Mercurial > hg > orthanc-stl
annotate Sources/Plugin.cpp @ 35:ee3bc8f7df5b
reorganization
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 04 Apr 2024 20:37:08 +0200 |
parents | bee2017f3088 |
children | 13698d34e059 |
rev | line source |
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1 /** |
24 | 2 * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
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3 * SPDX-License-Identifier: GPL-3.0-or-later |
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4 */ |
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5 |
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6 /** |
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7 * STL plugin for Orthanc |
24 | 8 * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
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9 * |
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10 * This program is free software: you can redistribute it and/or |
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11 * modify it under the terms of the GNU General Public License as |
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12 * published by the Free Software Foundation, either version 3 of the |
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13 * License, or (at your option) any later version. |
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14 * |
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15 * This program is distributed in the hope that it will be useful, but |
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16 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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18 * General Public License for more details. |
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19 * |
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20 * You should have received a copy of the GNU General Public License |
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21 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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22 **/ |
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23 |
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24 |
35 | 25 #include "StructureSetGeometry.h" |
26 #include "StructureSet.h" | |
34 | 27 #include "STLToolbox.h" |
33 | 28 #include "StructurePolygon.h" |
32 | 29 #include "VTKToolbox.h" |
30 #include "Vector3D.h" | |
31 #include "Toolbox.h" | |
32 #include "Extent2D.h" | |
33 | |
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34 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
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35 |
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36 #include <EmbeddedResources.h> |
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37 |
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38 #include <DicomFormat/DicomInstanceHasher.h> |
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39 #include <DicomParsing/FromDcmtkBridge.h> |
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40 #include <DicomParsing/ParsedDicomFile.h> |
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41 #include <Images/ImageProcessing.h> |
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42 #include <Logging.h> |
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43 #include <OrthancFramework.h> |
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44 #include <SerializationToolbox.h> |
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45 #include <SystemToolbox.h> |
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46 |
33 | 47 #include <vtkNew.h> |
48 | |
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49 #include <boost/thread/shared_mutex.hpp> |
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50 |
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51 #define ORTHANC_PLUGIN_NAME "stl" |
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52 |
6 | 53 |
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54 // Forward declaration |
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55 void ReadStaticAsset(std::string& target, |
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56 const std::string& path); |
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57 |
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58 |
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59 /** |
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60 * As the Three.js static assets are gzipped by the |
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61 * "EmbedStaticAssets.py" script, we use a cache to maintain the |
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62 * uncompressed assets in order to avoid multiple gzip decodings. |
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63 **/ |
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64 class ResourcesCache : public boost::noncopyable |
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65 { |
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66 private: |
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67 typedef std::map<std::string, std::string*> Content; |
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68 |
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69 boost::shared_mutex mutex_; |
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70 Content content_; |
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71 |
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72 public: |
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73 ~ResourcesCache() |
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74 { |
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75 for (Content::iterator it = content_.begin(); it != content_.end(); ++it) |
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76 { |
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77 assert(it->second != NULL); |
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78 delete it->second; |
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79 } |
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80 } |
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81 |
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82 void Answer(OrthancPluginRestOutput* output, |
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83 const std::string& path) |
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84 { |
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85 const std::string mime = Orthanc::EnumerationToString(Orthanc::SystemToolbox::AutodetectMimeType(path)); |
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86 |
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87 { |
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88 // Check whether the cache already contains the resource |
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89 boost::shared_lock<boost::shared_mutex> lock(mutex_); |
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90 |
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91 Content::const_iterator found = content_.find(path); |
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92 |
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93 if (found != content_.end()) |
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94 { |
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95 assert(found->second != NULL); |
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96 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, found->second->c_str(), found->second->size(), mime.c_str()); |
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97 return; |
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98 } |
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99 } |
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100 |
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101 // This resource has not been cached yet |
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102 |
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103 std::unique_ptr<std::string> item(new std::string); |
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104 ReadStaticAsset(*item, path); |
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105 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, item->c_str(), item->size(), mime.c_str()); |
