Mercurial > hg > orthanc-stl
annotate Sources/Plugin.cpp @ 31:ab231760799d
added button to import STL
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 04 Apr 2024 18:05:13 +0200 |
parents | 3570c23764d4 |
children | 976da5476810 |
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 |
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25 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
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26 |
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27 #include <EmbeddedResources.h> |
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28 |
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29 #include <DicomFormat/DicomInstanceHasher.h> |
6 | 30 #include <Compression/GzipCompressor.h> |
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31 #include <ChunkedBuffer.h> |
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32 #include <DicomParsing/FromDcmtkBridge.h> |
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33 #include <DicomParsing/ParsedDicomFile.h> |
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34 #include <Images/ImageProcessing.h> |
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35 #include <Logging.h> |
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36 #include <OrthancFramework.h> |
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37 #include <SerializationToolbox.h> |
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38 #include <SystemToolbox.h> |
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39 |
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40 #include <vtkImageConstantPad.h> |
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41 #include <vtkImageData.h> |
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42 #include <vtkImageResize.h> |
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43 #include <vtkMarchingCubes.h> |
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44 #include <vtkNew.h> |
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45 #include <vtkPolyData.h> |
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46 #include <vtkPolyDataNormals.h> |
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47 #include <vtkSmoothPolyDataFilter.h> |
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48 #include <vtkTriangle.h> |
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49 |
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50 #include <boost/thread/shared_mutex.hpp> |
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51 |
6 | 52 #include <nifti1_io.h> |
53 | |
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54 #define ORTHANC_PLUGIN_NAME "stl" |
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55 |
6 | 56 |
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57 // Forward declaration |
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58 void ReadStaticAsset(std::string& target, |
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59 const std::string& path); |
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60 |
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61 |
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62 /** |
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63 * As the Three.js static assets are gzipped by the |
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64 * "EmbedStaticAssets.py" script, we use a cache to maintain the |
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65 * uncompressed assets in order to avoid multiple gzip decodings. |
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66 **/ |
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67 class ResourcesCache : public boost::noncopyable |
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68 { |
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69 private: |
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70 typedef std::map<std::string, std::string*> Content; |
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71 |
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72 boost::shared_mutex mutex_; |
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73 Content content_; |
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74 |
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75 public: |
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76 ~ResourcesCache() |
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77 { |
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78 for (Content::iterator it = content_.begin(); it != content_.end(); ++it) |
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79 { |
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80 assert(it->second != NULL); |
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81 delete it->second; |
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82 } |
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83 } |
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84 |
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85 void Answer(OrthancPluginRestOutput* output, |
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86 const std::string& path) |
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87 { |
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88 const std::string mime = Orthanc::EnumerationToString(Orthanc::SystemToolbox::AutodetectMimeType(path)); |
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89 |
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90 { |
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91 // Check whether the cache already contains the resource |
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92 boost::shared_lock<boost::shared_mutex> lock(mutex_); |
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93 |
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94 Content::const_iterator found = content_.find(path); |
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95 |
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96 if (found != content_.end()) |
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97 { |
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98 assert(found->second != NULL); |
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99 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, found->second->c_str(), found->second->size(), mime.c_str()); |
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100 return; |
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101 } |
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102 } |
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103 |
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104 // This resource has not been cached yet |
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105 |
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106 std::unique_ptr<std::string> item(new std::string); |
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107 ReadStaticAsset(*item, path); |
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108 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, item->c_str(), item->size(), mime.c_str()); |
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109 |
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110 { |
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111 // Store the resource into the cache |
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112 boost::unique_lock<boost::shared_mutex> lock(mutex_); |
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113 |
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114 if (content_.find(path) == content_.end()) |
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115 { |
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116 content_[path] = item.release(); |
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117 } |
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118 } |
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119 } |
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120 }; |
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121 |
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122 |
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123 static ResourcesCache cache_; |
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124 static bool hasCreateDicomStl_; |
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125 |
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126 void ServeFile(OrthancPluginRestOutput* output, |
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127 const char* url, |
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128 const OrthancPluginHttpRequest* request) |
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129 { |
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130 if (request->method != OrthancPluginHttpMethod_Get) |
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131 { |
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132 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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133 return; |
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134 } |
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135 |
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136 std::string file = request->groups[0]; |
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137 |
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138 if (file == "viewer.html") |
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139 { |
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140 std::string s; |
