Mercurial > hg > orthanc
changeset 5043:ec5c203a97ea
returning sequences in MainDicomTags and RequestedTags
author | Alain Mazy <am@osimis.io> |
---|---|
date | Mon, 27 Jun 2022 15:22:19 +0200 |
parents | 120945ce48b6 |
children | 6fed78e13233 |
files | NEWS OrthancFramework/Resources/CMake/OrthancFrameworkConfiguration.cmake OrthancFramework/Sources/DicomFormat/DicomSequencesMap.cpp OrthancFramework/Sources/DicomFormat/DicomSequencesMap.h OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp OrthancServer/Sources/Database/StatelessDatabaseOperations.h OrthancServer/Sources/ServerContext.cpp |
diffstat | 7 files changed, 173 insertions(+), 93 deletions(-) [+] |
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--- a/NEWS Mon Jun 27 14:09:17 2022 +0200 +++ b/NEWS Mon Jun 27 15:22:19 2022 +0200 @@ -12,7 +12,8 @@ * "ExtraMainDicomTags" configuration now accepts Dicom Sequences. Sequences are stored in a dedicated new metadata "MainDicomSequences". This should improve DicomWeb QIDO-RS and avoid warnings like "Accessing Dicom tags from storage when - accessing series : 0040,0275" + accessing series : 0040,0275". + Main dicom sequences can now be returned in "MainDicomTags" and in "RequestedTags". Maintenance
--- a/OrthancFramework/Resources/CMake/OrthancFrameworkConfiguration.cmake Mon Jun 27 14:09:17 2022 +0200 +++ b/OrthancFramework/Resources/CMake/OrthancFrameworkConfiguration.cmake Mon Jun 27 15:22:19 2022 +0200 @@ -197,6 +197,7 @@ ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/DicomInstanceHasher.cpp ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/DicomIntegerPixelAccessor.cpp ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/DicomMap.cpp + ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/DicomSequencesMap.cpp ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/DicomStreamReader.cpp ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/DicomValue.cpp ${CMAKE_CURRENT_LIST_DIR}/../../Sources/DicomFormat/StreamBlockReader.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancFramework/Sources/DicomFormat/DicomSequencesMap.cpp Mon Jun 27 15:22:19 2022 +0200 @@ -0,0 +1,100 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics + * Department, University Hospital of Liege, Belgium + * Copyright (C) 2017-2022 Osimis S.A., Belgium + * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, 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. + * + * 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 "../PrecompiledHeaders.h" +#include "DicomSequencesMap.h" +#include "../Toolbox.h" + +namespace Orthanc +{ + +#if ORTHANC_ENABLE_DCMTK == 1 + + // copy all tags from Json (used to read from metadata) + void DicomSequencesMap::Deserialize(const Json::Value& serialized) + { + Json::Value::Members members = serialized.getMemberNames(); + for (size_t i = 0; i < members.size(); i++) + { + DicomTag tag(0, 0); + if (DicomTag::ParseHexadecimal(tag, members[i].c_str())) + { + sequences_[tag] = serialized[members[i]]; + } + } + } + +#endif + + // serialize a subet of tags (used to store in the metadata) + void DicomSequencesMap::Serialize(Json::Value& target, const std::set<DicomTag>& tags) const + { + // add the sequences to "target" + for (std::map<DicomTag, Json::Value>::const_iterator it = sequences_.begin(); + it != sequences_.end(); ++it) + { + if (tags.find(it->first) != tags.end()) + { + target[it->first.Format()] = it->second; + } + } + } + + // copy a subset of tags from Json + void DicomSequencesMap::FromDicomAsJson(const Json::Value& dicomAsJson, const std::set<DicomTag>& tags) + { + for (std::set<DicomTag>::const_iterator it = tags.begin(); + it != tags.end(); ++it) + { + std::string tag = it->Format(); + if (dicomAsJson.isMember(tag)) + { + sequences_[*it] = dicomAsJson[tag]; + } + } + } + + void DicomSequencesMap::ToJson(Json::Value& target, DicomToJsonFormat format, const std::set<DicomTag>& tags) const + { + // add the sequences to "target" + for (std::map<DicomTag, Json::Value>::const_iterator it = sequences_.begin(); + it != sequences_.end(); ++it) + { + Json::Value sequenceFullJson = Json::objectValue; + sequenceFullJson[it->first.Format()] = it->second; + + Json::Value& requestedFormatJson = sequenceFullJson; + Json::Value convertedJson; + + if (format != DicomToJsonFormat_Full) + { + Toolbox::SimplifyDicomAsJson(convertedJson, sequenceFullJson, format); + requestedFormatJson = convertedJson; + } + + Json::Value::Members keys = requestedFormatJson.getMemberNames(); + for (size_t i = 0; i < keys.size(); i++) // there should always be only one member in this JSON + { + target[keys[i]] = requestedFormatJson[keys[i]]; + } + } + } +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancFramework/Sources/DicomFormat/DicomSequencesMap.h Mon Jun 27 15:22:19 2022 +0200 @@ -0,0 +1,57 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics + * Department, University Hospital of Liege, Belgium + * Copyright (C) 2017-2022 Osimis S.A., Belgium + * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, 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. + * + * 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/>. + **/ + + +#pragma once + +#include "../../../OrthancFramework/Sources/DicomFormat/DicomTag.h" + +#include <json/value.h> +#include <boost/noncopyable.hpp> + +#include <map> + +namespace Orthanc +{ + class DatabaseLookup; + class ParsedDicomFile; + struct ServerIndexChange; + + /* + * contains a map of dicom sequences where: + * the key is a DicomTag + * the sequence is serialized in Json "full" format + */ + struct DicomSequencesMap : public boost::noncopyable + { + std::map<DicomTag, Json::Value> sequences_; + + void Deserialize(const Json::Value& serialized); + void Serialize(Json::Value& target, const std::set<DicomTag>& tagsSubset) const; + void FromDicomAsJson(const Json::Value& dicomAsJson, const std::set<DicomTag>& tagsSubset); + void ToJson(Json::Value& target, DicomToJsonFormat format, const std::set<DicomTag>& tagsSubset) const; + + size_t GetSize() const + { + return sequences_.size(); + } + }; +}
--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp Mon Jun 27 14:09:17 2022 +0200 +++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp Mon Jun 27 15:22:19 2022 +0200 @@ -45,71 +45,6 @@ namespace Orthanc { - // copy all tags from Json (used to read from metadata) - void DicomSequencesMap::Deserialize(const Json::Value& serialized) - { - Json::Value::Members members = serialized.getMemberNames(); - for (size_t i = 0; i < members.size(); i++) - { - DicomTag tag = FromDcmtkBridge::ParseTag(members[i].c_str()); - sequences_[tag] = serialized[members[i]]; - } - } - - // serialize a subet of tags (used to store in the metadata) - void DicomSequencesMap::Serialize(Json::Value& target, const std::set<DicomTag>& tags) const - { - // add the sequences to "target" - for (std::map<DicomTag, Json::Value>::const_iterator it = sequences_.begin(); - it != sequences_.end(); ++it) - { - if (tags.find(it->first) != tags.end()) - { - target[it->first.Format()] = it->second; - } - } - } - - // copy a subset of tags from Json - void DicomSequencesMap::FromDicomAsJson(const Json::Value& dicomAsJson, const std::set<DicomTag>& tags) - { - for (std::set<DicomTag>::const_iterator it = tags.begin(); - it != tags.end(); ++it) - { - std::string tag = it->Format(); - if (dicomAsJson.isMember(tag)) - { - sequences_[*it] = dicomAsJson[tag]; - } - } - } - - void DicomSequencesMap::ToJson(Json::Value& target, DicomToJsonFormat