Mercurial > hg > orthanc-wsi

annotate Applications/DicomToTiff.cpp @ 242:49f647ed1b4c

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added copyright UCLouvain
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 06 Dec 2021 16:05:42 +0100
parents 20bc074ec19a
children 20a730889ae2
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Affero General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Affero General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Affero General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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22
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23 #include "../Framework/DicomToolbox.h"
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24 #include "../Framework/ImageToolbox.h"
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25 #include "../Framework/Inputs/DicomPyramid.h"
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26 #include "../Framework/Inputs/TiledPyramidStatistics.h"
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27 #include "../Framework/Outputs/HierarchicalTiffWriter.h"
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28 #include "../Resources/Orthanc/Stone/OrthancHttpConnection.h"
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30 #include <Compatibility.h> // For std::unique_ptr
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31 #include <Logging.h>
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32 #include <OrthancException.h>
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33
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34 #include "ApplicationToolbox.h"
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37 static const char* OPTION_COLOR = "color";
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38 static const char* OPTION_HELP = "help";
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39 static const char* OPTION_INPUT = "input";
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40 static const char* OPTION_JPEG_QUALITY = "jpeg-quality";
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41 static const char* OPTION_OUTPUT = "output";
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42 static const char* OPTION_REENCODE = "reencode";
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43 static const char* OPTION_VERBOSE = "verbose";
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44 static const char* OPTION_VERSION = "version";
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45
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46 static bool ParseParameters(int& exitStatus,
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47 boost::program_options::variables_map& options,
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48 int argc,
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49 char* argv[])
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50 {
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51 // Declare the supported parameters
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52 boost::program_options::options_description generic("Generic options");
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53 generic.add_options()
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54 (OPTION_HELP, "Display this help and exit")
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55 (OPTION_VERSION, "Output version information and exit")
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56 (OPTION_VERBOSE, "Be verbose in logs")
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57 ;
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58
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59 boost::program_options::options_description source("Options for the source DICOM image");
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60 source.add_options()
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61 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
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62 "URL to the REST API of the target Orthanc server")
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63 ;
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64 OrthancWSI::ApplicationToolbox::AddRestApiOptions(source);
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66 boost::program_options::options_description target("Options for the target TIFF image");
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67 target.add_options()
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68 (OPTION_COLOR, boost::program_options::value<std::string>(),
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69 "Color of the background for missing tiles (e.g. \"255,0,0\")")
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70 (OPTION_REENCODE, boost::program_options::value<bool>(),
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71 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)")
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72 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(),
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73 "Set quality level for JPEG (0..100)")
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74 ;
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75
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76 boost::program_options::options_description hidden;
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77 hidden.add_options()
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78 (OPTION_INPUT, boost::program_options::value<std::string>(),
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79 "Orthanc identifier of the input series of interest")
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80 (OPTION_OUTPUT, boost::program_options::value<std::string>(),
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81 "Output TIFF file");
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82
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83 boost::program_options::options_description allWithoutHidden;
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84 allWithoutHidden.add(generic).add(source).add(target);
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85
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86 boost::program_options::options_description all = allWithoutHidden;
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87 all.add(hidden);
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88
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89 boost::program_options::positional_options_description positional;
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90 positional.add(OPTION_INPUT, 1);
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91 positional.add(OPTION_OUTPUT, 1);
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92
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93 bool error = false;
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94
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95 try
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96 {
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97 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
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98 options(all).positional(positional).run(), options);
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99 boost::program_options::notify(options);
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100 }
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101 catch (boost::program_options::error& e)
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102 {
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103 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
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104 error = true;
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105 }
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106
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107 if (!error &&
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108 options.count(OPTION_HELP) == 0 &&
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109 options.count(OPTION_VERSION) == 0)
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110 {
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111 if (options.count(OPTION_INPUT) != 1)
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112 {
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113 LOG(ERROR) << "No input series was specified";
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114 error = true;
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115 }
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116
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117 if (options.count(OPTION_OUTPUT) != 1)
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118 {
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119 LOG(ERROR) << "No output file was specified";
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120 error = true;
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121 }
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122 }
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123
128
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124 if (error || options.count(OPTION_HELP))
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125 {
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126 std::cout << std::endl
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127 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]"
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128 << std::endl
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129 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
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130 << std::endl << std::endl
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131 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl
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132 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)."
