Mercurial > hg > orthanc-stone
annotate RenderingPlugin/Sources/Plugin.cpp @ 1931:00f123df5de3
added more tolerance wrt. bad values of the Pixel Spacing (0028,0030) tag
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 31 Mar 2022 13:34:24 +0200 |
parents | bd527bbc34df |
children | a601b8abc1cb |
rev | line source |
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1 /** |
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2 * Stone of Orthanc |
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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) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 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 General Public License as |
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10 * published by the Free Software Foundation, either version 3 of the |
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11 * 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 * 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 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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21 |
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22 |
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23 #include "OrthancPluginConnection.h" |
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24 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
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25 |
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26 #include "../../OrthancStone/Sources/Toolbox/AffineTransform2D.h" |
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27 #include "../../OrthancStone/Sources/Toolbox/DicomInstanceParameters.h" |
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28 #include "../../OrthancStone/Sources/Toolbox/DicomStructureSet.h" |
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29 |
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30 #include <EmbeddedResources.h> |
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31 |
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32 #include <Images/Image.h> |
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33 #include <Images/ImageProcessing.h> |
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34 #include <Images/PngWriter.h> |
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35 #include <Images/NumpyWriter.h> |
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36 #include <Logging.h> |
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37 #include <SerializationToolbox.h> |
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38 #include <Toolbox.h> |
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39 |
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40 #include <boost/math/constants/constants.hpp> |
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41 |
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42 |
1916 | 43 static const char* const INSTANCES = "Instances"; |
44 static const char* const RT_STRUCT_IOD = "1.2.840.10008.5.1.4.1.1.481.3"; | |
45 static const char* const SOP_CLASS_UID = "0008,0016"; | |
46 static const char* const STRUCTURES = "Structures"; | |
47 | |
48 | |
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49 class DicomStructureCache : public boost::noncopyable |
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50 { |
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51 private: |
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52 boost::mutex mutex_; |
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53 std::string instanceId_; |
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54 std::unique_ptr<OrthancStone::DicomStructureSet> rtstruct_; |
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55 |
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56 DicomStructureCache() // Singleton design pattern |
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57 { |
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58 } |
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59 |
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60 public: |
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61 void Invalidate(const std::string& instanceId) |
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62 { |
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63 boost::mutex::scoped_lock lock(mutex_); |
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64 |
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65 if (instanceId_ == instanceId) |
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66 { |
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67 rtstruct_.reset(NULL); |
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68 } |
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69 } |
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70 |
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71 static DicomStructureCache& GetSingleton() |
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72 { |
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73 static DicomStructureCache instance; |
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74 return instance; |
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75 } |
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76 |
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77 class Accessor : public boost::noncopyable |
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78 { |
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79 private: |
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80 boost::mutex::scoped_lock lock_; |
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81 std::string instanceId_; |
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82 OrthancStone::DicomStructureSet* rtstruct_; |
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83 |
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84 public: |
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85 Accessor(DicomStructureCache& that, |
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86 const std::string& instanceId) : |
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87 lock_(that.mutex_), |
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88 instanceId_(instanceId), |
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89 rtstruct_(NULL) |
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90 { |
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91 if (that.instanceId_ == instanceId && |
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92 that.rtstruct_.get() != NULL) |
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93 { |
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94 rtstruct_ = that.rtstruct_.get(); |
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95 } |
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96 else |
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97 { |
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98 try |
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99 { |
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100 OrthancStone::OrthancPluginConnection connection; |
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101 OrthancStone::FullOrthancDataset dataset(connection, "/instances/" + instanceId + "/tags?ignore-length=3006-0050"); |
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102 that.rtstruct_.reset(new OrthancStone::DicomStructureSet(dataset)); |
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103 that.instanceId_ = instanceId; |
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104 rtstruct_ = that.rtstruct_.get(); |
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105 } |
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106 catch (Orthanc::OrthancException&) |
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107 { |
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108 } |
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109 } |
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110 } |
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111 |
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112 const std::string& GetInstanceId() const |
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113 { |
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114 return instanceId_; |
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115 } |
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116 |
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117 bool IsValid() const |
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118 { |
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119 return rtstruct_ != NULL; |
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120 } |
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121 |
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122 OrthancStone::DicomStructureSet& GetRtStruct() const |
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123 { |
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124 if (IsValid()) |