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106 |
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107 { |
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108 // Store the resource into the cache |
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109 boost::unique_lock<boost::shared_mutex> lock(mutex_); |
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110 |
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111 if (content_.find(path) == content_.end()) |
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112 { |
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113 content_[path] = item.release(); |
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114 } |
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115 } |
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116 } |
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117 }; |
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118 |
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119 |
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120 static ResourcesCache cache_; |
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121 static bool hasCreateDicomStl_; |
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122 |
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123 void ServeFile(OrthancPluginRestOutput* output, |
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124 const char* url, |
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125 const OrthancPluginHttpRequest* request) |
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126 { |
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127 if (request->method != OrthancPluginHttpMethod_Get) |
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128 { |
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129 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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130 return; |
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131 } |
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132 |
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133 std::string file = request->groups[0]; |
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134 |
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135 if (file == "viewer.html") |
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136 { |
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137 std::string s; |
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138 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_HTML); |
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139 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Html)); |
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140 } |
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141 else if (file == "viewer.js") |
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142 { |
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143 std::string s; |
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144 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_JS); |
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145 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_JavaScript)); |
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146 } |
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147 else |
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148 { |
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149 cache_.Answer(output, file); |
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150 } |
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151 } |
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152 |
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153 |
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154 |
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155 |
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156 #include <dcmtk/dcmdata/dcfilefo.h> |
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157 #include <dcmtk/dcmdata/dcsequen.h> |
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158 #include <dcmtk/dcmdata/dcuid.h> |
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159 |
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160 |
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161 class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller |
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162 { |
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163 private: |
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164 Orthanc::ImageAccessor& target_; |
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165 |
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166 public: |
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167 XorFiller(Orthanc::ImageAccessor& target) : |
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168 target_(target) |
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169 { |
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170 } |
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171 |
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172 virtual void Fill(int y, |
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173 int x1, |
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174 int x2) ORTHANC_OVERRIDE |
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175 { |
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176 assert(x1 <= x2); |
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177 |
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178 if (y >= 0 && |
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179 y < static_cast<int>(target_.GetHeight())) |
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180 { |
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181 x1 = std::max(x1, 0); |
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182 x2 = std::min(x2, static_cast<int>(target_.GetWidth()) - 1); |
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183 |
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184 uint8_t* p = reinterpret_cast<uint8_t*>(target_.GetRow(y)) + x1; |
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185 |
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186 for (int i = x1; i <= x2; i++, p++) |
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187 { |
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188 *p = (*p ^ 0xff); |
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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 |
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194 |
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195 static Orthanc::ParsedDicomFile* LoadInstance(const std::string& instanceId) |
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196 { |
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197 std::string dicom; |
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198 |
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199 if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false)) |
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200 { |
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201 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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202 } |
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203 else |
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204 { |
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205 return new Orthanc::ParsedDicomFile(dicom); |
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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 GetReferencedVolumeAxes(Vector3D& axisX, |
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211 Vector3D& axisY, |
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212 const StructureSet& structureSet) |
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213 { |
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214 // This is a rough guess for the X/Y axes |
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215 axisX = Vector3D(1, 0, 0); |
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216 axisY = Vector3D(0, 1, 0); |
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217 |
