Mercurial > hg > orthanc-dicomweb
view Plugin/WadoRsRetrieveFrames.cpp @ 415:e7b0c7f83fa7 OrthancDicomWeb-1.1
upgrade to Orthanc framework 1.7.0 in releases
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Mon, 25 May 2020 11:58:53 +0200 |
parents | 2977ef0eabbb |
children | 787c1d774b27 |
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) 2017-2020 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 "WadoRs.h" #include "GdcmParsedDicomFile.h" #include <Core/Toolbox.h> #include <Plugins/Samples/Common/OrthancPluginCppWrapper.h> #include <memory> #include <list> #include <gdcmImageReader.h> #include <gdcmImageWriter.h> #include <gdcmImageChangeTransferSyntax.h> #include <boost/algorithm/string/replace.hpp> #include <boost/lexical_cast.hpp> 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 void RemoveSurroundingQuotes(std::string& value) { if (!value.empty() && value[0] == '\"' && value[value.size() - 1] == '\"') { value = value.substr(1, value.size() - 2); } } static gdcm::TransferSyntax ParseTransferSyntax(const OrthancPluginHttpRequest* request, gdcm::TransferSyntax sourceTransferSyntax) { 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] == "*/*") { return gdcm::TransferSyntax::ExplicitVRLittleEndian; } if (tokens[0] != "multipart/related") { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, "expecting 'Accept: multipart/related' HTTP header"); } 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]; RemoveSurroundingQuotes(type); } if (parsed[0] == "transfer-syntax") { transferSyntax = parsed[1]; RemoveSurroundingQuotes(transferSyntax); } } if (type == "application/octet-stream") { if (transferSyntax.empty()) { return gdcm::TransferSyntax(gdcm::TransferSyntax::ExplicitVRLittleEndian); } else if (transferSyntax == "*") { // New in DICOMweb plugin 1.1.0 return sourceTransferSyntax; } else { throw Orthanc::OrthancException( Orthanc::ErrorCode_BadRequest, "DICOMweb RetrieveFrames: Cannot specify a transfer syntax (" + transferSyntax + ") for default Little Endian uncompressed pixel data"); } } else { /** * DICOM 2017c * http://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_6.1.1.8-3b **/ if (type == "image/jpeg" && (transferSyntax.empty() || // Default transferSyntax == "1.2.840.10008.1.2.4.70")) { return gdcm::TransferSyntax::JPEGLosslessProcess14_1; } else if (type == "image/jpeg" && transferSyntax == "1.2.840.10008.1.2.4.50") { return gdcm::TransferSyntax::JPEGBaselineProcess1; } else if (type == "image/jpeg" && transferSyntax == "1.2.840.10008.1.2.4.51") { return gdcm::TransferSyntax::JPEGExtendedProcess2_4; } else if (type == "image/jpeg" && transferSyntax == "1.2.840.10008.1.2.4.57") { return gdcm::TransferSyntax::JPEGLosslessProcess14; } else if (type == "image/x-dicom-rle" && (transferSyntax.empty() || // Default transferSyntax == "1.2.840.10008.1.2.5")) { return gdcm::TransferSyntax::RLELossless; } else if (type == "image/x-jls" && (transferSyntax.empty() || // Default transferSyntax == "1.2.840.10008.1.2.4.80")) { return gdcm::TransferSyntax::JPEGLSLossless; } else if (type == "image/x-jls" && transferSyntax == "1.2.840.10008.1.2.4.81") { return gdcm::TransferSyntax::JPEGLSNearLossless; } else if (type == "image/jp2" && (transferSyntax.empty() || // Default transferSyntax == "1.2.840.10008.1.2.4.90")) { return gdcm::TransferSyntax::JPEG2000Lossless; } else if (type == "image/jp2" && transferSyntax == "1.2.840.10008.1.2.4.91") { return gdcm::TransferSyntax::JPEG2000; } else if (type == "image/jpx" && (transferSyntax.empty() || // Default transferSyntax == "1.2.840.10008.1.2.4.92")) { return gdcm::TransferSyntax::JPEG2000Part2Lossless; } else if (type == "image/jpx" && transferSyntax == "1.2.840.10008.1.2.4.93") { return gdcm::TransferSyntax::JPEG2000Part2; } /** * Backward compatibility with DICOM 2014a * http://dicom.nema.org/medical/dicom/2014a/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; } throw Orthanc::OrthancException( Orthanc::ErrorCode_BadRequest, "DICOMweb