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125 { |
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126 return *rtstruct_; |
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127 } |
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128 else |
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129 { |
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130 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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131 } |
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132 } |
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133 }; |
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134 }; |
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135 |
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136 |
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137 static Orthanc::PixelFormat Convert(OrthancPluginPixelFormat format) |
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138 { |
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139 switch (format) |
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140 { |
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141 case OrthancPluginPixelFormat_RGB24: |
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142 return Orthanc::PixelFormat_RGB24; |
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143 |
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144 case OrthancPluginPixelFormat_Grayscale8: |
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145 return Orthanc::PixelFormat_Grayscale8; |
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146 |
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147 case OrthancPluginPixelFormat_Grayscale16: |
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148 return Orthanc::PixelFormat_Grayscale16; |
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149 |
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150 case OrthancPluginPixelFormat_SignedGrayscale16: |
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151 return Orthanc::PixelFormat_SignedGrayscale16; |
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152 |
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153 default: |
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154 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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155 } |
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156 } |
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157 |
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158 |
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159 static bool ParseBoolean(const std::string& key, |
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160 const std::string& value) |
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161 { |
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162 bool result; |
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163 |
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164 if (Orthanc::SerializationToolbox::ParseBoolean(result, value)) |
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165 { |
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166 return result; |
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167 } |
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168 else |
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169 { |
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170 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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171 "Bad value for " + key + ": " + value); |
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172 } |
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173 } |
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174 |
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175 |
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176 static double ParseDouble(const std::string& key, |
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177 const std::string& value) |
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178 { |
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179 double result; |
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180 |
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181 if (Orthanc::SerializationToolbox::ParseDouble(result, value)) |
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182 { |
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183 return result; |
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184 } |
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185 else |
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186 { |
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187 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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188 "Bad value for " + key + ": " + value); |
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189 } |
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190 } |
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191 |
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192 |
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193 static unsigned int ParseUnsignedInteger(const std::string& key, |
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194 const std::string& value) |
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195 { |
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196 uint32_t result; |
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197 |
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198 if (Orthanc::SerializationToolbox::ParseUnsignedInteger32(result, value)) |
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199 { |
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200 return result; |
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201 } |
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202 else |
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203 { |
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204 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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205 "Bad value for " + key + ": " + value); |
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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 |
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211 class DataAugmentationParameters : public boost::noncopyable |
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212 { |
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213 private: |
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214 double angleRadians_; |
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215 double scaling_; |
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216 double offsetX_; |
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217 double offsetY_; |
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218 bool flipX_; |
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219 bool flipY_; |
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220 bool hasResize_; |
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221 unsigned int targetWidth_; |
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222 unsigned int targetHeight_; |
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223 |
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224 void ApplyInternal(Orthanc::ImageAccessor& target, |
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225 const Orthanc::ImageAccessor& source) |
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226 { |
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227 if (source.GetWidth() == 0 || |
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228 source.GetHeight() == 0) |
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229 { |
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230 Orthanc::ImageProcessing::Set(target, 0); // Clear the image |
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231 } |
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232 else if (target.GetWidth() == 0 || |
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233 target.GetHeight() == 0) |
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234 { |
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235 // Nothing to do |
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236 } |
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237 else |
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238 { |
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239 OrthancStone::AffineTransform2D transform = ComputeTransform(source.GetWidth(), source.GetHeight()); |
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240 |
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241 OrthancStone::ImageInterpolation interpolation; |
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242 |
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243 if (source.GetFormat() == Orthanc::PixelFormat_RGB24) |