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141 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_HTML); |
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142 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Html)); |
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143 } |
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144 else if (file == "viewer.js") |
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145 { |
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146 std::string s; |
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147 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_JS); |
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148 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_JavaScript)); |
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149 } |
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150 else |
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151 { |
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152 cache_.Answer(output, file); |
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153 } |
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154 } |
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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 #include <dcmtk/dcmdata/dcdeftag.h> |
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160 #include <dcmtk/dcmdata/dcfilefo.h> |
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161 #include <dcmtk/dcmdata/dcitem.h> |
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162 #include <dcmtk/dcmdata/dcsequen.h> |
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163 #include <dcmtk/dcmdata/dcuid.h> |
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164 |
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165 class Extent2D : public boost::noncopyable |
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166 { |
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167 private: |
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168 bool isEmpty_; |
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169 double x1_; |
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170 double y1_; |
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171 double x2_; |
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172 double y2_; |
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173 |
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174 void CheckNotEmpty() const |
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175 { |
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176 if (isEmpty_) |
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177 { |
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178 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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179 } |
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180 } |
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181 |
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182 public: |
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183 Extent2D() : |
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184 isEmpty_(true), |
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185 x1_(0), |
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186 y1_(0), |
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187 x2_(0), |
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188 y2_(0) |
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189 { |
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190 } |
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191 |
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192 bool IsEmpty() const |
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193 { |
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194 return isEmpty_; |
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195 } |
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196 |
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197 double GetMinX() const |
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198 { |
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199 CheckNotEmpty(); |
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200 return x1_; |
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201 } |
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202 |
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203 double GetMaxX() const |
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204 { |
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205 CheckNotEmpty(); |
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206 return x2_; |
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207 } |
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208 |
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209 double GetMinY() const |
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210 { |
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211 CheckNotEmpty(); |
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212 return y1_; |
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213 } |
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214 |
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215 double GetMaxY() const |
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216 { |
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217 CheckNotEmpty(); |
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218 return y2_; |
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219 } |
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220 |
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221 double GetWidth() const |
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222 { |
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223 CheckNotEmpty(); |
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224 return x2_ - x1_; |
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225 } |
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226 |
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227 double GetHeight() const |
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228 { |
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229 CheckNotEmpty(); |
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230 return y2_ - y1_; |
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231 } |
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232 |
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233 void Add(double x, |
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234 double y) |
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235 { |
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236 if (isEmpty_) |
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237 { |
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238 x1_ = x2_ = x; |
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239 y1_ = y2_ = y; |
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240 isEmpty_ = false; |
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241 } |
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242 else |
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243 { |
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244 x1_ = std::min(x1_, x); |
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245 x2_ = std::max(x2_, x); |
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246 y1_ = std::min(y1_, y); |
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247 y2_ = std::max(y2_, y); |
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248 } |
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249 } |
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250 }; |
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251 |
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252 static std::string GetStringValue(DcmItem& item, |
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253 const DcmTagKey& key) |
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254 { |
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255 const char* s = NULL; |
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256 if (!item.findAndGetString(key, s).good() || |
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257 s == NULL) |
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258 { |
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259 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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260 } |
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261 else |
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262 { |
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263 return Orthanc::Toolbox::StripSpaces(s); |
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264 } |
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265 } |
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266 |
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267 |
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268 static void ListStructuresNames(std::set<std::string>& target, |
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269 Orthanc::ParsedDicomFile& source) |
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270 { |
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271 target.clear(); |
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272 |
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273 DcmSequenceOfItems* sequence = NULL; |
