Mercurial > hg > orthanc-dicomweb
view Plugin/QidoRs.cpp @ 20:d5cd40f12c86
fix VR extraction
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 20 May 2015 12:56:32 +0200 |
parents | d3dc9727c51e |
children | c1223564bc80 |
line wrap: on
line source
/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, 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 "Plugin.h" #include "StowRs.h" // For IsXmlExpected() #include "../Core/Dicom.h" #include "../Core/DicomResults.h" #include "../Core/Toolbox.h" #include "../Core/Configuration.h" #include "../Core/MultipartWriter.h" #include <gdcmTag.h> #include <list> #include <stdexcept> #include <boost/lexical_cast.hpp> #include <gdcmDict.h> #include <gdcmDicts.h> #include <gdcmGlobal.h> #include <gdcmDictEntry.h> #include <boost/regex.hpp> #include <boost/algorithm/string/replace.hpp> namespace { enum QueryLevel { QueryLevel_Study, QueryLevel_Series, QueryLevel_Instance }; class ModuleMatcher { private: typedef std::map<gdcm::Tag, std::string> Filters; const gdcm::Dict& dictionary_; bool fuzzy_; unsigned int offset_; unsigned int limit_; std::list<gdcm::Tag> includeFields_; bool includeAllFields_; Filters filters_; static inline uint16_t GetCharValue(char c) { if (c >= '0' && c <= '9') return c - '0'; else if (c >= 'a' && c <= 'f') return c - 'a' + 10; else if (c >= 'A' && c <= 'F') return c - 'A' + 10; else return 0; } static inline uint16_t GetTagValue(const char* c) { return ((GetCharValue(c[0]) << 12) + (GetCharValue(c[1]) << 8) + (GetCharValue(c[2]) << 4) + GetCharValue(c[3])); } gdcm::Tag ParseTag(const std::string& key) const { if (key.size() == 8 && isxdigit(key[0]) && isxdigit(key[1]) && isxdigit(key[2]) && isxdigit(key[3]) && isxdigit(key[4]) && isxdigit(key[5]) && isxdigit(key[6]) && isxdigit(key[7])) { return gdcm::Tag(GetTagValue(key.c_str()), GetTagValue(key.c_str() + 4)); } else { gdcm::Tag tag; dictionary_.GetDictEntryByKeyword(key.c_str(), tag); if (tag.IsIllegal() || tag.IsPrivate()) { if (key.find('.') != std::string::npos) { throw std::runtime_error("This QIDO-RS implementation does not support search over sequences: " + key); } else { throw std::runtime_error("Illegal tag name in QIDO-RS: " + key); } } return tag; } } static bool IsWildcard(const std::string& constraint) { return (constraint.find('-') != std::string::npos || constraint.find('*') != std::string::npos || constraint.find('\\') != std::string::npos || constraint.find('?') != std::string::npos); } static bool ApplyRangeConstraint(const std::string& value, const std::string& constraint) { size_t separator = constraint.find('-'); std::string lower(constraint.substr(0, separator)); std::string upper(constraint.substr(separator + 1)); std::string v(value); OrthancPlugins::ToLowerCase(lower); OrthancPlugins::ToLowerCase(upper); OrthancPlugins::ToLowerCase(v); if (lower.size() == 0 && upper.size() == 0) { return false; } if (lower.size() == 0) { return v <= upper; } if (upper.size() == 0) { return v >= lower; } return (v >= lower && v <= upper); } static bool ApplyListConstraint(const std::string& value, const std::string& constraint) { std::string v1(value); OrthancPlugins::ToLowerCase(v1); std::vector<std::string> items; OrthancPlugins::TokenizeString(items, constraint, '\\'); for (size_t i = 0; i < items.size(); i++) { std::string lower(items[i]); OrthancPlugins::ToLowerCase(lower); if (lower == v1) { return true; } } return false; } static std::string WildcardToRegularExpression(const std::string& source) { std::string result = source; // Escape all special characters boost::replace_all(result, "\\", "\\\\"); boost::replace_all(result, "^", "\\^"); boost::replace_all(result, ".", "\\."); boost::replace_all(result, "$", "\\$"); boost::replace_all(result, "|", "\\|"); boost::replace_all(result, "(", "\\("); boost::replace_all(result, ")", "\\)"); boost::replace_all(result, "[", "\\["); boost::replace_all(result, "]", "\\]"); boost::replace_all(result, "+", "\\+"); boost::replace_all(result, "/", "\\/"); boost::replace_all(result, "{", "\\{"); boost::replace_all(result, "}", "\\}"); // Convert wildcards '*' and '?' to their regex equivalents boost::replace_all(result, "?", "."); boost::replace_all(result, "*", ".