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244 { |
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245 LOG(WARNING) << "Bilinear interpolation for color images is not implemented yet"; |
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246 interpolation = OrthancStone::ImageInterpolation_Nearest; |
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247 } |
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248 else |
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249 { |
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250 interpolation = OrthancStone::ImageInterpolation_Bilinear; |
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251 } |
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252 |
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253 transform.Apply(target, source, interpolation, true /* clear */); |
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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 Orthanc::ImageAccessor* ApplyUnchecked(const Orthanc::ImageAccessor& source) |
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259 { |
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260 std::unique_ptr<Orthanc::ImageAccessor> target; |
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261 |
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262 if (hasResize_) |
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263 { |
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264 target.reset(new Orthanc::Image(source.GetFormat(), targetWidth_, targetHeight_, false)); |
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265 } |
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266 else |
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267 { |
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268 target.reset(new Orthanc::Image(source.GetFormat(), source.GetWidth(), source.GetHeight(), false)); |
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269 } |
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270 |
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271 ApplyInternal(*target, source); |
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272 return target.release(); |
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273 } |
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274 |
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275 |
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276 public: |
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277 DataAugmentationParameters() |
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278 { |
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279 Clear(); |
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280 } |
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281 |
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282 |
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283 void Clear() |
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284 { |
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285 angleRadians_ = 0; |
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286 scaling_ = 1; |
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287 offsetX_ = 0; |
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288 offsetY_ = 0; |
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289 flipX_ = false; |
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290 flipY_ = false; |
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291 hasResize_ = false; |
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292 targetWidth_ = 0; |
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293 targetHeight_ = 0; |
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294 } |
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295 |
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296 |
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297 OrthancStone::AffineTransform2D ComputeTransform(unsigned int sourceWidth, |
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298 unsigned int sourceHeight) const |
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299 { |
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300 unsigned int w = (hasResize_ ? targetWidth_ : sourceWidth); |
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301 unsigned int h = (hasResize_ ? targetHeight_ : sourceHeight); |
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302 |
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303 if (w == 0 || |
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304 h == 0 || |
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305 sourceWidth == 0 || |
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306 sourceHeight == 0) |
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307 { |
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308 // Division by zero |
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309 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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310 } |
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311 |
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312 double r = std::min(static_cast<double>(w) / static_cast<double>(sourceWidth), |
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313 static_cast<double>(h) / static_cast<double>(sourceHeight)); |
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314 |
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315 OrthancStone::AffineTransform2D resize = OrthancStone::AffineTransform2D::Combine( |
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316 OrthancStone::AffineTransform2D::CreateOffset(static_cast<double>(w) / 2.0, |
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317 static_cast<double>(h) / 2.0), |
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318 OrthancStone::AffineTransform2D::CreateScaling(r, r)); |
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319 |
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320 OrthancStone::AffineTransform2D dataAugmentation = OrthancStone::AffineTransform2D::Combine( |
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321 OrthancStone::AffineTransform2D::CreateScaling(scaling_, scaling_), |
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322 OrthancStone::AffineTransform2D::CreateOffset(offsetX_, offsetY_), |
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323 OrthancStone::AffineTransform2D::CreateRotation(angleRadians_), |
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324 OrthancStone::AffineTransform2D::CreateOffset(-static_cast<double>(sourceWidth) / 2.0, |
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325 -static_cast<double>(sourceHeight) / 2.0), |
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326 OrthancStone::AffineTransform2D::CreateFlip(flipX_, flipY_, sourceWidth, sourceHeight)); |
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327 |
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328 return OrthancStone::AffineTransform2D::Combine(resize, dataAugmentation); |
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329 } |
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330 |
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331 |
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332 bool ParseParameter(const std::string& key, |
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333 const std::string& value) |
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334 { |
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335 if (key == "angle") |
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336 { |
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337 double angle = ParseDouble(key, value); |
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338 angleRadians_ = angle / 180.0 * boost::math::constants::pi<double>(); |
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339 return true; |
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340 } |
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341 else if (key == "scaling") |
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342 { |
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343 scaling_ = ParseDouble(key, value); |
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344 return true; |
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345 } |
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346 else if (key == "offset-x") |
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347 { |
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348 offsetX_ = ParseDouble(key, value); |
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349 return true; |
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350 } |
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351 else if (key == "offset-y") |
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352 { |
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353 offsetY_ = ParseDouble(key, value); |
