Mercurial > hg > orthanc-dicomweb
view Plugin/WadoRs.cpp @ 88:e009c43f4dbb
switch between the media types
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 09 Dec 2015 11:30:05 +0100 |
parents | 58665d0b7609 |
children | 4667d4235791 |
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/** * 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 "Plugin.h" #include <boost/lexical_cast.hpp> #include "Configuration.h" #include "Dicom.h" #include "DicomResults.h" #include "../Orthanc/Core/Toolbox.h" #include "../Orthanc/Core/OrthancException.h" static bool AcceptMultipartDicom(const OrthancPluginHttpRequest* request) { std::string accept; if (!OrthancPlugins::LookupHttpHeader(accept, request, "accept")) { return true; // By default, return "multipart/related; type=application/dicom;" } std::string application; std::map<std::string, std::string> attributes; OrthancPlugins::ParseContentType(application, attributes, accept); if (application != "multipart/related" && application != "*/*") { std::string s = "This WADO-RS plugin cannot generate the following content type: " + accept; OrthancPluginLogError(context_, s.c_str()); return false; } if (attributes.find("type") != attributes.end()) { std::string s = attributes["type"]; Orthanc::Toolbox::ToLowerCase(s); if (s != "application/dicom") { std::string s = "This WADO-RS plugin only supports application/dicom return type for DICOM retrieval (" + accept + ")"; OrthancPluginLogError(context_, s.c_str()); return false; } } if (attributes.find("transfer-syntax") != attributes.end()) { std::string s = "This WADO-RS plugin cannot change the transfer syntax to " + attributes["transfer-syntax"]; OrthancPluginLogError(context_, s.c_str()); return false; } return true; } static bool AcceptMetadata(const OrthancPluginHttpRequest* request, bool& isXml) { isXml = true; std::string accept; if (!OrthancPlugins::LookupHttpHeader(accept, request, "accept")) { // By default, return "multipart/related; type=application/dicom+xml;" return true; } std::string application; std::map<std::string, std::string> attributes; OrthancPlugins::ParseContentType(application, attributes, accept); if (application == "application/json") { isXml = false; return true; } if (application != "multipart/related" && application != "*/*") { std::string s = "This WADO-RS plugin cannot generate the following content type: " + accept; OrthancPluginLogError(context_, s.c_str()); return false; } if (attributes.find("type") != attributes.end()) { std::string s = attributes["type"]; Orthanc::Toolbox::ToLowerCase(s); if (s != "application/dicom+xml") { std::string s = "This WADO-RS plugin only supports application/json or application/dicom+xml return types for metadata (" + accept + ")"; OrthancPluginLogError(context_, s.c_str()); return false; } } if (attributes.find("transfer-syntax") != attributes.end()) { std::string s = "This WADO-RS plugin cannot change the transfer syntax to " + attributes["transfer-syntax"]; OrthancPluginLogError(context_, s.c_str()); return false; } return true; } static bool AcceptBulkData(const OrthancPluginHttpRequest* request) { std::string accept; if (!OrthancPlugins::LookupHttpHeader(accept, request, "accept")) { return true; // By default, return "multipart/related; type=application/octet-stream;" } std::string application; std::map<std::string, std::string> attributes; OrthancPlugins::ParseContentType(application, attributes, accept); if (application != "multipart/related" && application != "*/*") { std::string s = "This WADO-RS plugin cannot generate the following bulk data type: " + accept; OrthancPluginLogError(context_, s.c_str()); return false; } if (attributes.find("type") != attributes.end()) { std::string s = attributes["type"]; Orthanc::Toolbox::ToLowerCase(s); if (s != "application/octet-stream") { std::string s = "This WADO-RS plugin only supports application/octet-stream