*"); return result; } static bool Matches(const std::string& value, const std::string& constraint) { // http://www.itk.org/Wiki/DICOM_QueryRetrieve_Explained // http://dicomiseasy.blogspot.be/2012/01/dicom-queryretrieve-part-i.html if (constraint.find('-') != std::string::npos) { return ApplyRangeConstraint(value, constraint); } if (constraint.find('\\') != std::string::npos) { return ApplyListConstraint(value, constraint); } if (constraint.find('*') != std::string::npos || constraint.find('?') != std::string::npos) { boost::regex pattern(WildcardToRegularExpression(constraint), boost::regex::icase /* case insensitive search */); return boost::regex_match(value, pattern); } else { std::string v(value), c(constraint); OrthancPlugins::ToLowerCase(v); OrthancPlugins::ToLowerCase(c); return v == c; } } static void AddResultAttributesForLevel(std::list<gdcm::Tag>& result, QueryLevel level) { switch (level) { case QueryLevel_Study: // http://medical.nema.org/medical/dicom/current/output/html/part18.html#table_6.7.1-2 result.push_back(gdcm::Tag(0x0008, 0x0005)); // Specific Character Set result.push_back(gdcm::Tag(0x0008, 0x0020)); // Study Date result.push_back(gdcm::Tag(0x0008, 0x0030)); // Study Time result.push_back(gdcm::Tag(0x0008, 0x0050)); // Accession Number result.push_back(gdcm::Tag(0x0008, 0x0056)); // Instance Availability result.push_back(gdcm::Tag(0x0008, 0x0061)); // Modalities in Study result.push_back(gdcm::Tag(0x0008, 0x0090)); // Referring Physician's Name result.push_back(gdcm::Tag(0x0008, 0x0201)); // Timezone Offset From UTC //result.push_back(gdcm::Tag(0x0008, 0x1190)); // Retrieve URL => SPECIAL CASE result.push_back(gdcm::Tag(0x0010, 0x0010)); // Patient's Name result.push_back(gdcm::Tag(0x0010, 0x0020)); // Patient ID result.push_back(gdcm::Tag(0x0010, 0x0030)); // Patient's Birth Date result.push_back(gdcm::Tag(0x0010, 0x0040)); // Patient's Sex result.push_back(gdcm::Tag(0x0020, 0x000D)); // Study Instance UID result.push_back(gdcm::Tag(0x0020, 0x0010)); // Study ID result.push_back(gdcm::Tag(0x0020, 0x1206)); // Number of Study Related Series result.push_back(gdcm::Tag(0x0020, 0x1208)); // Number of Study Related Instances break; case QueryLevel_Series: // http://medical.nema.org/medical/dicom/current/output/html/part18.html#table_6.7.1-2a result.push_back(gdcm::Tag(0x0008, 0x0005)); // Specific Character Set result.push_back(gdcm::Tag(0x0008, 0x0056)); // Modality result.push_back(gdcm::Tag(0x0008, 0x0201)); // Timezone Offset From UTC result.push_back(gdcm::Tag(0x0008, 0x103E)); // Series Description //result.push_back(gdcm::Tag(0x0008, 0x1190)); // Retrieve URL => SPECIAL CASE result.push_back(gdcm::Tag(0x0020, 0x000E)); // Series Instance UID result.push_back(gdcm::Tag(0x0020, 0x0011)); // Series Number result.push_back(gdcm::Tag(0x0020, 0x1209)); // Number of Series Related Instances result.push_back(gdcm::Tag(0x0040, 0x0244)); // Performed Procedure Step Start Date result.push_back(gdcm::Tag(0x0040, 0x0245)); // Performed Procedure Step Start Time result.push_back(gdcm::Tag(0x0040, 0x0275)); // Request Attribute Sequence break; case QueryLevel_Instance: // http://medical.nema.org/medical/dicom/current/output/html/part18.html#table_6.7.1-2b result.push_back(gdcm::Tag(0x0008, 