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354 return true; |
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355 } |
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356 else if (key == "flip-x") |
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357 { |
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358 flipX_ = ParseBoolean(key, value); |
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359 return true; |
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360 } |
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361 else if (key == "flip-y") |
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362 { |
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363 flipY_ = ParseBoolean(key, value); |
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364 return true; |
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365 } |
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366 else if (key == "resize") |
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367 { |
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368 std::vector<std::string> tokens; |
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369 Orthanc::Toolbox::TokenizeString(tokens, value, ','); |
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370 if (tokens.size() != 2) |
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371 { |
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372 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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373 "Must provide two integers separated by commas in " + key + ": " + value); |
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374 } |
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375 else |
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376 { |
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377 targetWidth_ = ParseUnsignedInteger(key, tokens[0]); |
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378 targetHeight_ = ParseUnsignedInteger(key, tokens[1]); |
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379 hasResize_ = true; |
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380 return true; |
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381 } |
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382 } |
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383 else |
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384 { |
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385 return false; |
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386 } |
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387 } |
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388 |
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389 |
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390 Orthanc::ImageAccessor* Apply(const Orthanc::ImageAccessor& source) |
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391 { |
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392 if (source.GetFormat() != Orthanc::PixelFormat_RGB24 && |
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393 source.GetFormat() != Orthanc::PixelFormat_Float32) |
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394 { |
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395 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); |
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396 } |
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397 else |
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398 { |
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399 return ApplyUnchecked(source); |
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400 } |
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401 } |
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402 |
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403 |
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404 Orthanc::ImageAccessor* ApplyBinaryMask(const Orthanc::ImageAccessor& source) |
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405 { |
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406 if (source.GetFormat() != Orthanc::PixelFormat_Grayscale8) |
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407 { |
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408 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat, |
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409 "A segmentation mask should be a grayscale image"); |
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410 } |
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411 else |
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412 { |
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413 std::unique_ptr<Orthanc::ImageAccessor> target(ApplyUnchecked(source)); |
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414 |
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415 const unsigned int h = target->GetHeight(); |
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416 const unsigned int w = target->GetWidth(); |
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417 |
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418 // Apply thresholding to get back a binary image |
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419 for (unsigned int y = 0; y < h; y++) |
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420 { |
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421 uint8_t* p = reinterpret_cast<uint8_t*>(target->GetRow(y)); |
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422 for (unsigned int x = 0; x < w; x++, p++) |
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423 { |
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424 if (*p < 128) |
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425 { |
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426 *p = 0; |
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427 } |
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428 else |
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429 { |
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430 *p = 255; |
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431 } |
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432 } |
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433 } |
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434 |
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435 return target.release(); |
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436 } |
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437 } |
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438 }; |
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439 |
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440 |
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441 static OrthancStone::DicomInstanceParameters* GetInstanceParameters(const std::string& orthancId) |
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442 { |
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443 OrthancPlugins::MemoryBuffer tags; |
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444 if (!tags.RestApiGet("/instances/" + orthancId + "/tags", false)) |
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445 { |
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446 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem); |
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447 } |
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448 |
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449 Json::Value json; |
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450 tags.ToJson(json); |
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451 |
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452 Orthanc::DicomMap m; |
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453 m.FromDicomAsJson(json); |
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454 |
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455 return new OrthancStone::DicomInstanceParameters(m); |
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456 } |
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457 |
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458 |
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459 static void AnswerNumpyImage(OrthancPluginRestOutput* output, |
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460 const Orthanc::ImageAccessor& image, |
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461 bool compress) |
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462 { |
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463 std::string answer; |
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464 Orthanc::NumpyWriter writer; |
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465 writer.SetCompressed(compress); |
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466 Orthanc::IImageWriter::WriteToMemory(writer, answer, image); |
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467 |