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218 // Look for one instance from the referenced volume |
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219 const std::string& sopInstanceUid = structureSet.GetPolygon(0).GetReferencedSopInstanceUid(); |
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220 |
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221 Json::Value response; |
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222 if (OrthancPlugins::RestApiPost(response, "/tools/lookup", sopInstanceUid, false)) |
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223 { |
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224 if (response.type() != Json::arrayValue) |
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225 { |
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226 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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227 } |
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228 |
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229 bool first = true; |
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230 |
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231 for (Json::Value::ArrayIndex i = 0; i < response.size(); i++) |
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232 { |
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233 if (response[i].type() != Json::objectValue) |
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234 { |
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235 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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236 } |
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237 |
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238 if (Orthanc::SerializationToolbox::ReadString(response[i], "Type") == "Instance") |
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239 { |
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240 if (first) |
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241 { |
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242 const std::string& instanceId = Orthanc::SerializationToolbox::ReadString(response[i], "ID"); |
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243 std::unique_ptr<Orthanc::ParsedDicomFile> reference(LoadInstance(instanceId)); |
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244 |
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245 std::string imageOrientation; |
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246 if (reference->GetTagValue(imageOrientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT)) |
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247 { |
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248 std::vector<std::string> items; |
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249 Orthanc::Toolbox::TokenizeString(items, imageOrientation, '\\'); |
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250 |
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251 double x1, x2, x3, y1, y2, y3; |
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252 |
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253 if (items.size() == 6 && |
33 | 254 STLToolbox::MyParseDouble(x1, items[0]) && |
255 STLToolbox::MyParseDouble(x2, items[1]) && | |
256 STLToolbox::MyParseDouble(x3, items[2]) && | |
257 STLToolbox::MyParseDouble(y1, items[3]) && | |
258 STLToolbox::MyParseDouble(y2, items[4]) && | |
259 STLToolbox::MyParseDouble(y3, items[5])) | |
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260 { |
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261 axisX = Vector3D(x1, x2, x3); |
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262 axisY = Vector3D(y1, y2, y3); |
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263 } |
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264 } |
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265 } |
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266 else |
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267 { |
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268 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, |
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269 "Multiple instances with the same SOP Instance UID"); |
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270 } |
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271 } |
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272 } |
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273 } |
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274 } |
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275 |
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276 |
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277 static bool EncodeStructureSetMesh(std::string& stl, |
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278 const StructureSet& structureSet, |
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279 const StructureSetGeometry& geometry, |
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280 const std::set<std::string>& roiNames, |
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281 unsigned int resolution, |
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282 bool smooth) |
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283 { |
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284 if (resolution < 1 || |
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285 structureSet.GetPolygonsCount() < 1) |
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286 { |
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287 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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288 } |
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289 |
33 | 290 if (!STLToolbox::IsNear(1, geometry.GetSlicesNormal().ComputeNorm())) |
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291 { |
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292 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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293 } |
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294 |
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295 Vector3D axisX, axisY; |
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296 GetReferencedVolumeAxes(axisX, axisY, structureSet); |
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297 |
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298 Vector3D axisZ = Vector3D::CrossProduct(axisX, axisY); |
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299 |
33 | 300 if (!STLToolbox::IsNear(1, axisX.ComputeNorm()) || |
301 !STLToolbox::IsNear(1, axisY.ComputeNorm()) || | |
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302 !Vector3D::AreParallel(axisZ, geometry.GetSlicesNormal())) |
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303 { |
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304 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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305 } |
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306 |
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307 Extent2D extent; |
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308 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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309 { |
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310 structureSet.GetPolygon(i).Add(extent, axisX, axisY); |
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311 } |
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312 |
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313 const int depth = geometry.GetSlicesCount(); |
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314 |
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315 vtkNew<vtkImageData> volume; |
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316 volume->SetDimensions(resolution, resolution, depth); |
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317 volume->AllocateScalars(VTK_UNSIGNED_CHAR, 1); |
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318 |
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319 assert(sizeof(unsigned char) == 1); |