0x0005)); // Specific Character Set result.push_back(gdcm::Tag(0x0008, 0x0016)); // SOP Class UID result.push_back(gdcm::Tag(0x0008, 0x0018)); // SOP Instance UID result.push_back(gdcm::Tag(0x0008, 0x0056)); // Instance Availability result.push_back(gdcm::Tag(0x0008, 0x0201)); // Timezone Offset From UTC result.push_back(gdcm::Tag(0x0008, 0x1190)); // Retrieve URL result.push_back(gdcm::Tag(0x0020, 0x0013)); // Instance Number result.push_back(gdcm::Tag(0x0028, 0x0010)); // Rows result.push_back(gdcm::Tag(0x0028, 0x0011)); // Columns result.push_back(gdcm::Tag(0x0028, 0x0100)); // Bits Allocated result.push_back(gdcm::Tag(0x0028, 0x0008)); // Number of Frames break; default: throw std::runtime_error("Internal error"); } } public: ModuleMatcher(const OrthancPluginHttpRequest* request) : dictionary_(gdcm::Global::GetInstance().GetDicts().GetPublicDict()), fuzzy_(false), offset_(0), limit_(0), includeAllFields_(false) { for (int32_t i = 0; i < request->getCount; i++) { std::string key(request->getKeys[i]); std::string value(request->getValues[i]); 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 std::runtime_error("Not a proper value for fuzzy matching (true or false): " + value); } } else if (key == "includefield") { if (key == "all") { includeAllFields_ = true; } else { // Split a comma-separated list of tags std::vector<std::string> tags; OrthancPlugins::TokenizeString(tags, value, ','); for (size_t i = 0; i < tags.size(); i++) { includeFields_.push_back(ParseTag(tags[i])); } } } else { filters_[ParseTag(key)] = value; } } } unsigned int GetLimit() const { return limit_; } unsigned int GetOffset() const { return offset_; } void AddFilter(const gdcm::Tag& tag, const std::string& constraint) { filters_[tag] = constraint; } bool LookupExactFilter(std::string& constraint, const gdcm::Tag& tag) const { Filters::const_iterator it = filters_.find(tag); if (it != filters_.end() && !IsWildcard(it->second)) { constraint = it->second; return true; } else { return false; } } bool Matches(const OrthancPlugins::ParsedDicomFile& dicom) const { for (Filters::const_iterator it = filters_.begin(); it != filters_.end(); ++it) { std::string value; if (!dicom.GetTag(value, it->first, true)) { return false; } if (!Matches(value, it->second)) { return false; } } return true; } void ExtractFields(gdcm::DataSet& result, const OrthancPlugins::ParsedDicomFile& dicom, const std::string& wadoBase, QueryLevel level) const { std::list<gdcm::Tag> 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 == QueryLevel_Instance || level == QueryLevel_Series) && filters_.find(OrthancPlugins::DICOM_TAG_STUDY_INSTANCE_UID) == filters_.end() ) { AddResultAttributesForLevel(fields, QueryLevel_Study); } // For instances, add all Series-level attributes if // {SeriesInstanceUID} is not specified. if (level == QueryLevel_Instance && filters_.find(OrthancPlugins::DICOM_TAG_SERIES_INSTANCE_UID) == filters_.end() ) { AddResultAttributesForLevel(fields, QueryLevel_Series); } // Copy all the required fields to the target for (std::list<gdcm::Tag>::const_iterator it = fields.begin(); it != fields.end(); it++) { if (dicom.GetDataSet().FindDataElement(*it)) { const gdcm::DataElement& element = dicom.GetDataSet().GetDataElement(*it); result.Replace(element); } } // Set the retrieve URL for WADO-RS std::string url = (wadoBase + "/studies/" + dicom.GetTagWithDefault(OrthancPlugins::DICOM_TAG_STUDY_INSTANCE_UID, "", true)); if (level == QueryLevel_Series || level == QueryLevel_Instance) { url += "/series/" + dicom.GetTagWithDefault(OrthancPlugins::DICOM_TAG_SERIES_INSTANCE_UID, "", true); } if (level == QueryLevel_Instance) { url += "/instances/" + dicom.GetTagWithDefault(OrthancPlugins::DICOM_TAG_SOP_INSTANCE_UID, "", true); } gdcm::DataElement