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468 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, |
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469 answer.c_str(), answer.size(), "application/octet-stream"); |
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470 } |
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471 |
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472 |
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473 static void RenderNumpyFrame(OrthancPluginRestOutput* output, |
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474 const char* url, |
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475 const OrthancPluginHttpRequest* request) |
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476 { |
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477 DataAugmentationParameters dataAugmentation; |
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478 bool compress = false; |
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479 |
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480 for (uint32_t i = 0; i < request->getCount; i++) |
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481 { |
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482 std::string key(request->getKeys[i]); |
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483 std::string value(request->getValues[i]); |
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484 |
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485 if (!dataAugmentation.ParseParameter(key, value)) |
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486 { |
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487 if (key == "compress") |
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488 { |
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489 compress = ParseBoolean(key, value); |
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490 } |
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491 else |
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492 { |
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493 LOG(WARNING) << "Unsupported option for data augmentation: " << key; |
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494 } |
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495 } |
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496 } |
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497 |
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498 std::unique_ptr<OrthancStone::DicomInstanceParameters> parameters(GetInstanceParameters(request->groups[0])); |
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499 |
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500 OrthancPlugins::MemoryBuffer dicom; |
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501 dicom.GetDicomInstance(request->groups[0]); |
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502 |
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503 unsigned int frame = boost::lexical_cast<unsigned int>(request->groups[1]); |
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504 |
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505 OrthancPlugins::OrthancImage image; |
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506 image.DecodeDicomImage(dicom.GetData(), dicom.GetSize(), frame); |
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507 |
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508 Orthanc::ImageAccessor source; |
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509 source.AssignReadOnly(Convert(image.GetPixelFormat()), image.GetWidth(), image.GetHeight(), |
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510 image.GetPitch(), image.GetBuffer()); |
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511 |
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512 std::unique_ptr<Orthanc::ImageAccessor> modified; |
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513 |
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514 if (parameters->GetSopClassUid() == OrthancStone::SopClassUid_DicomSeg) |
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515 { |
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516 modified.reset(dataAugmentation.ApplyBinaryMask(source)); |
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517 } |
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518 else if (source.GetFormat() == Orthanc::PixelFormat_RGB24) |
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519 { |
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520 modified.reset(dataAugmentation.Apply(source)); |
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521 } |
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522 else |
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523 { |
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524 std::unique_ptr<Orthanc::ImageAccessor> converted(parameters->ConvertToFloat(source)); |
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525 assert(converted.get() != NULL); |
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526 |
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527 modified.reset(dataAugmentation.Apply(*converted)); |
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528 } |
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|
529 |
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|
530 assert(modified.get() != NULL); |
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|
531 AnswerNumpyImage(output, *modified, compress); |
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532 } |
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|
533 |
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534 |
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535 static bool IsRtStruct(const std::string& instanceId) |
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536 { |
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537 std::string s; |
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538 if (OrthancPlugins::RestApiGetString(s, "/instances/" + instanceId + "/content/" + SOP_CLASS_UID, false) && |
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539 !s.empty()) |
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540 { |
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541 if (s[s.size() - 1] == '\0') // Deal with DICOM padding |
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542 { |
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543 s.resize(s.size() - 1); |
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544 } |
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545 |
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546 return s == RT_STRUCT_IOD; |
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547 } |
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548 else |
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549 { |
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550 return false; |
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551 } |
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552 } |
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553 |
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554 |
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555 static void ListRtStruct(OrthancPluginRestOutput* output, |
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556 const char* url, |
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557 const OrthancPluginHttpRequest* request) |
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558 { |
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559 // This is a quick version of "/tools/find" on "SOPClassUID" (the |
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560 // latter would load all the DICOM files from disk) |
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561 |
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562 Json::Value series; |
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563 OrthancPlugins::RestApiGet(series, "/series?expand", false); |
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564 |
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565 if (series.type() != Json::arrayValue) |
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566 { |
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567 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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568 } |
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569 |
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570 Json::Value answer = Json::arrayValue; |
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571 |
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572 for (Json::Value::ArrayIndex i = 0; i < series.size(); i++) |
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573 { |
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574 if (series[i].type() != Json::objectValue || |
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575 !series[i].isMember(INSTANCES) || |