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320 memset(volume->GetScalarPointer(), 0, resolution * resolution * depth); |
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321 |
30 | 322 const double pixelSpacingX = extent.GetWidth() / static_cast<double>(resolution); |
323 const double pixelSpacingY = extent.GetHeight() / static_cast<double>(resolution); | |
324 const double pixelSpacingZ = geometry.GetSlicesSpacing(); | |
325 | |
326 bool first = true; | |
327 | |
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328 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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329 { |
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330 const StructurePolygon& polygon = structureSet.GetPolygon(i); |
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331 if (roiNames.find(polygon.GetRoiName()) != roiNames.end()) |
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332 { |
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333 // This polygon corresponds to a ROI of interest |
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334 |
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335 size_t z; |
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336 if (geometry.LookupSliceIndex(z, polygon)) |
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337 { |
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338 std::vector<Orthanc::ImageProcessing::ImagePoint> points; |
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339 points.reserve(polygon.GetPointsCount()); |
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340 |
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341 for (size_t j = 0; j < polygon.GetPointsCount(); j++) |
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342 { |
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343 const Vector3D& point = polygon.GetPoint(j); |
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344 double x = (Vector3D::DotProduct(point, axisX) - extent.GetMinX()) / extent.GetWidth() * static_cast<double>(resolution); |
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345 double y = (Vector3D::DotProduct(point, axisY) - extent.GetMinY()) / extent.GetHeight() * static_cast<double>(resolution); |
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346 points.push_back(Orthanc::ImageProcessing::ImagePoint(static_cast<int32_t>(std::floor(x)), |
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347 static_cast<int32_t>(std::floor(y)))); |
30 | 348 |
349 if (first) | |
350 { | |
351 first = false; | |
352 volume->SetOrigin(point.GetX() - x * pixelSpacingX, | |
353 point.GetY() - y * pixelSpacingY, | |
354 point.GetZ() - z * pixelSpacingZ); | |
355 } | |
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356 } |
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357 |
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358 Orthanc::ImageAccessor slice; |
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359 slice.AssignWritable(Orthanc::PixelFormat_Grayscale8, resolution, resolution, resolution /* pitch */, |
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360 reinterpret_cast<uint8_t*>(volume->GetScalarPointer()) + z * resolution * resolution); |
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361 |
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362 XorFiller filler(slice); |
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363 Orthanc::ImageProcessing::FillPolygon(filler, points); |
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364 } |
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365 } |
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366 } |
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367 |
30 | 368 volume->SetSpacing(pixelSpacingX, pixelSpacingY, pixelSpacingZ); |
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369 |
32 | 370 return VTKToolbox::EncodeVolume(stl, volume.Get(), resolution, smooth); |
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371 } |
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372 |
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373 |
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374 void ListStructures(OrthancPluginRestOutput* output, |
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375 const char* url, |
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376 const OrthancPluginHttpRequest* request) |
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377 { |
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378 if (request->method != OrthancPluginHttpMethod_Get) |
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379 { |
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380 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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381 return; |
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382 } |
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383 |
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384 const std::string instanceId(request->groups[0]); |
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385 |
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386 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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387 |
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388 std::set<std::string> names; |
33 | 389 StructureSet::ListStructuresNames(names, *dicom); |
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390 |
3
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391 Json::Value answer = Json::arrayValue; |
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392 |
3
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393 for (std::set<std::string>::const_iterator it = names.begin(); it != names.end(); ++it) |
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394 { |
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395 answer.append(*it); |
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396 } |
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397 |
3
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398 std::string s = answer.toStyledString(); |
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399 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
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400 } |
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401 |
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402 |
4
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403 static void AddDefaultTagValue(Json::Value& target, |
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404 const Orthanc::DicomTag& tag, |
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405 const std::string& value) |
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406 { |
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407 if (!target.isMember(tag.Format())) |
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408 { |
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409 target[tag.Format()] = value; |
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410 } |
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411 } |
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412 |
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413 |
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414 static void AddDefaultTagValue(Json::Value& target, |
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415 const DcmTagKey& tag, |
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416 const std::string& value) |
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417 { |
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418 AddDefaultTagValue(target, Orthanc::DicomTag(tag.getGroup(), tag.getElement()), value); |
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419 } |
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420 |
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421 |
7 | 422 static void CallCreateDicom(Json::Value& answer, |
423 const std::string& stl, | |
424 const Json::Value& body, | |
425 const std::string& parentStudy, | |
426 const std::string& defaultSeriesDescription, | |
427 const std::string& defaultFrameOfReferenceUid, | |