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274 if (!source.GetDcmtkObject().getDataset()->findAndGetSequence(DCM_StructureSetROISequence, sequence).good() || |
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275 sequence == NULL) |
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276 { |
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277 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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278 } |
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279 |
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280 for (unsigned long i = 0; i < sequence->card(); i++) |
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281 { |
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282 DcmItem* item = sequence->getItem(i); |
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283 if (item == NULL) |
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284 { |
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285 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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286 } |
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287 else |
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288 { |
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289 target.insert(GetStringValue(*item, DCM_ROIName)); |
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290 } |
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291 } |
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292 } |
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293 |
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294 |
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295 static bool IsNear(double a, |
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296 double b) |
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297 { |
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298 return std::abs(a - b) < 10.0 * std::numeric_limits<double>::epsilon(); |
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299 } |
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300 |
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301 |
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302 class Vector3D |
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303 { |
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304 private: |
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305 double x_; |
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306 double y_; |
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307 double z_; |
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308 |
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309 public: |
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310 Vector3D() : |
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311 x_(0), |
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312 y_(0), |
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313 z_(0) |
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314 { |
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315 } |
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316 |
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317 Vector3D(double x, |
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318 double y, |
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319 double z) : |
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320 x_(x), |
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321 y_(y), |
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322 z_(z) |
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323 { |
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324 } |
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325 |
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326 Vector3D(const Vector3D& from, |
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327 const Vector3D& to) : |
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328 x_(to.x_ - from.x_), |
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329 y_(to.y_ - from.y_), |
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330 z_(to.z_ - from.z_) |
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331 { |
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332 } |
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333 |
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334 double GetX() const |
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335 { |
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336 return x_; |
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337 } |
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338 |
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339 double GetY() const |
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340 { |
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341 return y_; |
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342 } |
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343 |
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344 double GetZ() const |
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345 { |
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346 return z_; |
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347 } |
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348 |
29
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349 double ComputeSquaredNorm() const |
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350 { |
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351 return x_ * x_ + y_ * y_ + z_ * z_; |
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352 } |
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353 |
1
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354 double ComputeNorm() const |
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355 { |
29
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356 return sqrt(ComputeSquaredNorm()); |
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357 } |
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358 |
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359 void Normalize() |
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360 { |
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361 double norm = ComputeNorm(); |
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362 if (!IsNear(norm, 0)) |
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363 { |
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364 x_ /= norm; |
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365 y_ /= norm; |
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366 z_ /= norm; |
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367 } |
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368 } |
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369 |
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370 static Vector3D CrossProduct(const Vector3D& u, |
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371 const Vector3D& v) |
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372 { |
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373 return Vector3D(u.GetY() * v.GetZ() - u.GetZ() * v.GetY(), |
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374 u.GetZ() * v.GetX() - u.GetX() * v.GetZ(), |
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375 u.GetX() * v.GetY() - u.GetY() * v.GetX()); |
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376 } |
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377 |
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378 static double DotProduct(const Vector3D& a, |
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379 const Vector3D& b) |
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380 { |
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381 return a.GetX() * b.GetX() + a.GetY() * b.GetY() + a.GetZ() * b.GetZ(); |
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382 } |
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383 |
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384 static bool AreParallel(const Vector3D& a, |
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385 const Vector3D& b) |
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386 { |
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387 if (IsNear(a.ComputeSquaredNorm(), 1) && |
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388 IsNear(b.ComputeSquaredNorm(), 1)) |
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389 { |
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390 return IsNear(std::abs(Vector3D::DotProduct(a, b)), 1); |
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391 } |
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392 else |
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393 { |
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394 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
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395 "Only applicable to normalized vectors"); |
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396 } |
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397 } |
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398 }; |
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399 |
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400 |
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401 |
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402 static bool MyParseDouble(double& value, |
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403 const std::string& s) |