element(OrthancPlugins::DICOM_TAG_RETRIEVE_URL); element.SetByteValue(url.c_str(), url.size()); result.Replace(element); } }; class CandidateResources { private: typedef std::set<std::string> Resources; bool all_; QueryLevel level_; Resources resources_; static bool CallLookup(std::string& orthancId, const std::string& dicomId, char* (lookup) (OrthancPluginContext*, const char*)) { bool result = false; char* tmp = lookup(context_, dicomId.c_str()); if (tmp != NULL) { orthancId = tmp; result = true; } OrthancPluginFreeString(context_, tmp); return result; } void FilterByIdentifierInternal(const ModuleMatcher& matcher, const gdcm::Tag& tag, char* (lookup) (OrthancPluginContext*, const char*)) { std::string orthancId, dicomId; if (!matcher.LookupExactFilter(dicomId, tag)) { // There is no restriction at this level return; } if (CallLookup(orthancId, dicomId, lookup) && (all_ || resources_.find(orthancId) != resources_.end())) { // There remains a single candidate resource resources_.clear(); resources_.insert(orthancId); } else { // No matching resource remains resources_.clear(); } all_ = false; } bool PickOneInstance(std::string& instance, const std::string& resource) const { if (level_ == QueryLevel_Instance) { instance = resource; return true; } std::string uri; if (level_ == QueryLevel_Study) { uri = "/studies/" + resource + "/instances"; } else { assert(level_ == QueryLevel_Series); uri = "/series/" + resource + "/instances"; } Json::Value instances; if (!OrthancPlugins::RestApiGetJson(instances, context_, uri) || instances.type() != Json::arrayValue || instances.size() == 0) { return false; } else { instance = instances[0]["ID"].asString(); return true; } } public: CandidateResources() : all_(true), level_(QueryLevel_Study) { } void GoDown() { std::string baseUri; std::string nextLevel; switch (level_) { case QueryLevel_Study: baseUri = "/studies/"; nextLevel = "Series"; break; case QueryLevel_Series: baseUri = "/series/"; nextLevel = "Instances"; break; default: throw std::runtime_error("Internal error"); } if (!all_) { Resources children; for (Resources::const_iterator it = resources_.begin(); it != resources_.end(); it++) { Json::Value tmp; if (OrthancPlugins::RestApiGetJson(tmp, context_, baseUri + *it) && tmp.type() == Json::objectValue && tmp.isMember(nextLevel) && tmp[nextLevel].type() == Json::arrayValue) { for (Json::Value::ArrayIndex i = 0; i < tmp[nextLevel].size(); i++) { children.insert(tmp[nextLevel][i].asString()); } } } resources_ = children; } switch (level_) { case QueryLevel_Study: level_ = QueryLevel_Series; break; case QueryLevel_Series: level_ = QueryLevel_Instance; break; default: throw std::runtime_error("Internal error"); } } void FilterByIdentifier(const ModuleMatcher& matcher) { switch (level_) { case QueryLevel_Study: FilterByIdentifierInternal(matcher, OrthancPlugins::DICOM_TAG_STUDY_INSTANCE_UID, OrthancPluginLookupStudy); FilterByIdentifierInternal(matcher, OrthancPlugins::DICOM_TAG_ACCESSION_NUMBER, OrthancPluginLookupStudyWithAccessionNumber); break; case QueryLevel_Series: FilterByIdentifierInternal(matcher, OrthancPlugins::DICOM_TAG_SERIES_INSTANCE_UID, OrthancPluginLookupSeries); break; case QueryLevel_Instance: FilterByIdentifierInternal(matcher, OrthancPlugins::DICOM_TAG_SOP_INSTANCE_UID, OrthancPluginLookupInstance); break; default: throw std::runtime_error("Internal error"); } } void Flatten(std::list<std::string>& result) const { std::string instance; result.clear(); if (all_) { std::string uri; switch (level_) { case QueryLevel_Study: uri = "/studies/"; break; case QueryLevel_Series: uri = "/series/"; break; case QueryLevel_Instance: uri = "/instances/"; break; default: throw std::runtime_error("Internal error"); } Json::Value