428 const std::string& defaultTitle) | |
429 { | |
430 static const char* const KEY_TAGS = "Tags"; | |
431 | |
432 Json::Value normalized = Json::objectValue; | |
433 | |
434 if (body.isMember(KEY_TAGS)) | |
435 { | |
436 const Json::Value& tags = body[KEY_TAGS]; | |
437 | |
438 if (tags.type() != Json::objectValue) | |
439 { | |
440 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Tags must be provided as a JSON object"); | |
441 } | |
442 | |
443 std::vector<std::string> keys = tags.getMemberNames(); | |
444 for (size_t i = 0; i < keys.size(); i++) | |
445 { | |
446 const Orthanc::DicomTag tag = Orthanc::FromDcmtkBridge::ParseTag(keys[i]); | |
447 normalized[tag.Format()] = tags[keys[i]]; | |
448 } | |
449 } | |
450 | |
451 if (!normalized.isMember(Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format())) | |
452 { | |
453 normalized[Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format()] = defaultSeriesDescription; | |
454 } | |
455 | |
456 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_SERIES_NUMBER, "1"); | |
457 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, defaultFrameOfReferenceUid); | |
458 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_INSTANCE_NUMBER, "1"); | |
459 | |
460 AddDefaultTagValue(normalized, DCM_BurnedInAnnotation, "NO"); | |
461 AddDefaultTagValue(normalized, DCM_DeviceSerialNumber, ORTHANC_STL_VERSION); | |
462 AddDefaultTagValue(normalized, DCM_DocumentTitle, defaultTitle); | |
463 AddDefaultTagValue(normalized, DCM_Manufacturer, "Orthanc STL plugin"); | |
464 AddDefaultTagValue(normalized, DCM_ManufacturerModelName, "Orthanc STL plugin"); | |
465 AddDefaultTagValue(normalized, DCM_PositionReferenceIndicator, ""); | |
466 AddDefaultTagValue(normalized, DCM_SoftwareVersions, ORTHANC_STL_VERSION); | |
467 AddDefaultTagValue(normalized, DCM_ConceptNameCodeSequence, ""); | |
468 | |
469 std::string date, time; | |
470 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); | |
471 AddDefaultTagValue(normalized, DCM_AcquisitionDateTime, date + time); | |
472 | |
473 const Orthanc::DicomTag MEASUREMENT_UNITS_CODE_SEQUENCE(DCM_MeasurementUnitsCodeSequence.getGroup(), | |
474 DCM_MeasurementUnitsCodeSequence.getElement()); | |
475 | |
476 if (!normalized.isMember(MEASUREMENT_UNITS_CODE_SEQUENCE.Format())) | |
477 { | |
478 Json::Value item; | |
479 item["CodeValue"] = "mm"; | |
480 item["CodingSchemeDesignator"] = "UCUM"; | |
481 item["CodeMeaning"] = defaultTitle; | |
482 | |
483 normalized[MEASUREMENT_UNITS_CODE_SEQUENCE.Format()].append(item); | |
484 } | |
485 | |
486 std::string content; | |
487 Orthanc::Toolbox::EncodeDataUriScheme(content, Orthanc::MIME_STL, stl); | |
488 | |
489 Json::Value create; | |
490 create["Content"] = content; | |
491 create["Parent"] = parentStudy; | |
492 create["Tags"] = normalized; | |
493 | |
494 if (!OrthancPlugins::RestApiPost(answer, "/tools/create-dicom", create.toStyledString(), false)) | |
495 { | |
496 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Cannot create DICOM from STL"); | |
497 } | |
498 } | |
499 | |
500 | |
501 void EncodeStructureSet(OrthancPluginRestOutput* output, | |
502 const char* url, | |
503 const OrthancPluginHttpRequest* request) | |
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504 { |
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505 static const char* const KEY_INSTANCE = "Instance"; |
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506 static const char* const KEY_RESOLUTION = "Resolution"; |
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507 static const char* const KEY_ROI_NAMES = "RoiNames"; |
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508 static const char* const KEY_SMOOTH = "Smooth"; |
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509 static const char* const KEY_STRICT = "Strict"; |
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510 |
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511 if (request->method != OrthancPluginHttpMethod_Post) |
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512 { |
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513 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
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514 return; |
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515 } |
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516 |
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517 Json::Value body; |
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518 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
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519 { |
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520 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
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521 } |
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522 |
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523 const std::string instanceId = Orthanc::SerializationToolbox::ReadString(body, KEY_INSTANCE); |
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524 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
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525 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
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526 true /* smooth by default */); |
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527 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
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528 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
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529 256 /* default value */); |
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530 const bool strict = (body.isMember(KEY_STRICT) ? |
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531 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_STRICT) : |
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532 true /* strict by default */); |
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533 |
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534 std::set<std::string> roiNames; |
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535 Orthanc::SerializationToolbox::ReadSetOfStrings(roiNames, body, KEY_ROI_NAMES); |
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536 |
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537 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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538 |
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539 StructureSet structureSet(*dicom); |
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540 |
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541 StructureSetGeometry geometry(structureSet, strict); |
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542 |
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543 std::string stl; |
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544 if (!EncodeStructureSetMesh(stl, structureSet, geometry, roiNames, resolution, smooth)) |
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545 { |
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546 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from RT-STRUCT"); |
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547 } |
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|
548 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
549 { |
7 | 550 std::string seriesDescription; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
551 |
7 | 552 if (dicom->GetTagValue(seriesDescription, Orthanc::DICOM_TAG_SERIES_DESCRIPTION)) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
553 { |
7 | 554 seriesDescription += ": "; |
555 } | |
556 else | |
557 { | |
558 seriesDescription.clear(); | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
559 } |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
560 |
7 | 561 bool first = true; |
562 for (std::set<std::string>::const_iterator it = roiNames.begin(); it != roiNames.end(); ++it) | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
563 { |
7 | 564 if (first) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
565 { |
7 | 566 first = false; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
567 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
