result.push_back(Orthanc::DicomTag(0x0008, 0x0056)); // Instance Availability result.push_back(Orthanc::DicomTag(0x0008, 0x0201)); // Timezone Offset From UTC result.push_back(Orthanc::DicomTag(0x0008, 0x1190)); // Retrieve URL result.push_back(Orthanc::DicomTag(0x0020, 0x0013)); // Instance Number result.push_back(Orthanc::DicomTag(0x0028, 0x0010)); // Rows result.push_back(Orthanc::DicomTag(0x0028, 0x0011)); // Columns result.push_back(Orthanc::DicomTag(0x0028, 0x0100)); // Bits Allocated result.push_back(Orthanc::DicomTag(0x0028, 0x0008)); // Number of Frames break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } public: explicit ModuleMatcher(const OrthancPluginHttpRequest* request) : fuzzy_(false), offset_(0), limit_(0), includeAllFields_(false) { std::string args; for (uint32_t i = 0; i < request->getCount; i++) { std::string key(request->getKeys[i]); std::string value(request->getValues[i]); args += " [" + key + "=" + value + "]"; if (key == "limit") { limit_ = boost::lexical_cast<unsigned int>(value); } else if (key == "offset") { offset_ = boost::lexical_cast<unsigned int>(value); } else if (key == "fuzzymatching") { if (value == "true") { fuzzy_ = true; } else if (value == "false") { fuzzy_ = false; } else { throw Orthanc::OrthancException( Orthanc::ErrorCode_BadRequest, "Not a proper value for fuzzy matching (true or false): " + value); } } else if (key == "includefield") { if (value == "all") { includeAllFields_ = true; } else { // Split a comma-separated list of tags std::vector<std::string> tags; Orthanc::Toolbox::TokenizeString(tags, value, ','); for (size_t i = 0; i < tags.size(); i++) { Orthanc::DicomTag tag(0, 0); if (OrthancPlugins::ParseTag(tag, tags[i])) { includeFields_.push_back(tag); } } } } else { Orthanc::DicomTag tag(0, 0); if (OrthancPlugins::ParseTag(tag, key)) { filters_[tag] = value; } } } OrthancPlugins::LogInfo("Arguments of QIDO-RS request:" + args); } unsigned int GetLimit() const { return limit_; } unsigned int GetOffset() const { return offset_; } void AddFilter(const Orthanc::DicomTag& tag, const std::string& constraint) { filters_[tag] = constraint; } void Print(std::ostream& out) const { for (Filters::const_iterator it = filters_.begin(); it != filters_.end(); ++it) { printf("Filter [%04x,%04x] = [%s]\n", it->first.GetGroup(), it->first.GetElement(), it->second.c_str()); } } void ConvertToOrthanc(Json::Value& result, Orthanc::ResourceType level) const { result = Json::objectValue; switch (level) { case Orthanc::ResourceType_Study: result["Level"] = "Study"; break; case Orthanc::ResourceType_Series: result["Level"] = "Series"; break; case Orthanc::ResourceType_Instance: result["Level"] = "Instance"; break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } result["Expand"] = false; result["CaseSensitive"] = OrthancPlugins::Configuration::GetBooleanValue("QidoCaseSensitive", true); result["Query"] = Json::objectValue; result["Limit"] = limit_; result["Since"] = offset_; if (offset_ != 0 && !OrthancPlugins::CheckMinimalOrthancVersion(1, 3, 0)) { OrthancPlugins::LogError( "QIDO-RS request with \"offset\" argument: " "Only available if the Orthanc core version is >= 1.3.0"); } for (Filters::const_iterator it = filters_.begin(); it != filters_.end(); ++it) { result["Query"][it->first.Format()] = it->second; } } void ComputeDerivedTags(Filters& target, Orthanc::ResourceType level, const std::string& resource) const { target.clear(); switch (level) { case Orthanc::ResourceType_Study: { Json::Value series, instances; if (OrthancPlugins::RestApiGet(series, "/studies/" + resource + "/series?expand", false) && OrthancPlugins::RestApiGet(instances, "/studies/" + resource + "/instances", false)) { target[Orthanc::DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES] = boost::lexical_cast<std::string>(series.size()); target[Orthanc::DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES] = boost::lexical_cast<std::string>(instances.size()); // Collect the Modality of all the child series std::set<std::string> modalities; for (Json::Value::ArrayIndex i = 0; i < series.size(); i++) { if (series[i].isMember("MainDicomTags") && series[i]["MainDicomTags"].isMember("Modality")) { modalities.insert(series[i]["MainDicomTags"]["Modality"].asString()); } } std::string s; for (std::set<std::string>::const_iterator it = modalities.begin(); it != modalities.end(); ++it) { if (!s.empty()) { s += "\\"; } s += *it; } target[Orthanc::DICOM_TAG_MODALITIES_IN_STUDY] = s; } else { target[Orthanc::DICOM_TAG_MODALITIES_IN_STUDY] = ""; target[Orthanc::DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES] = "0"; target[Orthanc::DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES] = "0"; } break; } case Orthanc::ResourceType_Series: { Json::Value instances; if (OrthancPlugins::RestApiGet(instances, "/series/" + resource + "/instances", false)) { // Number of Series Related Instances target[Orthanc::DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES] = boost::lexical_cast<std::string>(instances.size()); } else { target[Orthanc::DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES] = "0"; } break; } default: break; } } void ExtractFields(Json::Value& result, const Json::Value& source, const std::string& wadoBase, Orthanc::ResourceType level) const { result = Json::objectValue; std::list<Orthanc::DicomTag> fields = includeFields_; // The list of