tmp; if (OrthancPlugins::RestApiGetJson(tmp, context_, uri) && tmp.type() == Json::arrayValue) { for (Json::Value::ArrayIndex i = 0; i < tmp.size(); i++) { if (PickOneInstance(instance, tmp[i].asString())) { result.push_back(instance); } } } } else { for (Resources::const_iterator it = resources_.begin(); it != resources_.end(); it++) { if (PickOneInstance(instance, *it)) { result.push_back(instance); } } } } }; } static void ApplyMatcher(OrthancPluginRestOutput* output, const OrthancPluginHttpRequest* request, const ModuleMatcher& matcher, const CandidateResources& candidates, QueryLevel level) { std::list<std::string> resources; candidates.Flatten(resources); std::string wadoBase = OrthancPlugins::Configuration::GetBaseUrl(configuration_, request) + "/wado-rs"; OrthancPlugins::DicomResults results(*dictionary_, IsXmlExpected(request), true); for (std::list<std::string>::const_iterator it = resources.begin(); it != resources.end(); it++) { std::string file; if (OrthancPlugins::RestApiGetString(file, context_, "/instances/" + *it + "/file")) { OrthancPlugins::ParsedDicomFile dicom(file); if (matcher.Matches(dicom)) { std::auto_ptr<gdcm::DataSet> result(new gdcm::DataSet); matcher.ExtractFields(*result, dicom, wadoBase, level); results.Add(dicom.GetFile(), *result); } } } results.Answer(context_, output); } int32_t SearchForStudies(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { try { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context_, output, "GET"); return 0; } ModuleMatcher matcher(request); CandidateResources candidates; candidates.FilterByIdentifier(matcher); ApplyMatcher(output, request, matcher, candidates, QueryLevel_Study); return 0; } catch (std::runtime_error& e) { OrthancPluginLogError(context_, e.what()); return -1; } catch (boost::bad_lexical_cast& e) { OrthancPluginLogError(context_, e.what()); return -1; } } int32_t SearchForSeries(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { try { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context_, output, "GET"); return 0; } ModuleMatcher matcher(request); if (request->groupsCount == 1) { // The "StudyInstanceUID" is provided by the regular expression matcher.AddFilter(OrthancPlugins::DICOM_TAG_STUDY_INSTANCE_UID, request->groups[0]); } CandidateResources candidates; candidates.FilterByIdentifier(matcher); candidates.GoDown(); candidates.FilterByIdentifier(matcher); ApplyMatcher(output, request, matcher, candidates, QueryLevel_Series); return 0; } catch (std::runtime_error& e) { OrthancPluginLogError(context_, e.what()); return -1; } catch (boost::bad_lexical_cast& e) { OrthancPluginLogError(context_, e.what()); return -1; } } int32_t SearchForInstances(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { try { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context_, output, "GET"); return 0; } ModuleMatcher matcher(request); if (request->groupsCount == 1 || request->groupsCount == 2) { // The "StudyInstanceUID" is provided by the regular expression matcher.AddFilter(OrthancPlugins::DICOM_TAG_STUDY_INSTANCE_UID, request->groups[0]); } if (request->groupsCount == 2) { // The "SeriesInstanceUID" is provided by the regular expression matcher.AddFilter(OrthancPlugins::DICOM_TAG_SERIES_INSTANCE_UID, request->groups[1]); } CandidateResources candidates; candidates.FilterByIdentifier(matcher); candidates.GoDown(); candidates.FilterByIdentifier(matcher); candidates.GoDown(); candidates.FilterByIdentifier(matcher); ApplyMatcher(output, request, matcher, candidates, QueryLevel_Instance); return 0; } catch (std::runtime_error& e) { OrthancPluginLogError(context_, e.what()); return -1; } catch (boost::bad_lexical_cast& e) { OrthancPluginLogError(context_, e.what()); return -1; } }