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576 series[i][INSTANCES].type() != Json::arrayValue) |
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577 { |
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578 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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579 } |
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580 |
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|
581 const Json::Value& instances = series[i][INSTANCES]; |
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582 |
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583 for (Json::Value::ArrayIndex j = 0; j < instances.size(); j++) |
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584 { |
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585 if (instances[j].type() != Json::stringValue) |
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586 { |
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587 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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588 } |
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589 } |
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590 |
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591 if (instances.size() > 0 && |
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592 IsRtStruct(instances[0].asString())) |
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593 { |
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594 for (Json::Value::ArrayIndex j = 0; j < instances.size(); j++) |
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595 { |
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596 answer.append(instances[j].asString()); |
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597 } |
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598 } |
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599 } |
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600 |
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601 std::string s = answer.toStyledString(); |
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602 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json"); |
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603 } |
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604 |
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605 |
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606 static void GetRtStruct(OrthancPluginRestOutput* output, |
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607 const char* url, |
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608 const OrthancPluginHttpRequest* request) |
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609 { |
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610 DicomStructureCache::Accessor accessor(DicomStructureCache::GetSingleton(), request->groups[0]); |
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611 |
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612 if (!accessor.IsValid()) |
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613 { |
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614 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem); |
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615 } |
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616 |
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617 Json::Value answer; |
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618 answer[STRUCTURES] = Json::arrayValue; |
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619 |
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620 for (size_t i = 0; i < accessor.GetRtStruct().GetStructuresCount(); i++) |
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621 { |
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622 Json::Value color = Json::arrayValue; |
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623 color.append(accessor.GetRtStruct().GetStructureColor(i).GetRed()); |
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624 color.append(accessor.GetRtStruct().GetStructureColor(i).GetGreen()); |
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625 color.append(accessor.GetRtStruct().GetStructureColor(i).GetBlue()); |
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626 |
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627 Json::Value structure; |
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628 structure["Name"] = accessor.GetRtStruct().GetStructureName(i); |
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629 structure["Interpretation"] = accessor.GetRtStruct().GetStructureInterpretation(i); |
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630 structure["Color"] = color; |
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631 |
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632 answer[STRUCTURES].append(structure); |
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633 } |
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634 |
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635 std::set<std::string> sopInstanceUids; |
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636 accessor.GetRtStruct().GetReferencedInstances(sopInstanceUids); |
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637 |
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638 answer[INSTANCES] = Json::arrayValue; |
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639 for (std::set<std::string>::const_iterator it = sopInstanceUids.begin(); it != sopInstanceUids.end(); ++it) |
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640 { |
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641 OrthancPlugins::OrthancString s; |
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642 s.Assign(OrthancPluginLookupInstance(OrthancPlugins::GetGlobalContext(), it->c_str())); |
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643 |
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644 std::string t; |
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645 s.ToString(t); |
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646 |
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647 answer[INSTANCES].append(t); |
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648 } |
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649 |
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650 std::string s = answer.toStyledString(); |
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651 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json"); |
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652 } |
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653 |
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654 |
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655 |
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656 static void RenderRtStruct(OrthancPluginRestOutput* output, |
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657 const char* url, |
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658 const OrthancPluginHttpRequest* request) |
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659 { |
1894
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660 class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller |
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661 { |
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662 private: |
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663 Orthanc::Image image_; |
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664 |
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665 public: |
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666 XorFiller(unsigned int width, |
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667 unsigned int height) : |
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668 image_(Orthanc::PixelFormat_Grayscale8, width, height, false) |
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669 { |
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670 Orthanc::ImageProcessing::Set(image_, 0); |
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671 } |
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672 |
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673 const Orthanc::ImageAccessor& GetImage() const |
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674 { |
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675 return image_; |
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676 } |
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677 |
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678 virtual void Fill(int y, |
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679 int x1, |
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680 int x2) ORTHANC_OVERRIDE |
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681 { |
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682 assert(x1 > 0 && |
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683 x1 <= x2 && |