attributes for this query level AddResultAttributesForLevel(fields, level); // All other attributes passed as query keys for (Filters::const_iterator it = filters_.begin(); it != filters_.end(); ++it) { fields.push_back(it->first); } // For instances and series, add all Study-level attributes if // {StudyInstanceUID} is not specified. if ((level == Orthanc::ResourceType_Instance || level == Orthanc::ResourceType_Series) && filters_.find(Orthanc::DICOM_TAG_STUDY_INSTANCE_UID) == filters_.end() ) { AddResultAttributesForLevel(fields, Orthanc::ResourceType_Study); } // For instances, add all Series-level attributes if // {SeriesInstanceUID} is not specified. if (level == Orthanc::ResourceType_Instance && filters_.find(Orthanc::DICOM_TAG_SERIES_INSTANCE_UID) == filters_.end() ) { AddResultAttributesForLevel(fields, Orthanc::ResourceType_Series); } // Copy all the required fields to the target for (std::list<Orthanc::DicomTag>::const_iterator it = fields.begin(); it != fields.end(); ++it) { // Complies to the JSON produced internally by Orthanc char tag[16]; sprintf(tag, "%04x,%04x", it->GetGroup(), it->GetElement()); if (source.isMember(tag)) { result[tag] = source[tag]; } } // Set the retrieve URL for WADO-RS std::string url = (wadoBase + "studies/" + GetOrthancTag(source, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, "")); if (level == Orthanc::ResourceType_Series || level == Orthanc::ResourceType_Instance) { url += "/series/" + GetOrthancTag(source, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, ""); } if (level == Orthanc::ResourceType_Instance) { url += "/instances/" + GetOrthancTag(source, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, ""); } static const Orthanc::DicomTag DICOM_TAG_RETRIEVE_URL(0x0008, 0x1190); result[DICOM_TAG_RETRIEVE_URL.Format()] = url; } }; } static void ApplyMatcher(OrthancPluginRestOutput* output, const OrthancPluginHttpRequest* request, const ModuleMatcher& matcher, Orthanc::ResourceType level) { Json::Value find; matcher.ConvertToOrthanc(find, level); std::string body; { Json::FastWriter writer; body = writer.write(find); } Json::Value resources; if (!OrthancPlugins::RestApiPost(resources, "/tools/find", body, false) || resources.type() != Json::arrayValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } typedef std::list< std::pair<std::string, std::string> > ResourcesAndInstances; ResourcesAndInstances resourcesAndInstances; std::string root = (level == Orthanc::ResourceType_Study ? "/studies/" : "/series/"); for (Json::Value::ArrayIndex i = 0; i < resources.size(); i++) { const std::string resource = resources[i].asString(); if (level == Orthanc::ResourceType_Study || level == Orthanc::ResourceType_Series) { // Find one child instance of this resource Json::Value tmp; if (OrthancPlugins::RestApiGet(tmp, root + resource + "/instances", false) && tmp.type() == Json::arrayValue && tmp.size() > 0) { resourcesAndInstances.push_back(std::make_pair(resource, tmp[0]["ID"].asString())); } } else { resourcesAndInstances.push_back(std::make_pair(resource, resource)); } } std::string wadoBase = OrthancPlugins::Configuration::GetBaseUrl(request); OrthancPlugins::DicomWebFormatter::HttpWriter writer(output, IsXmlExpected(request)); // Fix of issue #13 for (ResourcesAndInstances::const_iterator it = resourcesAndInstances.begin(); it != resourcesAndInstances.end(); ++it) { Json::Value tags; if (OrthancPlugins::RestApiGet(tags, "/instances/" + it->second + "/tags?short", false)) { std::string wadoUrl = OrthancPlugins::Configuration::GetWadoUrl( wadoBase, GetOrthancTag(tags, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, ""), GetOrthancTag(tags, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, ""), GetOrthancTag(tags, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, "")); Json::Value result; matcher.ExtractFields(result, tags, wadoBase, level); // Inject the derived tags ModuleMatcher::Filters derivedTags; matcher.ComputeDerivedTags(derivedTags, level, it->first); for (ModuleMatcher::Filters::const_iterator tag = derivedTags.begin(); tag != derivedTags.end(); ++tag) { result[tag->first.Format()] = tag->second; } writer.AddJson(result); } } writer.Send(); } void SearchForStudies(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); } else { ModuleMatcher matcher(request); ApplyMatcher(output, request, matcher, Orthanc::ResourceType_Study); } } void SearchForSeries(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); } else { ModuleMatcher matcher(request); if (request->groupsCount == 1) { // The "StudyInstanceUID" is provided by the regular expression matcher.AddFilter(Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, request->groups[0]); } ApplyMatcher(output, request, matcher, Orthanc::ResourceType_Series); } } void SearchForInstances(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); } else { ModuleMatcher matcher(request); if (request->groupsCount == 1 || request->groupsCount == 2) { // The "StudyInstanceUID" is provided by the regular expression matcher.AddFilter(Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, request->groups[0]); } if (request->groupsCount == 2) { // The "SeriesInstanceUID" is provided by the regular expression matcher.AddFilter(Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, request->groups[1]); } ApplyMatcher(output, request, matcher, Orthanc::ResourceType_Instance); } }