RetrieveFrames: Transfer syntax \"" + transferSyntax + "\" is incompatible with media type \"" + type + "\""); } } } // By default, DICOMweb expectes Little Endian uncompressed pixel data return gdcm::TransferSyntax::ExplicitVRLittleEndian; } static void ParseFrameList(std::list<unsigned int>& frames, const OrthancPluginHttpRequest* request) { frames.clear(); if (request->groupsCount <= 3 || request->groups[3] == NULL) { return; } std::string source(request->groups[3]); Orthanc::Toolbox::ToLowerCase(source); boost::replace_all(source, "%2c", ","); std::vector<std::string> tokens; Orthanc::Toolbox::TokenizeString(tokens, source, ','); for (size_t i = 0; i < tokens.size(); i++) { int frame = boost::lexical_cast<int>(tokens[i]); if (frame <= 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, "Invalid frame number (must be > 0): " + tokens[i]); } frames.push_back(static_cast<unsigned int>(frame - 1)); } } static const char* GetMimeType(const gdcm::TransferSyntax& syntax) { // http://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_6.1.1.8-3b // http://dicom.nema.org/MEDICAL/dicom/2019a/output/chtml/part18/chapter_6.html#table_6.1.1.8-3b switch (syntax) { case gdcm::TransferSyntax::ImplicitVRLittleEndian: // The "transfer-syntax" info was added in version 1.1 of the plugin return "application/octet-stream; transfer-syntax=1.2.840.10008.1.2"; case gdcm::TransferSyntax::ExplicitVRLittleEndian: return "application/octet-stream; transfer-syntax=1.2.840.10008.1.2.1"; case gdcm::TransferSyntax::JPEGBaselineProcess1: return "image/jpeg; transfer-syntax=1.2.840.10008.1.2.4.50"; case gdcm::TransferSyntax::JPEGExtendedProcess2_4: return "image/jpeg; transfer-syntax=1.2.840.10008.1.2.4.51"; case gdcm::TransferSyntax::JPEGLosslessProcess14: return "image/jpeg; transfer-syntax=1.2.840.10008.1.2.4.57"; case gdcm::TransferSyntax::JPEGLosslessProcess14_1: return "image/jpeg; transferSyntax=1.2.840.10008.1.2.4.70"; case gdcm::TransferSyntax::RLELossless: return "image/x-dicom-rle; transferSyntax=1.2.840.10008.1.2.5"; case gdcm::TransferSyntax::JPEGLSLossless: return "image/x-jls; transferSyntax=1.2.840.10008.1.2.4.80"; case gdcm::TransferSyntax::JPEGLSNearLossless: return "image/x-jls; transfer-syntax=1.2.840.10008.1.2.4.81"; case gdcm::TransferSyntax::JPEG2000Lossless: return "image/jp2; transferSyntax=1.2.840.10008.1.2.4.90"; case gdcm::TransferSyntax::JPEG2000: return "image/jp2; transfer-syntax=1.2.840.10008.1.2.4.91"; case gdcm::TransferSyntax::JPEG2000Part2Lossless: return "image/jpx; transferSyntax=1.2.840.10008.1.2.4.92"; case gdcm::TransferSyntax::JPEG2000Part2: return "image/jpx; transfer-syntax=1.2.840.10008.1.2.4.93"; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } static void ConvertYbrToRgb(uint8_t rgb[3], const uint8_t ybr[3]) { // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2 // https://en.wikipedia.org/wiki/YCbCr#JPEG_conversion const float Y = ybr[0]; const float Cb = ybr[1]; const float Cr = ybr[2]; const float result[3] = { Y + 1.402f * (Cr - 128.0f), Y - 0.344136f * (Cb - 128.0f) - 0.714136f * (Cr - 128.0f), Y + 1.772f * (Cb - 128.0f) }; for (uint8_t i = 0; i < 3 ; i++) { if (result[i] < 0) { rgb[i] = 0; } else if (result[i] > 255) { rgb[i] = 255; } else { rgb[i] = static_cast<uint8_t>(result[i]); } } } static void AnswerSingleFrame(OrthancPluginRestOutput* output, const OrthancPluginHttpRequest* request, const OrthancPlugins::GdcmParsedDicomFile& dicom, const char* frame, size_t size, unsigned int frameIndex, bool convertYbr) { /** * Fix the photometric interpretation, typically needed for some * multiframe US images (as the one in issue 164). Also check out * the "Plugins/Samples/GdcmDecoder/GdcmImageDecoder.cpp" file in * the source distribution of Orthanc, and Osimis issue WVB-319 * ("Some images are not loading in US_MF"). **/ std::vector<uint8_t> copied; // Don't move this variable inside the // "if", as "frame" might point