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684 x2 < static_cast<int>(image_.GetWidth()) && |
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685 y > 0 && |
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686 y < static_cast<int>(image_.GetHeight())); |
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687 |
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688 uint8_t* p = reinterpret_cast<uint8_t*>(image_.GetRow(y)) + x1; |
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689 |
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690 for (int i = x1; i <= x2; i++, p++) |
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691 { |
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692 *p = (*p ^ 0xff); |
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693 } |
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694 } |
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695 }; |
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696 |
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697 DataAugmentationParameters dataAugmentation; |
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698 std::string structureName; |
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699 std::string instanceId; |
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700 bool compress = false; |
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701 |
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702 for (uint32_t i = 0; i < request->getCount; i++) |
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703 { |
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704 std::string key(request->getKeys[i]); |
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705 std::string value(request->getValues[i]); |
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706 |
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707 if (!dataAugmentation.ParseParameter(key, value)) |
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708 { |
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709 if (key == "structure") |
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710 { |
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711 structureName = value; |
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712 } |
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713 else if (key == "instance") |
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714 { |
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715 instanceId = value; |
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716 } |
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717 else if (key == "compress") |
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718 { |
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719 compress = ParseBoolean(key, value); |
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720 } |
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721 else |
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722 { |
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723 LOG(WARNING) << "Unsupported option: " << key; |
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724 } |
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725 } |
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726 } |
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|
727 |
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728 if (structureName.empty()) |
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729 { |
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730 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol, |
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731 "Missing option \"structure\" to provide the structure name"); |
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732 } |
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733 |
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734 if (instanceId.empty()) |
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735 { |
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736 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol, |
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737 "Missing option \"instance\" to provide the Orthanc identifier of the instance of interest"); |
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738 } |
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739 |
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740 std::unique_ptr<OrthancStone::DicomInstanceParameters> parameters(GetInstanceParameters(instanceId)); |
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741 |
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742 std::list< std::vector<OrthancStone::Vector> > polygons; |
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743 |
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744 { |
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745 DicomStructureCache::Accessor accessor(DicomStructureCache::GetSingleton(), request->groups[0]); |
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746 |
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747 if (!accessor.IsValid()) |
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748 { |
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749 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem); |
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750 } |
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751 |
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752 size_t structureIndex; |
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753 bool found = false; |
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754 for (size_t i = 0; i < accessor.GetRtStruct().GetStructuresCount(); i++) |
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755 { |
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756 if (accessor.GetRtStruct().GetStructureName(i) == structureName) |
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757 { |
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758 structureIndex = i; |
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759 found = true; |
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|
760 break; |
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|
761 } |
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|
762 } |
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|
763 |
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|
764 if (!found) |
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|
765 { |
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|
766 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, |
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|
767 "Unknown structure name: " + structureName); |
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|
768 } |
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|
769 |
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770 accessor.GetRtStruct().GetStructurePoints(polygons, structureIndex, parameters->GetSopInstanceUid()); |
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771 } |
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changeset
|
772 |
1895
14c8f339d480
removed redundant definitions Point2D, Point3D and Vector3D from DicomStructureSetUtils.h
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1894
diff
changeset
|
773 // We use a "XOR" filler for the polygons in order to deal with holes in the RT-STRUCT |
1894
438071a29f77
xor polygon filler for holes in rt-struct
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diff
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|
774 XorFiller filler(parameters->GetWidth(), parameters->GetHeight()); |
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775 OrthancStone::AffineTransform2D transform = dataAugmentation.ComputeTransform(parameters->GetWidth(), parameters->GetHeight()); |
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|
776 |
1888
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|
777 for (std::list< std::vector<OrthancStone::Vector> >::const_iterator |
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778 it = polygons.begin(); it != polygons.end(); ++it) |
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779 { |
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|
780 std::vector<Orthanc::ImageProcessing::ImagePoint> points; |
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781 points.reserve(it->size()); |
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782 |
1888
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|
783 for (size_t i = 0; i < it->size(); i++) |
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|
784 { |
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|
785 double x, y; |
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|
786 parameters->GetGeometry().ProjectPoint(x, y, (*it) [i]); |
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787 x /= parameters->GetPixelSpacingX(); |