format) const - { - // add the sequences to "target" - for (std::map<DicomTag, Json::Value>::const_iterator it = sequences_.begin(); - it != sequences_.end(); ++it) - { - Json::Value sequenceForConversion = Json::objectValue; - sequenceForConversion[it->first.Format()] = it->second; - - Json::Value& requestedFormatJson = sequenceForConversion; - Json::Value convertedJson; - - if (format != DicomToJsonFormat_Full) - { - Toolbox::SimplifyDicomAsJson(convertedJson, sequenceForConversion, format); - requestedFormatJson = convertedJson; - } - - Json::Value::Members keys = requestedFormatJson.getMemberNames(); - for (size_t i = 0; i < keys.size(); i++) // there should always be only one member in this JSON - { - target[keys[i]] = requestedFormatJson[keys[i]]; - } - } - } - namespace { /**
--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.h Mon Jun 27 14:09:17 2022 +0200 +++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.h Mon Jun 27 15:22:19 2022 +0200 @@ -23,6 +23,7 @@ #pragma once #include "../../../OrthancFramework/Sources/DicomFormat/DicomMap.h" +#include "../../../OrthancFramework/Sources/DicomFormat/DicomSequencesMap.h" #include "IDatabaseWrapper.h" #include "../DicomInstanceOrigin.h" @@ -37,31 +38,11 @@ class ParsedDicomFile; struct ServerIndexChange; - /* - * contains a map of dicom sequences where: - * the key is a DicomTag - * the sequence is serialized in Json "full" format - */ - struct DicomSequencesMap : public boost::noncopyable - { - std::map<DicomTag, Json::Value> sequences_; - - void Deserialize(const Json::Value& serialized); - void Serialize(Json::Value& target, const std::set<DicomTag>& tags) const; - void FromDicomAsJson(const Json::Value& dicomAsJson, const std::set<DicomTag>& tags); - void ToJson(Json::Value& target, DicomToJsonFormat format) const; - - size_t GetSize() const - { - return sequences_.size(); - } - }; - struct ExpandedResource : public boost::noncopyable { std::string id_; DicomMap tags_; // all tags from DB (only leaf tags, not sequences !) - DicomSequencesMap sequences_; // the requested sequences + DicomSequencesMap sequences_; // the requested sequences (from MainDicomTags or RequestedTags) std::string mainDicomTagsSignature_; std::string parentId_; std::list<std::string> childrenIds_;
--- a/OrthancServer/Sources/ServerContext.cpp Mon Jun 27 14:09:17 2022 +0200 +++ b/OrthancServer/Sources/ServerContext.cpp Mon Jun 27 15:22:19 2022 +0200 @@ -2083,10 +2083,11 @@ target[MAIN_DICOM_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], mainDicomTags, format); - {// TODO add the sequences to the main dicom tags - // const std::set<DicomTag>& mainDicomTags = DicomMap::MainDicomTagsConfiguration::GetInstance().GetMainDicomTagsByLevel(resource.type_); - // mainDicomTags. - // resource.sequences_.ToJson(target[MAIN_DICOM_TAGS], format); + {// add the main DICOM sequences to the main dicom tags + const std::set<DicomTag>& mainDicomTags = DicomMap::GetMainDicomTags(resource.type_); + std::set<DicomTag> mainDicomSequences; + DicomMap::ExtractSequences(mainDicomSequences, mainDicomTags); + resource.sequences_.ToJson(target[MAIN_DICOM_TAGS], format, mainDicomSequences); } if (resource.type_ == ResourceType_Study) @@ -2108,8 +2109,12 @@ target[REQUESTED_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[REQUESTED_TAGS], tags, format); - // add the sequences to the requested tags - resource.sequences_.ToJson(target[REQUESTED_TAGS], format); + {// add the requested sequences to the requested tags + std::set<DicomTag> requestedDicomSequences; + DicomMap::ExtractSequences(requestedDicomSequences, requestedTags); + resource.sequences_.ToJson(target[REQUESTED_TAGS], format, requestedDicomSequences); + } + } }