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comparison Applications/Dicomizer.cpp @ 279:77afef2cf64b

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automated extraction of the imaged volume if using OpenSlide
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 12 Jul 2023 18:06:34 +0200
parents 20a730889ae2
children 34b507959e32 b5b9719ef1c0
comparison
equal deleted inserted replaced
278:169f168ba07a 279:77afef2cf64b
641 "URL to the REST API of the target Orthanc server") 641 "URL to the REST API of the target Orthanc server")
642 ; 642 ;
643 643
644 boost::program_options::options_description volumeOptions("Description of the imaged volume"); 644 boost::program_options::options_description volumeOptions("Description of the imaged volume");
645 volumeOptions.add_options() 645 volumeOptions.add_options()
646 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), 646 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(),
647 "Width of the specimen (in mm)") 647 "Width of the specimen (in mm), defaults to 15mm if missing")
648 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), 648 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(),
649 "Height of the specimen (in mm)") 649 "Height of the specimen (in mm), defaults to 15mm if missing")
650 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), 650 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1),
651 "Depth of the specimen (in mm)") 651 "Depth of the specimen (in mm)")
652 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), 652 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20),
653 "X offset the specimen, wrt. slide coordinates origin (in mm)") 653 "X offset the specimen, wrt. slide coordinates origin (in mm)")
654 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), 654 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40),
1008 } 1008 }
1009 1009
1010 1010
1011 1011
1012 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, 1012 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression,
1013 OrthancWSI::ImagedVolumeParameters& volume,
1013 const std::string& path, 1014 const std::string& path,
1014 const OrthancWSI::DicomizerParameters& parameters) 1015 const OrthancWSI::DicomizerParameters& parameters)
1015 { 1016 {
1016 if (parameters.IsCytomineSource()) 1017 if (parameters.IsCytomineSource())
1017 { 1018 {
1070 1071
1071 try 1072 try
1072 { 1073 {
1073 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; 1074 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide";
1074 sourceCompression = OrthancWSI::ImageCompression_Unknown; 1075 sourceCompression = OrthancWSI::ImageCompression_Unknown;
1075 return new OrthancWSI::OpenSlidePyramid(path, 1076
1076 parameters.GetTargetTileWidth(512), 1077 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide(
1077 parameters.GetTargetTileHeight(512)); 1078 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512),
1079 parameters.GetTargetTileHeight(512)));
1080
1081 float volumeWidth, volumeHeight;
1082 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight))
1083 {
1084 if (!volume.HasWidth())
1085 {
1086 volume.SetWidth(volumeWidth);
1087 }
1088
1089 if (!volume.HasHeight())
1090 {
1091 volume.SetHeight(volumeHeight);
1092 }
1093 }
1094
1095 return openslide.release();
1078 } 1096 }
1079 catch (Orthanc::OrthancException&) 1097 catch (Orthanc::OrthancException&)
1080 { 1098 {
1081 LOG(ERROR) << "This file is not supported by OpenSlide"; 1099 LOG(ERROR) << "This file is not supported by OpenSlide";
1082 return NULL; 1100 return NULL;
1099 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) 1117 if (ParseParameters(exitStatus, parameters, volume, argc, argv))
1100 { 1118 {
1101 OrthancWSI::ImageCompression sourceCompression; 1119 OrthancWSI::ImageCompression sourceCompression;
1102 std::unique_ptr<OrthancWSI::ITiledPyramid> source; 1120 std::unique_ptr<OrthancWSI::ITiledPyramid> source;
1103 1121
1104 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); 1122 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters));
1105 if (source.get() == NULL) 1123 if (source.get() == NULL)
1106 { 1124 {
1107 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); 1125 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
1108 } 1126 }
1109 1127