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788 y /= parameters->GetPixelSpacingY(); |
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|
789 |
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790 transform.Apply(x, y); |
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|
791 |
1888
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|
792 points.push_back(Orthanc::ImageProcessing::ImagePoint(x, y)); |
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|
793 } |
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|
794 |
1894
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1892
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changeset
|
795 Orthanc::ImageProcessing::FillPolygon(filler, points); |
1885
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796 } |
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|
797 |
1894
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changeset
|
798 AnswerNumpyImage(output, filler.GetImage(), compress); |
1885
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|
799 } |
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|
800 |
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|
801 |
1890
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added classes BucketAccumulator1D/2D
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diff
changeset
|
802 |
1885
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|
803 OrthancPluginErrorCode OnChangeCallback(OrthancPluginChangeType changeType, |
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804 OrthancPluginResourceType resourceType, |
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805 const char* resourceId) |
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|
806 { |
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|
807 switch (changeType) |
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|
808 { |
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|
809 case OrthancPluginChangeType_Deleted: |
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|
810 if (resourceType == OrthancPluginResourceType_Instance) |
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|
811 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
812 DicomStructureCache::GetSingleton().Invalidate(resourceId); |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
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|
813 } |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
814 |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
815 break; |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
816 |
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1889
diff
changeset
|
817 case OrthancPluginChangeType_OrthancStarted: |
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1889
diff
changeset
|
818 { |
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1889
diff
changeset
|
819 DicomStructureCache::Accessor accessor(DicomStructureCache::GetSingleton(), "54460695-ba3885ee-ddf61ac0-f028e31d-a6e474d9"); |
1892
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
820 OrthancStone::LinearAlgebra::Print(accessor.GetRtStruct().GetEstimatedNormal()); |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
821 printf("Slice thickness: %f\n", accessor.GetRtStruct().GetEstimatedSliceThickness()); |
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1889
diff
changeset
|
822 break; |
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
823 } |
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1889
diff
changeset
|
824 |
1885
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
825 default: |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
826 break; |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
827 } |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
828 |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
829 return OrthancPluginErrorCode_Success; |
1882
4e80b8afd0da
numpy in rendering plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1877
diff
changeset
|
830 } |
4e80b8afd0da
numpy in rendering plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1877
diff
changeset
|
831 |
1877
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
832 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
833 extern "C" |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
834 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
835 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
836 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
837 OrthancPlugins::SetGlobalContext(context); |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
838 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
839 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
840 Orthanc::Logging::InitializePluginContext(context); |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
841 #else |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
842 Orthanc::Logging::Initialize(context); |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
843 #endif |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
844 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
845 /* Check the version of the Orthanc core */ |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
846 if (OrthancPluginCheckVersion(context) == 0) |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
847 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
848 char info[1024]; |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
849 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
850 context->orthancVersion, |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
851 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
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skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
852 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
853 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
854 OrthancPluginLogError(context, info); |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
855 return -1; |
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skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
856 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
857 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
858 try |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
859 { |
1882
4e80b8afd0da
numpy in rendering plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1877
diff
changeset
|
860 OrthancPlugins::RegisterRestCallback<RenderNumpyFrame>("/stone/instances/([^/]+)/frames/([0-9]+)/numpy", true); |
1885
ddaee6b96501
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
861 OrthancPlugins::RegisterRestCallback<ListRtStruct>("/stone/rt-struct", true); |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
862 OrthancPlugins::RegisterRestCallback<GetRtStruct>("/stone/rt-struct/([^/]+)/info", true); |
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retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
863 OrthancPlugins::RegisterRestCallback<RenderRtStruct>("/stone/rt-struct/([^/]+)/numpy", true); |
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1884
diff
changeset
|
864 OrthancPluginRegisterOnChangeCallback(context, OnChangeCallback); |
1877
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
865 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
866 catch (...) |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
867 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
868 OrthancPlugins::LogError("Exception while initializing the Stone Web viewer plugin"); |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
869 return -1; |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
870 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
871 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
872 return 0; |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
873 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
874 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
875 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
876 ORTHANC_PLUGINS_API void OrthancPluginFinalize() |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
877 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
878 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
879 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
880 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
881 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
882 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
883 return PLUGIN_NAME; |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
884 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
885 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
886 |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
887 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
888 { |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
889 return PLUGIN_VERSION; |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
890 } |
a2955abe4c2e
skeleton for the RenderingPlugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
891 } |