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133 << std::endl;
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134
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135 std::cout << allWithoutHidden << "\n";
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136
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137 if (error)
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138 {
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139 exitStatus = -1;
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140 }
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141
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142 return false;
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143 }
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144
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145 if (options.count(OPTION_VERSION))
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146 {
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147 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]);
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148 return false;
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149 }
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150
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151 if (options.count(OPTION_VERBOSE))
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152 {
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153 Orthanc::Logging::EnableInfoLevel(true);
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154 }
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155
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156 return true;
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157 }
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158
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159
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160
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161 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer,
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162 const boost::program_options::variables_map& options)
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163 {
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164 std::unique_ptr<Orthanc::ImageAccessor> tile
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165 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(),
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166 writer.GetTileWidth(),
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167 writer.GetTileHeight()));
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168
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169 uint8_t red = 255;
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170 uint8_t green = 255;
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171 uint8_t blue = 255;
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172
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173 if (options.count(OPTION_COLOR))
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174 {
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175 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options[OPTION_COLOR].as<std::string>());
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176 }
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177
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178 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue);
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179
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180 return tile.release();
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181 }
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182
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183
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184
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185 static void Run(OrthancWSI::ITiledPyramid& source,
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186 const boost::program_options::variables_map& options)
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187 {
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188 bool reencode = (options.count(OPTION_REENCODE) &&
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189 options[OPTION_REENCODE].as<bool>());
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190
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191 Orthanc::PhotometricInterpretation targetPhotometric;
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192
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193 if (reencode)
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194 {
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195 // The DicomToTiff tool only creates TIFF images with JPEG tiles (*)
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196 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422;
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197 }
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198 else
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199 {
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200 targetPhotometric = source.GetPhotometricInterpretation();
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201 }
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202
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203 OrthancWSI::ImageToolbox::CheckConstantTileSize(source); // (**)
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204 OrthancWSI::HierarchicalTiffWriter target(options[OPTION_OUTPUT].as<std::string>(),
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205 source.GetPixelFormat(),
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206 OrthancWSI::ImageCompression_Jpeg, // (*)
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207 source.GetTileWidth(0), // (**)
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208 source.GetTileHeight(0), // (**)
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209 targetPhotometric);
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210
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211 if (options.count(OPTION_JPEG_QUALITY))
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212 {
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213 target.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>());
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214 }
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215
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216 LOG(WARNING) << "Source photometric interpretation: " << EnumerationToString(source.GetPhotometricInterpretation());
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217 LOG(WARNING) << "Target photometric interpretation: " << EnumerationToString(targetPhotometric);
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218
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219 std::unique_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
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220
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221 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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222 {
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223 LOG(WARNING) << "Creating level " << level << " of size "
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224 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
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225 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
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226 }
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227
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228 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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229 {
163
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230 LOG(WARNING) << std::string(reencode ? "Re-encoding" : "Transcoding")
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231 << " level " << level;
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232
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233 unsigned int countX = OrthancWSI::CeilingDivision
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234 (source.GetLevelWidth(level), source.GetTileWidth(level));
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235
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236 unsigned int countY = OrthancWSI::CeilingDivision
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237 (source.GetLevelHeight(level), source.GetTileHeight(level));
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238
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239 for (unsigned int tileY = 0; tileY < countY; tileY++)
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240 {
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241 for (unsigned int tileX = 0; tileX < countX; tileX++)
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242 {
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243 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
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244
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245 bool missing = false;
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246 bool success = true;
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247
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248 std::string tile;
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249 OrthancWSI::ImageCompression compression;
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250
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251 if (source.ReadRawTile(tile, compression, level, tileX, tileY))
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252 {
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253 if (compression == OrthancWSI::ImageCompression_Jpeg)
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254 {
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255 // Transcoding of JPEG tiles
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256 target.WriteRawTile(tile, compression, level, tileX, tileY);
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257 }
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258 else if (reencode)
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259 {
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260 std::unique_ptr<Orthanc::ImageAccessor> decoded;
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261
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262 if (compression == OrthancWSI::ImageCompression_None)
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263 {
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264 decoded.reset(OrthancWSI::ImageToolbox::DecodeRawTile(
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265 tile, source.GetPixelFormat(),
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266 source.GetTileWidth(level), source.GetTileHeight(level)));
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267 }
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268 else
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269 {
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270 decoded.reset(OrthancWSI::ImageToolbox::DecodeTile(tile, compression));
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271 }
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272
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273 target.EncodeTile(*decoded, level, tileX, tileY);
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274 }
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275 else
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276 {
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277 success = false; // Re-encoding is mandatory
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278 }
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279 }
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280 else
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281 {
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282 // Unable to read the raw tile: The tile is missing (sparse tiling)
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283 missing = true;
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284 }
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285
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286 if (!success)
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287 {
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288 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is "
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289 << OrthancWSI::EnumerationToString(compression)
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290 << "), please use the --" << OPTION_REENCODE << "=1 option";
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291 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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292 }
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293
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294 if (missing)
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295 {
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296 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile ("
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297 << tileX << "," << tileY << ") at level " << level;
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298 target.EncodeTile(*empty, level, tileX, tileY);
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299 }
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300 }
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301 }
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302
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303 target.Flush();
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304 }
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305 }
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306
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307
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308
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309 int main(int argc, char* argv[])
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310 {
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311 OrthancWSI::ApplicationToolbox::GlobalInitialize();
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312 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]);
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313
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314 int exitStatus = 0;
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315 boost::program_options::variables_map options;
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316
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317 try
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318 {
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319 if (ParseParameters(exitStatus, options, argc, argv))
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320 {
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321 Orthanc::WebServiceParameters params;
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322
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323 OrthancWSI::ApplicationToolbox::SetupRestApi(params, options);
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324
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325 OrthancStone::OrthancHttpConnection orthanc(params);
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326 OrthancWSI::DicomPyramid source(orthanc, options[OPTION_INPUT].as<std::string>(),
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327 false /* don't use cached metadata */);
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328
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329 OrthancWSI::TiledPyramidStatistics stats(source);
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330 Run(stats, options);
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331 }
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332 }
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333 catch (Orthanc::OrthancException& e)
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334 {
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335 LOG(ERROR) << "Terminating on exception: " << e.What();
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336
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337 if (options.count(OPTION_REENCODE) == 0)
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338 {
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339 LOG(ERROR) << "Consider using option \"--" << OPTION_REENCODE << "\"";
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340 }
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341
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342 exitStatus = -1;
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343 }
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344
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345 OrthancWSI::ApplicationToolbox::GlobalFinalize();
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346
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347 return exitStatus;
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348 }