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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 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU Affero General Public License
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8 * as published by the Free Software Foundation, either version 3 of
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9 * the License, or (at your option) any later version.
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10 *
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11 * This program is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty of
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13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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14 * Affero General Public License for more details.
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15 *
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16 * You should have received a copy of the GNU Affero General Public License
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17 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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18 **/
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19
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20
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21 #include "../Framework/DicomToolbox.h"
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22 #include "../Framework/ImageToolbox.h"
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23 #include "../Framework/Inputs/DicomPyramid.h"
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24 #include "../Framework/Messaging/CurlOrthancConnection.h"
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25 #include "../Framework/Orthanc/Core/Logging.h"
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26 #include "../Framework/Orthanc/Core/OrthancException.h"
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27 #include "../Framework/Outputs/HierarchicalTiffWriter.h"
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28
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29 #include "ApplicationToolbox.h"
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30
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31 #include <boost/program_options.hpp>
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32
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33
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34 static bool ParseParameters(int& exitStatus,
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35 boost::program_options::variables_map& options,
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36 int argc,
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37 char* argv[])
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38 {
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39 // Declare the supported parameters
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40 boost::program_options::options_description generic("Generic options");
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41 generic.add_options()
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42 ("help", "Display this help and exit")
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43 ("verbose", "Be verbose in logs")
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44 ;
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45
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46 boost::program_options::options_description source("Options for the source DICOM image");
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47 source.add_options()
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48 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
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49 "URL to the REST API of the target Orthanc server")
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50 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server")
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51 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server")
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52 ;
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53
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54 boost::program_options::options_description target("Options for the target TIFF image");
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55 target.add_options()
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56 ("color", boost::program_options::value<std::string>(), "Color of the background for missing tiles (e.g. \"255,0,0\")")
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57 ("reencode", boost::program_options::value<bool>(),
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58 "Whether to reencode each tile in JPEG (no transcoding, much slower) (Boolean)")
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59 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)")
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60 ;
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61
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62 boost::program_options::options_description hidden;
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63 hidden.add_options()
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64 ("input", boost::program_options::value<std::string>(), "Orthanc identifier of the input series of interest")
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65 ("output", boost::program_options::value<std::string>(), "Output TIFF file");
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66 ;
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67
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68 boost::program_options::options_description allWithoutHidden;
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69 allWithoutHidden.add(generic).add(source).add(target);
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70
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71 boost::program_options::options_description all = allWithoutHidden;
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72 all.add(hidden);
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73
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74 boost::program_options::positional_options_description positional;
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75 positional.add("input", 1);
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76 positional.add("output", 1);
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77
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78 bool error = false;
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79
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80 try
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81 {
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82 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
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83 options(all).positional(positional).run(), options);
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84 boost::program_options::notify(options);
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85 }
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86 catch (boost::program_options::error& e)
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87 {
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88 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
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89 error = true;
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90 }
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91
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92 if (!error &&
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93 options.count("help") == 0)
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94 {
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95 if (options.count("input") != 1)
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96 {
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97 LOG(ERROR) << "No input series was specified";
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98 error = true;
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99 }
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100
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101 if (options.count("output") != 1)
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102 {
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103 LOG(ERROR) << "No output file was specified";
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104 error = true;
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105 }
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106 }
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107
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108 if (error || options.count("help"))
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109 {
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110 std::cout << std::endl
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111 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]"
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112 << std::endl
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113 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
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114 << std::endl << std::endl
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115 << "Convert a DICOM for digital pathology stored in some Orthanc server as a standard hierarchical TIFF."