return type for bulk data retrieval (" + accept + ")"; OrthancPluginLogError(context_, s.c_str()); return false; } } if (attributes.find("ra,ge") != attributes.end()) { std::string s = "This WADO-RS plugin does not support Range retrieval, it can only return entire bulk data object"; OrthancPluginLogError(context_, s.c_str()); return false; } return true; } static OrthancPluginErrorCode AnswerListOfDicomInstances(OrthancPluginRestOutput* output, const std::string& resource) { Json::Value instances; if (!OrthancPlugins::RestApiGetJson(instances, context_, resource + "/instances")) { // Internal error OrthancPluginSendHttpStatusCode(context_, output, 400); return OrthancPluginErrorCode_Success; } if (OrthancPluginStartMultipartAnswer(context_, output, "related", "application/dicom")) { return OrthancPluginErrorCode_Plugin; } for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) { std::string uri = "/instances/" + instances[i]["ID"].asString() + "/file"; std::string dicom; if (OrthancPlugins::RestApiGetString(dicom, context_, uri) && OrthancPluginSendMultipartItem(context_, output, dicom.c_str(), dicom.size()) != 0) { return OrthancPluginErrorCode_Plugin; } } return OrthancPluginErrorCode_Success; } static void AnswerMetadata(OrthancPluginRestOutput* output, const OrthancPluginHttpRequest* request, const std::string& resource, bool isInstance, bool isXml) { std::list<std::string> files; if (isInstance) { files.push_back(resource + "/file"); } else { Json::Value instances; if (!OrthancPlugins::RestApiGetJson(instances, context_, resource + "/instances")) { // Internal error OrthancPluginSendHttpStatusCode(context_, output, 400); return; } for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) { files.push_back("/instances/" + instances[i]["ID"].asString() + "/file"); } } const std::string wadoBase = OrthancPlugins::Configuration::GetBaseUrl(configuration_, request); OrthancPlugins::DicomResults results(context_, output, wadoBase, *dictionary_, isXml, true); for (std::list<std::string>::const_iterator it = files.begin(); it != files.end(); ++it) { std::string content; if (OrthancPlugins::RestApiGetString(content, context_, *it)) { OrthancPlugins::ParsedDicomFile dicom(content); results.Add(dicom.GetFile()); } } results.Answer(); } static bool LocateStudy(OrthancPluginRestOutput* output, std::string& uri, const OrthancPluginHttpRequest* request) { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context_, output, "GET"); return false; } std::string id; { char* tmp = OrthancPluginLookupStudy(context_, request->groups[0]); if (tmp == NULL) { std::string s = "Accessing an inexistent study with WADO-RS: " + std::string(request->groups[0]); OrthancPluginLogError(context_, s.c_str()); OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } id.assign(tmp); OrthancPluginFreeString(context_, tmp); } uri = "/studies/" + id; return true; } static bool LocateSeries(OrthancPluginRestOutput* output, std::string& uri, const OrthancPluginHttpRequest* request) { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context_, output, "GET"); return false; } std::string id; { char* tmp = OrthancPluginLookupSeries(context_, request->groups[1]); if (tmp == NULL) { std::string s = "Accessing an inexistent series with WADO-RS: " + std::string(request->groups[1]); OrthancPluginLogError(context_, s.c_str()); OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } id.assign(tmp); OrthancPluginFreeString(context_, tmp); } Json::Value study; if (!OrthancPlugins::RestApiGetJson(study, context_, "/series/" + id + "/study")) { OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } if (study["MainDicomTags"]["StudyInstanceUID"].asString() != std::string(request->groups[0])) { std::string s = "No series " + std::string(request->groups[1]) + " in study " + std::string(request->groups[0]); OrthancPluginLogError(context_, s.c_str()); OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } uri = "/series/" + id; return true; } static bool LocateInstance(OrthancPluginRestOutput* output, std::string& uri, const OrthancPluginHttpRequest* request) { if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context_, output, "GET"); return false; } std::string id; { char* tmp = OrthancPluginLookupInstance(context_, request->groups[2]); if (tmp == NULL) { std::string s = "Accessing an inexistent instance with WADO-RS: " + std::string(request->groups[2]); OrthancPluginLogError(context_, s.c_str()); OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } id.assign(tmp); OrthancPluginFreeString(context_, tmp); } Json::Value study, series; if (!OrthancPlugins::RestApiGetJson(series, context_, "/instances/" + id + "/series") || !OrthancPlugins::RestApiGetJson(study, context_, "/instances/" + id + "/study")) { OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } if (study["MainDicomTags"]["StudyInstanceUID"].asString() != std::string(request->groups[0]) || series["MainDicomTags"]["SeriesInstanceUID"].asString() != std::string(request->groups[1])) { std::string s = ("No instance " + std::string(request->groups[2]) + " in study " + std::string(request->groups[0]) + " or " + " in series " + std::string(request->groups[1])); OrthancPluginLogError(context_, s.c_str()); OrthancPluginSendHttpStatusCode(context_, output, 404); return false; } uri = "/instances/" + id; return true; } OrthancPluginErrorCode RetrieveDicomStudy(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri; if (LocateStudy(output, uri, request)) { AnswerListOfDicomInstances(output, uri); } return OrthancPluginErrorCode_Success; } OrthancPluginErrorCode RetrieveDicomSeries(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri; if (LocateSeries(output, uri, request)) { AnswerListOfDicomInstances(output, uri); } return OrthancPluginErrorCode_Success; } OrthancPluginErrorCode RetrieveDicomInstance(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri; if (LocateInstance(output, uri, request)) { if (OrthancPluginStartMultipartAnswer(context_, output, "related", "application/dicom")) { return OrthancPluginErrorCode_Plugin; } std::string dicom; if (OrthancPlugins::RestApiGetString(dicom, context_, uri + "/file") && OrthancPluginSendMultipartItem(context_, output, dicom.c_str(), dicom.size()) != 0) { return OrthancPluginErrorCode_Plugin; } } return OrthancPluginErrorCode_Success; } OrthancPluginErrorCode RetrieveStudyMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri; if (LocateStudy(output, uri, request)) { AnswerMetadata(output, request, uri, false, isXml); } return OrthancPluginErrorCode_Success; } OrthancPluginErrorCode RetrieveSeriesMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri; if (LocateSeries(output, uri, request)) { AnswerMetadata(output, request, uri, false, isXml); } return OrthancPluginErrorCode_Success; } OrthancPluginErrorCode RetrieveInstanceMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri; if (LocateInstance(output, uri, request)) { AnswerMetadata(output, request, uri, true, isXml); } return OrthancPluginErrorCode_Success; } static uint32_t Hex2Dec(char c) { return (c >= '0' && c <= '9') ? c - '0' : c - 'a' + 10; } static bool ParseBulkTag(gdcm::Tag& tag, const std::string& s) { if (s.size() != 8) { return false; } for (size_t i = 0; i < 8; i++) { if ((s[i] < '0' || s[i] > '9') && (s[i] < 'a' || s[i] > 'f')) { return false; } } uint32_t g = ((Hex2Dec(s[0]) << 12) + (Hex2Dec(s[1]) << 8) + (Hex2Dec(s[2]) << 4) + Hex2Dec(s[3])); uint32_t e = ((Hex2Dec(s[4]) << 12) + (Hex2Dec(s[5]) << 8) + (Hex2Dec(s[6]) << 4) + Hex2Dec(s[7])); tag = gdcm::Tag(g, e); return true; } static bool ExploreBulkData(std::string& content, const std::vector<std::string>& path, size_t position, const gdcm::DataSet& dataset) { gdcm::Tag tag; if (!ParseBulkTag(tag, path[position]) || !dataset.FindDataElement(tag)) { return false; } const gdcm::DataElement& element = dataset.GetDataElement(tag); if (position + 1 == path.size()) { const gdcm::ByteValue* data = element.GetByteValue(); if (!data) { content.clear(); } else { content.assign(data->GetPointer(), data->GetLength()); } return true; } return false; } OrthancPluginErrorCode RetrieveBulkData(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptBulkData(request)) { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); return OrthancPluginErrorCode_Success; } std::string uri, content; if (LocateInstance(output, uri, request) && OrthancPlugins::RestApiGetString(content, context_, uri + "/file")) { OrthancPlugins::ParsedDicomFile dicom(content); std::vector<std::string> path; Orthanc::Toolbox::TokenizeString(path, request->groups[3], '/'); std::string result; if (path.size() % 2 == 1 && ExploreBulkData(result, path, 0, dicom.GetDataSet())) { if (OrthancPluginStartMultipartAnswer(context_, output, "related", "application/octet-stream") != 0 || OrthancPluginSendMultipartItem(context_, output, result.c_str(), result.size()) != 0) { return OrthancPluginErrorCode_Plugin; } } else { OrthancPluginSendHttpStatusCode(context_, output, 400 /* Bad request */); } } return OrthancPluginErrorCode_Success; } #include <gdcmImageReader.h> #include <gdcmImageWriter.h> #include <gdcmImageChangeTransferSyntax.h> #include <gdcmJPEG2000Codec.h> static bool Test(const gdcm::DataSet& dicom) { if (!dicom.FindDataElement(OrthancPlugins::DICOM_TAG_PIXEL_DATA)) { return OrthancPluginErrorCode_IncompatibleImageFormat; } const gdcm::DataElement& pixelData = dicom.GetDataElement(OrthancPlugins::DICOM_TAG_PIXEL_DATA); const gdcm::SequenceOfFragments* fragments = pixelData.GetSequenceOfFragments(); if (fragments == NULL) { printf("Single-frame image\n"); printf("%d\n", pixelData.GetByteValue()->GetLength()); } else { printf("Multi-frame image (%d fragments)\n", fragments->GetNumberOfFragments()); for (gdcm::SequenceOfFragments::SizeType i = 0; i < fragments->GetNumberOfFragments(); i++) { printf("%d: %d\n", i, fragments->GetFragment(i).GetByteValue()->GetLength()); } } return true; } static void TokenizeAndNormalize(std::vector<std::string>& tokens, const std::string& source, char separator) { Orthanc::Toolbox::TokenizeString(tokens, source, separator); for (size_t i = 0; i < tokens.size(); i++) { tokens[i] = Orthanc::Toolbox::StripSpaces(tokens[i]); Orthanc::Toolbox::ToLowerCase(tokens[i]); } } static gdcm::TransferSyntax GetTransferSyntax(const OrthancPluginHttpRequest* request) { for (uint32_t i = 0; i < request->headersCount; i++) { std::string key(request->headersKeys[i]); Orthanc::Toolbox::ToLowerCase(key); if (key == "accept") { std::vector<std::string> tokens; TokenizeAndNormalize(tokens, request->headersValues[i], ';'); if (tokens.size() < 0 || tokens[0] != "multipart/related") { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } std::string type("application/octet-stream"); std::string transferSyntax; for (size_t j = 1; j < tokens.size(); j++) { std::vector<std::string> parsed; TokenizeAndNormalize(parsed, tokens[j], '='); if (parsed.size() != 2) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); } if (parsed[0] == "type") { type = parsed[1]; } if (parsed[0] == "transfer-syntax") { transferSyntax = parsed[1]; } } if (type == "application/octet-stream") { if (transferSyntax.empty()) { return gdcm::TransferSyntax(gdcm::TransferSyntax::ImplicitVRLittleEndian); } else { std::string s = ("DICOMweb RetrieveFrames: Cannot specify a transfer syntax (" + transferSyntax + ") for default Little Endian uncompressed pixel data"); OrthancPluginLogError(context_, s.c_str()); throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); } } else { // http://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_6.5-1 if (type == "image/dicom+jpeg" && transferSyntax == "1.2.840.10008.1.2.4.50") { return gdcm::TransferSyntax::JPEGBaselineProcess1; } else if (type == "image/dicom+jpeg" && transferSyntax == "1.2.840.10008.1.2.4.51") { return gdcm::TransferSyntax::JPEGExtendedProcess2_4; } else if (type == "image/dicom+jpeg" && transferSyntax == "1.2.840.10008.1.2.4.57") { return gdcm::TransferSyntax::JPEGLosslessProcess14; } else if (type == "image/dicom+jpeg" && (transferSyntax.empty() || transferSyntax == "1.2.840.10008.1.2.4.70")) { return gdcm::TransferSyntax::JPEGLosslessProcess14_1; } else if (type == "image/dicom+rle" && (transferSyntax.empty() || transferSyntax == "1.2.840.10008.1.2.5")) { return gdcm::TransferSyntax::RLELossless; } else if (type == "image/dicom+jpeg-ls" && (transferSyntax.empty() || transferSyntax == "1.2.840.10008.1.2.4.80")) { return gdcm::TransferSyntax::JPEGLSLossless; } else if (type == "image/dicom+jpeg-ls" && transferSyntax == "1.2.840.10008.1.2.4.81") { return gdcm::TransferSyntax::JPEGLSNearLossless; } else if (type == "image/dicom+jp2" && (transferSyntax.empty() || transferSyntax == "1.2.840.10008.1.2.4.90")) { return gdcm::TransferSyntax::JPEG2000Lossless; } else if (type == "image/dicom+jp2" && transferSyntax == "1.2.840.10008.1.2.4.91") { return gdcm::TransferSyntax::JPEG2000; } else if (type == "image/dicom+jpx" && (transferSyntax.empty() || transferSyntax == "1.2.840.10008.1.2.4.92")) { return gdcm::TransferSyntax::JPEG2000Part2Lossless; } else if (type == "image/dicom+jpx" && transferSyntax == "1.2.840.10008.1.2.4.93") { return gdcm::TransferSyntax::JPEG2000Part2; } else { std::string s = ("DICOMweb RetrieveFrames: Transfer syntax \"" + transferSyntax + "\" is incompatible with media type \"" + type + "\""); OrthancPluginLogError(context_, s.c_str()); throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); } } } } // By default, DICOMweb expectes Little Endian uncompressed pixel data return gdcm::TransferSyntax::ImplicitVRLittleEndian; } OrthancPluginErrorCode RetrieveFrames(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { // storescu -xs localhost 4242 ~/Subversion/orthanc-tests/Database/Multiframe.dcm // curl http://localhost:8042/dicom-web/studies/1.3.51.0.1.1.192.168.29.133.1681753.1681732/series/1.3.12.2.1107.5.2.33.37097.2012041612474981424569674.0.0.0/instances/1.3.12.2.1107.5.2.33.37097.2012041612485517294169680/frames/0 // curl http://localhost:8042/dicom-web/studies/1.3.46.670589.7.5.8.80001255161.20000323.151537.1/series/1.3.46.670589.7.5.7.80001255161.20000323.151537.1/instances/1.3.46.670589.7.5.1.981501.20000323.16172540.1.1.13/frames/0 // http://gdcm.sourceforge.net/html/CompressLossyJPEG_8cs-example.html printf("T: %s\n", GetTransferSyntax(request).GetString()); std::string uri, content; if (LocateInstance(output, uri, request) && OrthancPlugins::RestApiGetString(content, context_, uri + "/file")) { { OrthancPlugins::ParsedDicomFile dicom(content); Test(dicom.GetDataSet()); //return OrthancPluginErrorCode_Success; } printf("RetrieveFrames: [%s] [%s]\n", uri.c_str(), request->groups[3]); gdcm::ImageChangeTransferSyntax change; change.SetTransferSyntax(gdcm::TransferSyntax::JPEG2000Lossless); gdcm::JPEG2000Codec codec; if (!codec.CanCode(change.GetTransferSyntax())) { return OrthancPluginErrorCode_Plugin; } //codec.SetLossless(true); change.SetUserCodec(&codec); std::stringstream stream(content); gdcm::ImageReader reader; reader.SetStream(stream); printf("Read: %d\n", reader.Read()); change.SetInput(reader.GetImage()); printf("Change: %d\n", change.Change()); gdcm::ImageWriter writer; writer.SetImage(change.GetOutput()); writer.SetFile(reader.GetFile()); std::stringstream ss; writer.SetStream(ss); printf("Write: %d\n", writer.Write()); gdcm::Reader reader2; reader2.SetStream(ss); printf("Read: %d\n", reader2.Read()); Test(reader2.GetFile().GetDataSet()); } return OrthancPluginErrorCode_Success; }