Mercurial > hg > orthanc-neuro
view Sources/Plugin/Plugin.cpp @ 28:b440931aff64 default tip
added CITATION.cff
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Sat, 06 Apr 2024 17:25:43 +0200 |
parents | af9c718230ca |
children |
line wrap: on
line source
/** * Neuroimaging plugin for Orthanc * Copyright (C) 2021-2024 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 "PluginFrameDecoder.h" #include "../Framework/NeuroToolbox.h" #include "../Framework/NiftiWriter.h" #include <EmbeddedResources.h> #include <Logging.h> #include <SystemToolbox.h> #define ORTHANC_PLUGIN_NAME "neuro" static void CreateNifti(std::string& target, const Neuro::DicomInstancesCollection& collection, bool compress) { nifti_image nifti; std::vector<Neuro::Slice> slices; collection.CreateNiftiHeader(nifti, slices); Neuro::NiftiWriter writer; writer.WriteHeader(nifti); Neuro::PluginFrameDecoder decoder(collection); Neuro::IDicomFrameDecoder::Apply(writer, decoder, slices); writer.Flatten(target, compress); } static Neuro::InputDicomInstance* AcquireInstance(const std::string& instanceId) { #if 0 /** * This version uses DCMTK. It should be avoided for performance, as * it requires reading the entire DICOM files from the disk, whereas * "OrthancPluginDicomInstanceToJson()" will only read the DICOM * files up to pixel data, and will take advantage of the caching * mechanisms implemented inside the Orthanc core. **/ OrthancPlugins::MemoryBuffer dicom; dicom.GetDicomInstance(instanceId); Orthanc::ParsedDicomFile parsed(dicom.GetData(), dicom.GetSize()); return new Neuro::InputDicomInstance(parsed); #else Orthanc::DicomMap tags; { OrthancPlugins::OrthancString s; s.Assign(OrthancPluginDicomInstanceToJson( OrthancPlugins::GetGlobalContext(), instanceId.c_str(), OrthancPluginDicomToJsonFormat_Full, static_cast<OrthancPluginDicomToJsonFlags>(OrthancPluginDicomToJsonFlags_IncludePrivateTags | OrthancPluginDicomToJsonFlags_IncludeUnknownTags | OrthancPluginDicomToJsonFlags_StopAfterPixelData | OrthancPluginDicomToJsonFlags_SkipGroupLengths), 0)); Json::Value json; if (s.GetContent() == NULL || !OrthancPlugins::ReadJson(json, s.GetContent())) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Missing instance: " + instanceId); } tags.FromDicomAsJson(json); } std::unique_ptr<Neuro::InputDicomInstance> instance(new Neuro::InputDicomInstance(tags)); switch (instance->GetManufacturer()) { case Neuro::Manufacturer_Siemens: { std::string csa; if (OrthancPlugins::RestApiGetString(csa, "/instances/" + instanceId + "/content/" + Neuro::DICOM_TAG_SIEMENS_CSA_HEADER.Format(), false)) { instance->GetCSAHeader().Load(csa); } break; } case Neuro::Manufacturer_UIH: { const std::string uri = "/instances/" + instanceId + "/content/" + Neuro::DICOM_TAG_UIH_MR_VFRAME_SEQUENCE.Format(); Json::Value uih; if (OrthancPlugins::RestApiGet(uih, uri, false) && uih.type() == Json::arrayValue) { for (Json::Value::ArrayIndex i = 0; i < uih.size(); i++) { Json::Value tags2; if (uih[i].type() != Json::stringValue || !OrthancPlugins::RestApiGet(tags2, uri + "/" + uih[i].asString(), false) || tags2.type() != Json::arrayValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } Orthanc::DicomMap m; for (Json::Value::ArrayIndex j = 0; j < tags2.size(); j++) { Orthanc::DicomTag tag(0, 0); std::string value; if (tags2[j].type() != Json::stringValue || !Orthanc::DicomTag::ParseHexadecimal(tag, tags2[j].asCString()) || !OrthancPlugins::RestApiGetString(value, uri + "/" + uih[i].asString() + "/" + tags2[j].asString(), false)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } else { m.SetValue(tag, value, false); } } instance->AddUIHFrameSequenceItem(m); } } break; } default: break; } return instance.release(); #endif } static bool HasBooleanFlag(const OrthancPluginHttpRequest* request, const std::string& flag) { for (uint32_t i = 0; i < request->getCount; i++) { if (std::string(request->getKeys[i]) == flag) { return true; } } return false; } void SeriesToNifti(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { static const char* const KEY_INSTANCES = "Instances"; OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); } else { const std::string seriesId(request->groups[0]); Json::Value series; if (!OrthancPlugins::RestApiGet(series, "/series/" + seriesId, false)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Missing series: " + seriesId); } if (series.type() != Json::objectValue || !series.isMember(KEY_INSTANCES) || series[KEY_INSTANCES].type() != Json::arrayValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } Neuro::DicomInstancesCollection collection; for (Json::Value::ArrayIndex i = 0; i < series[KEY_INSTANCES].size(); i++) { if (series[KEY_INSTANCES][i].type() != Json::stringValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } else { const std::string id = series[KEY_INSTANCES][i].asString(); collection.AddInstance(AcquireInstance(id), id); } } const bool compress = HasBooleanFlag(request, "compress"); std::string nifti; CreateNifti(nifti, collection, compress); std::string filename = seriesId + ".nii"; if (compress) { filename += ".gz"; } const std::string contentDisposition = "filename=\"" + filename + "\""; OrthancPluginSetHttpHeader(context, output, "Content-Disposition", contentDisposition.c_str()); OrthancPluginAnswerBuffer(context, output, nifti.c_str(), nifti.size(), "application/octet-stream"); } } void InstanceToNifti(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); } else { const std::string instanceId(request->groups[0]); Neuro::DicomInstancesCollection collection; collection.AddInstance(AcquireInstance(instanceId), instanceId); const bool compress = HasBooleanFlag(request, "compress"); std::string nifti; CreateNifti(nifti, collection, compress); std::string filename = instanceId + ".nii"; if (compress) { filename += ".gz"; } const std::string contentDisposition = "filename=\"" + filename + "\""; OrthancPluginSetHttpHeader(context, output, "Content-Disposition", contentDisposition.c_str()); OrthancPluginAnswerBuffer(context, output, nifti.c_str(), nifti.size(), "application/octet-stream"); } } extern "C" { ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) { OrthancPlugins::SetGlobalContext(context); Orthanc::Logging::InitializePluginContext(context); Orthanc::Logging::EnableInfoLevel(true); /* Check the version of the Orthanc core */ if (OrthancPluginCheckVersion(context) == 0) { OrthancPlugins::ReportMinimalOrthancVersion(ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); return -1; } OrthancPlugins::SetDescription(ORTHANC_PLUGIN_NAME, "Add support for NIfTI in Orthanc."); OrthancPlugins::RegisterRestCallback<SeriesToNifti>("/series/(.*)/nifti", true /* thread safe */); OrthancPlugins::RegisterRestCallback<InstanceToNifti>("/instances/(.*)/nifti", true /* thread safe */); { std::string explorer; Orthanc::EmbeddedResources::GetFileResource( explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); OrthancPlugins::ExtendOrthancExplorer(ORTHANC_PLUGIN_NAME, explorer); } return 0; } ORTHANC_PLUGINS_API void OrthancPluginFinalize() { } ORTHANC_PLUGINS_API const char* OrthancPluginGetName() { return ORTHANC_PLUGIN_NAME; } ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() { return ORTHANC_PLUGIN_VERSION; } }