568 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
569 { |
7 | 570 seriesDescription += ", "; |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
571 } |
2
2bdb9acb7dcf
added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
572 |
7 | 573 seriesDescription += *it; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
574 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
575 |
7 | 576 std::string frameOfReferenceUid; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
577 if (structureSet.HasFrameOfReferenceUid()) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
578 { |
7 | 579 frameOfReferenceUid = structureSet.GetFrameOfReferenceUid(); |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
580 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
581 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
582 { |
7 | 583 frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
584 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
585 |
7 | 586 Json::Value answer; |
587 CallCreateDicom(answer, stl, body, structureSet.HashStudy(), seriesDescription, | |
588 frameOfReferenceUid, "STL model generated from DICOM RT-STRUCT"); | |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
589 |
7 | 590 std::string s = answer.toStyledString(); |
591 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
592 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
593 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
594 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
595 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
596 void ExtractStl(OrthancPluginRestOutput* output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
597 const char* url, |
0fb06c6a6c87
added route "/instances/{id}/stl"
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diff
changeset
|
598 const OrthancPluginHttpRequest* request) |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
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diff
changeset
|
599 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
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diff
changeset
|
600 if (request->method != OrthancPluginHttpMethod_Get) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
601 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
602 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
0fb06c6a6c87
added route "/instances/{id}/stl"
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diff
changeset
|
603 return; |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
2
diff
changeset
|
604 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
605 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
606 const std::string instanceId(request->groups[0]); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
607 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
608 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
609 DcmDataset& dataset = *dicom->GetDcmtkObject().getDataset(); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
610 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
611 std::string stl; |
33 | 612 if (STLToolbox::GetStringValue(dataset, DCM_MIMETypeOfEncapsulatedDocument) != Orthanc::MIME_STL || |
613 STLToolbox::GetStringValue(dataset, DCM_SOPClassUID) != UID_EncapsulatedSTLStorage || | |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
614 !dicom->GetTagValue(stl, Orthanc::DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
615 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
616 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "DICOM instance not encapsulating a STL model: " + instanceId); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
617 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
618 else |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
619 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
620 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
621 stl.empty() ? NULL : stl.c_str(), stl.size(), Orthanc::MIME_STL); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
622 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
623 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
624 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
625 |
6 | 626 |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
627 void EncodeNifti(OrthancPluginRestOutput* output, |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
628 const char* url, |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
629 const OrthancPluginHttpRequest* request) |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
630 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
631 static const char* const KEY_NIFTI = "Nifti"; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
632 static const char* const KEY_RESOLUTION = "Resolution"; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
633 static const char* const KEY_PARENT_STUDY = "ParentStudy"; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
634 static const char* const KEY_SMOOTH = "Smooth"; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
635 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
636 if (request->method != OrthancPluginHttpMethod_Post) |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
637 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
638 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
639 return; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
640 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
641 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
642 Json::Value body; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
643 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
644 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
645 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
646 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
647 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
648 std::string mime, nifti; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
649 if (!Orthanc::Toolbox::DecodeDataUriScheme(mime, nifti, Orthanc::SerializationToolbox::ReadString(body, KEY_NIFTI))) |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
650 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
651 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Missing the \"Nifti\" argument containing the NIfTI file"); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
652 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
653 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
654 const std::string parentStudy = Orthanc::SerializationToolbox::ReadString(body, KEY_PARENT_STUDY); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
655 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
656 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
657 true /* smooth by default */); |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
658 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
659 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
660 256 /* default value */); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
661 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
662 vtkNew<vtkImageData> volume; |
32 | 663 VTKToolbox::LoadNifti(volume.Get(), nifti); |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
664 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
665 std::string stl; |
32 | 666 if (!VTKToolbox::EncodeVolume(stl, volume.Get(), resolution, smooth)) |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
667 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
668 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from NIfTI"); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
669 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
670 else |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
671 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
672 const std::string title = "STL model generated from NIfTI"; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
673 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
674 const std::string frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
675 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
676 Json::Value answer; |
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677 CallCreateDicom(answer, stl, body, parentStudy, title, frameOfReferenceUid, title); |