to it if (convertYbr && size > 0) { copied.resize(size); memcpy(&copied[0], frame, size); uint8_t *p = &copied[0]; for (size_t i = 0; i < size / 3; i++) { uint8_t ybr[3], rgb[3]; ybr[0] = p[0]; ybr[1] = p[1]; ybr[2] = p[2]; ConvertYbrToRgb(rgb, ybr); p[0] = rgb[0]; p[1] = rgb[1]; p[2] = rgb[2]; p += 3; } frame = reinterpret_cast<const char*>(&copied[0]); } OrthancPluginErrorCode error; #if HAS_SEND_MULTIPART_ITEM_2 == 1 std::string location = dicom.GetWadoUrl(request) + "frames/" + boost::lexical_cast<std::string>(frameIndex + 1); const char *keys[] = { "Content-Location" }; const char *values[] = { location.c_str() }; error = OrthancPluginSendMultipartItem2(OrthancPlugins::GetGlobalContext(), output, frame, size, 1, keys, values); #else error = OrthancPluginSendMultipartItem(OrthancPlugins::GetGlobalContext(), output, frame, size); #endif if (error != OrthancPluginErrorCode_Success) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } } static bool AnswerFrames(OrthancPluginRestOutput* output, const OrthancPluginHttpRequest* request, const OrthancPlugins::GdcmParsedDicomFile& dicom, const gdcm::TransferSyntax& syntax, std::list<unsigned int>& frames) { static const gdcm::Tag DICOM_TAG_BITS_ALLOCATED(0x0028, 0x0100); static const gdcm::Tag DICOM_TAG_COLUMNS(0x0028, 0x0011); static const gdcm::Tag DICOM_TAG_PIXEL_DATA(0x7fe0, 0x0010); static const gdcm::Tag DICOM_TAG_ROWS(0x0028, 0x0010); static const gdcm::Tag DICOM_TAG_SAMPLES_PER_PIXEL(0x0028, 0x0002); static const gdcm::Tag DICOM_TAG_PHOTOMETRIC_INTERPRETATION(0x0028, 0x0004); if (!dicom.GetDataSet().FindDataElement(DICOM_TAG_PIXEL_DATA)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); } const gdcm::DataElement& pixelData = dicom.GetDataSet().GetDataElement(DICOM_TAG_PIXEL_DATA); const gdcm::SequenceOfFragments* fragments = pixelData.GetSequenceOfFragments(); if (OrthancPluginStartMultipartAnswer(OrthancPlugins::GetGlobalContext(), output, "related", GetMimeType(syntax)) != OrthancPluginErrorCode_Success) { return false; } int samplesPerPixel; if (!dicom.GetIntegerTag(samplesPerPixel, DICOM_TAG_SAMPLES_PER_PIXEL)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } bool convertYbr = false; { std::string photometric; if (samplesPerPixel == 3 && dicom.GetStringTag(photometric, DICOM_TAG_PHOTOMETRIC_INTERPRETATION, true) && photometric == "YBR_FULL") { convertYbr = true; } } if (fragments == NULL) { // Single-fragment image if (pixelData.GetByteValue() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, "Image was not properly decoded"); } int width, height, bits; if (!dicom.GetIntegerTag(height, DICOM_TAG_ROWS) || !dicom.GetIntegerTag(width, DICOM_TAG_COLUMNS) || !dicom.GetIntegerTag(bits, DICOM_TAG_BITS_ALLOCATED)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } size_t frameSize = height * width * bits * samplesPerPixel / 8; if (frameSize == 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); } /** * The number of bytes in "pixelData" might not be divisible by * "frameSize", because "pixelData" might contain one padding byte * to have an even number of bytes. * https://bitbucket.org/sjodogne/orthanc/issues/164/ **/ if (pixelData.GetByteValue()->GetLength() % frameSize != 0 && (/* allow one padding byte to be present */ pixelData.GetByteValue()->GetLength() % 2 == 0 && pixelData.GetByteValue()->GetLength() % frameSize != 1)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } size_t framesCount = pixelData.GetByteValue()->GetLength() / frameSize; if (frames.empty()) { // If no frame is provided, return all the frames (this is an extension) for (size_t i = 0; i < framesCount; i++) { frames.push_back(i); } } const char* buffer = pixelData.GetByteValue()->GetPointer(); assert(sizeof(char) == 1); for (std::list<unsigned int>::const_iterator frame = frames.begin(); frame != frames.end(); ++frame) { if (*frame >= framesCount) { throw Orthanc::OrthancException( Orthanc::ErrorCode_ParameterOutOfRange, "Trying to access