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116 << std::endl;
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117
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118 std::cout << allWithoutHidden << "\n";
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119
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120 if (error)
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121 {
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122 exitStatus = -1;
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123 }
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124
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125 return false;
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126 }
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127
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128 if (options.count("verbose"))
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129 {
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130 Orthanc::Logging::EnableInfoLevel(true);
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131 }
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132
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133 return true;
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134 }
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135
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136
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137
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138 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer,
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139 const boost::program_options::variables_map& options)
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140 {
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141 std::auto_ptr<Orthanc::ImageAccessor> tile
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142 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(),
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143 writer.GetTileWidth(),
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144 writer.GetTileHeight()));
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145
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146 uint8_t red = 255;
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147 uint8_t green = 255;
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148 uint8_t blue = 255;
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149
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150 if (options.count("color"))
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151 {
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152 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options["color"].as<std::string>());
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153 }
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154
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155 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue);
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156
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157 return tile.release();
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158 }
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159
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160
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161
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162 static void RunTranscode(OrthancWSI::ITiledPyramid& source,
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163 const boost::program_options::variables_map& options)
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164 {
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165 OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(),
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166 source.GetPixelFormat(),
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167 source.GetImageCompression(),
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168 source.GetTileWidth(),
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169 source.GetTileHeight());
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170
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171 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
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172
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173 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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174 {
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175 LOG(WARNING) << "Creating level " << level << " of size "
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176 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
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177 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
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178 }
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179
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180 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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181 {
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182 LOG(WARNING) << "Transcoding level " << level;
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183
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184 unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth());
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185 unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight());
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186
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187 for (unsigned int tileY = 0; tileY < countY; tileY++)
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188 {
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189 for (unsigned int tileX = 0; tileX < countX; tileX++)
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190 {
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191 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
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192 std::string tile;
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193
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194 if (source.ReadRawTile(tile, level, tileX, tileY))
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195 {
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196 target.WriteRawTile(tile, source.GetImageCompression(), level, tileX, tileY);
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197 }
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198 else
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199 {
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200 target.EncodeTile(*empty, level, tileX, tileY);
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201 }
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202 }
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203 }
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204
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205 target.Flush();
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206 }
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207 }
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208
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209
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210 static void RunReencode(OrthancWSI::ITiledPyramid& source,
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211 const boost::program_options::variables_map& options)
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212 {
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213 OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(),
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214 source.GetPixelFormat(),
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215 OrthancWSI::ImageCompression_Jpeg,
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216 source.GetTileWidth(),
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217 source.GetTileHeight());
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218
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219 if (options.count("jpeg-quality"))
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220 {
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221 target.SetJpegQuality(options["jpeg-quality"].as<int>());
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222 }
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223
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224 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
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225
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226 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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227 {
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228 LOG(WARNING) << "Creating level " << level << " of size "
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229 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
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230 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
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231 }
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232
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233 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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234 {
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235 LOG(WARNING) << "Reencoding level " << level;
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236
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237 unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth());
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238 unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight());
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239
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240 for (unsigned int tileY = 0; tileY < countY; tileY++)
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241 {
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242 for (unsigned int tileX = 0; tileX < countX; tileX++)
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243 {
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244 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
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245
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246 std::auto_ptr<Orthanc::ImageAccessor> tile(source.DecodeTile(level, tileX, tileY));
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247 if (tile.get() == NULL)
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248 {
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249 target.EncodeTile(*empty, level, tileX, tileY);
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250 }
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251 else
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252 {
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253 target.EncodeTile(*tile, level, tileX, tileY);
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254 }
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255 }
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256 }
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257
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258 target.Flush();
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259 }
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260 }
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261
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262
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263
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264 int main(int argc, char* argv[])
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265 {
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266 OrthancWSI::ApplicationToolbox::GlobalInitialize();
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267
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268 int exitStatus = 0;
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269 boost::program_options::variables_map options;
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270
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271 try
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272 {
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273 if (ParseParameters(exitStatus, options, argc, argv))
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274 {
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275 Orthanc::WebServiceParameters params;
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276
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277 if (options.count("orthanc"))
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278 {
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279 params.SetUrl(options["orthanc"].as<std::string>());
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280 }
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281
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282 if (options.count("username"))
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283 {
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284 params.SetUsername(options["username"].as<std::string>());
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285 }
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286
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287 if (options.count("password"))
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288 {
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289 params.SetPassword(options["password"].as<std::string>());
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290 }
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291
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292 OrthancWSI::CurlOrthancConnection orthanc(params);
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293 OrthancWSI::DicomPyramid source(orthanc, options["input"].as<std::string>());
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294
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295 if (options.count("reencode") &&
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296 options["reencode"].as<bool>())
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297 {
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298 RunReencode(source, options);
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299 }
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300 else
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301 {
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302 RunTranscode(source, options);
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303 }
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304 }
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305 }
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306 catch (Orthanc::OrthancException& e)
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307 {
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308 LOG(ERROR) << "Terminating on exception: " << e.What();
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309
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310 if (options.count("reencode") == 0)
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311 {
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312 LOG(ERROR) << "Consider using option \"--reencode\"";
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313 }
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314
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315 exitStatus = -1;
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316 }
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317
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318 OrthancWSI::ApplicationToolbox::GlobalFinalize();
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319
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320 return exitStatus;
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321 }
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