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678 |
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679 std::string s = answer.toStyledString(); |
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680 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
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681 } |
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682 } |
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683 |
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684 |
0
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685 extern "C" |
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686 { |
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687 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) |
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688 { |
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689 OrthancPlugins::SetGlobalContext(context); |
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690 |
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691 /* Check the version of the Orthanc core */ |
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692 if (OrthancPluginCheckVersion(OrthancPlugins::GetGlobalContext()) == 0) |
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693 { |
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694 char info[1024]; |
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695 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", |
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696 OrthancPlugins::GetGlobalContext()->orthancVersion, |
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697 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
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698 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, |
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699 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); |
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700 OrthancPluginLogError(OrthancPlugins::GetGlobalContext(), info); |
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701 return -1; |
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702 } |
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703 |
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704 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
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705 Orthanc::Logging::InitializePluginContext(context); |
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706 #else |
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707 Orthanc::Logging::Initialize(context); |
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708 #endif |
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709 |
1
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710 Orthanc::InitializeFramework("", false); |
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711 |
0
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712 hasCreateDicomStl_ = OrthancPlugins::CheckMinimalOrthancVersion(1, 12, 1); |
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713 |
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714 if (!hasCreateDicomStl_) |
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715 { |
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716 LOG(WARNING) << "Your version of Orthanc (" << std::string(context->orthancVersion) |
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717 << ") is insufficient to create DICOM STL, it should be above 1.12.1"; |
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718 } |
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719 |
25
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720 OrthancPlugins::SetDescription(ORTHANC_PLUGIN_NAME, "STL plugin for Orthanc."); |
0
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721 |
1
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722 OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/app/(.*)", true); |
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723 OrthancPlugins::RegisterRestCallback<ExtractStl>("/instances/([0-9a-f-]+)/stl", true); |
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724 OrthancPlugins::RegisterRestCallback<ListStructures>("/stl/rt-struct/([0-9a-f-]+)", true); |
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725 |
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726 if (hasCreateDicomStl_) |
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727 { |
8
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728 OrthancPlugins::RegisterRestCallback<EncodeStructureSet>("/stl/encode-rtstruct", true); |
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729 OrthancPlugins::RegisterRestCallback<EncodeNifti>("/stl/encode-nifti", true); |
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730 } |
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|
731 |
31
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|
732 OrthancPlugins::OrthancConfiguration globalConfiguration; |
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733 OrthancPlugins::OrthancConfiguration configuration; |
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734 globalConfiguration.GetSection(configuration, "STL"); |
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735 |
2
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736 // Extend the default Orthanc Explorer with custom JavaScript for STL |
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737 std::string explorer; |
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738 |
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|
739 { |
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740 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); |
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741 |
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742 std::map<std::string, std::string> dictionary; |
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743 dictionary["HAS_CREATE_DICOM_STL"] = (hasCreateDicomStl_ ? "true" : "false"); |
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744 dictionary["SHOW_NIFTI_BUTTON"] = (configuration.GetBooleanValue("NIfTI", false) ? "true" : "false"); |
2
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745 explorer = Orthanc::Toolbox::SubstituteVariables(explorer, dictionary); |
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|
746 |
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747 OrthancPlugins::ExtendOrthancExplorer(ORTHANC_PLUGIN_NAME, explorer); |
2
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748 } |
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|
749 |
0
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|
750 return 0; |
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|
751 } |
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|
752 |
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|
753 |
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754 ORTHANC_PLUGINS_API void OrthancPluginFinalize() |
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755 { |
1
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756 Orthanc::FinalizeFramework(); |
0
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757 } |
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|
758 |
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|
759 |
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760 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() |
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|
761 { |
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|
762 return ORTHANC_PLUGIN_NAME; |
0
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|
763 } |
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|
764 |
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diff
changeset
|
765 |
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766 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() |
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767 { |
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768 return ORTHANC_STL_VERSION; |
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|
769 } |
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770 } |