frame number " + boost::lexical_cast<std::string>(*frame + 1) + " of an image with " + boost::lexical_cast<std::string>(framesCount) + " frames"); } else { const char* p = buffer + (*frame) * frameSize; AnswerSingleFrame(output, request, dicom, p, frameSize, *frame, convertYbr); } } } else { // Multi-fragment image, we assume that each fragment corresponds to one frame if (frames.empty()) { // If no frame is provided, return all the frames (this is an extension) for (size_t i = 0; i < fragments->GetNumberOfFragments(); i++) { frames.push_back(i); } } for (std::list<unsigned int>::const_iterator frame = frames.begin(); frame != frames.end(); ++frame) { if (*frame >= fragments->GetNumberOfFragments()) { // TODO A frame is not a fragment, looks like a bug throw Orthanc::OrthancException( Orthanc::ErrorCode_ParameterOutOfRange, "Trying to access frame number " + boost::lexical_cast<std::string>(*frame + 1) + " of an image with " + boost::lexical_cast<std::string>(fragments->GetNumberOfFragments()) + " frames"); } else { AnswerSingleFrame(output, request, dicom, fragments->GetFragment(*frame).GetByteValue()->GetPointer(), fragments->GetFragment(*frame).GetByteValue()->GetLength(), *frame, convertYbr); } } } return true; } void RetrieveFrames(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { std::list<unsigned int> frames; ParseFrameList(frames, request); Json::Value header; std::string orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid; OrthancPlugins::MemoryBuffer content; if (LocateInstance(output, orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid, request) && content.RestApiGet("/instances/" + orthancId + "/file", false) && OrthancPlugins::RestApiGet(header, "/instances/" + orthancId + "/header?simplify", false)) { { std::string s = "DICOMweb RetrieveFrames on " + orthancId + ", frames: "; for (std::list<unsigned int>::const_iterator frame = frames.begin(); frame != frames.end(); ++frame) { s += boost::lexical_cast<std::string>(*frame + 1) + " "; } OrthancPlugins::LogInfo(s); } std::auto_ptr<OrthancPlugins::GdcmParsedDicomFile> source; gdcm::TransferSyntax sourceSyntax; if (header.type() == Json::objectValue && header.isMember("TransferSyntaxUID")) { sourceSyntax = gdcm::TransferSyntax::GetTSType(header["TransferSyntaxUID"].asCString()); } else { source.reset(new OrthancPlugins::GdcmParsedDicomFile(content)); sourceSyntax = source->GetFile().GetHeader().GetDataSetTransferSyntax(); } gdcm::TransferSyntax targetSyntax(ParseTransferSyntax(request, sourceSyntax)); if (sourceSyntax == targetSyntax) { // No need to change the transfer syntax if (source.get() == NULL) { source.reset(new OrthancPlugins::GdcmParsedDicomFile(content)); } AnswerFrames(output, request, *source, targetSyntax, frames); } else { // Need to convert the transfer syntax { OrthancPlugins::LogInfo("DICOMweb RetrieveFrames: Transcoding instance " + orthancId + " from transfer syntax " + std::string(sourceSyntax.GetString()) + " to " + std::string(targetSyntax.GetString())); } gdcm::ImageChangeTransferSyntax change; change.SetTransferSyntax(targetSyntax); // TODO Avoid this unnecessary memcpy by defining a stream over the MemoryBuffer std::string dicom(content.GetData(), content.GetData() + content.GetSize()); std::stringstream stream(dicom); gdcm::ImageReader reader; reader.SetStream(stream); if (!reader.Read()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot decode the image"); } change.SetInput(reader.GetImage()); if (!change.Change()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, "Cannot change the transfer syntax of the image"); } gdcm::ImageWriter writer; writer.SetImage(change.GetOutput()); writer.SetFile(reader.GetFile()); std::stringstream ss; writer.SetStream(ss); if (!writer.Write()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotEnoughMemory); } OrthancPlugins::GdcmParsedDicomFile transcoded(ss.str()); AnswerFrames(output, request, transcoded, targetSyntax, frames); } } }