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404 { |
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405 #if 1 |
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406 // This version is much faster, as "ParseDouble()" internally uses |
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407 // "boost::lexical_cast<double>()" |
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408 char* end = NULL; |
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409 value = strtod(s.c_str(), &end); |
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410 return (end == s.c_str() + s.size()); |
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411 #else |
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412 return Orthanc::SerializationToolbox::ParseDouble(value, s); |
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413 #endif |
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414 } |
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415 |
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416 |
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417 class StructurePolygon : public boost::noncopyable |
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418 { |
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419 private: |
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420 std::string roiName_; |
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421 std::string referencedSopInstanceUid_; |
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422 uint8_t red_; |
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423 uint8_t green_; |
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424 uint8_t blue_; |
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425 std::vector<Vector3D> points_; |
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426 |
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427 public: |
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428 StructurePolygon(Orthanc::ParsedDicomFile& dicom, |
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429 unsigned long roiIndex, |
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430 unsigned long contourIndex) |
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431 { |
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432 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
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433 |
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434 DcmItem* structure = NULL; |
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435 DcmItem* roi = NULL; |
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436 DcmItem* contour = NULL; |
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437 DcmSequenceOfItems* referenced = NULL; |
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438 |
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439 if (!dataset.findAndGetSequenceItem(DCM_StructureSetROISequence, structure, roiIndex).good() || |
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440 structure == NULL || |
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441 !dataset.findAndGetSequenceItem(DCM_ROIContourSequence, roi, roiIndex).good() || |
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442 roi == NULL || |
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443 !roi->findAndGetSequenceItem(DCM_ContourSequence, contour, contourIndex).good() || |
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444 contour == NULL || |
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445 !contour->findAndGetSequence(DCM_ContourImageSequence, referenced).good() || |
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446 referenced == NULL || |
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447 referenced->card() != 1) |
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448 { |
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449 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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450 } |
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451 |
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452 roiName_ = GetStringValue(*structure, DCM_ROIName); |
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453 referencedSopInstanceUid_ = GetStringValue(*referenced->getItem(0), DCM_ReferencedSOPInstanceUID); |
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454 |
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455 if (GetStringValue(*contour, DCM_ContourGeometricType) != "CLOSED_PLANAR") |
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456 { |
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457 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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458 } |
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459 |
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460 { |
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461 std::vector<std::string> tokens; |
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462 Orthanc::Toolbox::TokenizeString(tokens, GetStringValue(*roi, DCM_ROIDisplayColor), '\\'); |
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463 |
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464 uint32_t r, g, b; |
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465 if (tokens.size() != 3 || |
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466 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(r, tokens[0]) || |
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467 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(g, tokens[1]) || |
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468 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(b, tokens[2]) || |
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469 r > 255 || |
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470 g > 255 || |
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471 b > 255) |
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472 { |
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473 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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474 } |
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475 |
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476 red_ = r; |
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477 green_ = g; |
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478 blue_ = b; |
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479 } |
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480 |
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481 { |
3
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482 std::vector<std::string> tokens; |
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483 Orthanc::Toolbox::TokenizeString(tokens, GetStringValue(*contour, DCM_ContourData), '\\'); |
1
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484 |
3
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485 const std::string s = GetStringValue(*contour, DCM_NumberOfContourPoints); |
1
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486 |
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487 uint32_t countPoints; |
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488 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(countPoints, s) || |
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489 tokens.size() != 3 * countPoints) |
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490 { |
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encoding of RT-STRUCT as STL
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491 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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492 } |
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493 |
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494 points_.reserve(countPoints); |
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495 |
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encoding of RT-STRUCT as STL
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496 for (size_t i = 0; i < tokens.size(); i += 3) |
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497 { |
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498 double x, y, z; |
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499 if (!MyParseDouble(x, tokens[i]) || |
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diff
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500 !MyParseDouble(y, tokens[i + 1]) || |
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501 !MyParseDouble(z, tokens[i + 2])) |
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encoding of RT-STRUCT as STL
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502 { |
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encoding of RT-STRUCT as STL
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503 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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504 } |
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encoding of RT-STRUCT as STL
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505 |
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506 points_.push_back(Vector3D(x, y, z)); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
507 } |
0f03a8a0bd6f
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diff
changeset
|
508 |
0f03a8a0bd6f
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|
509 assert(points_.size() == countPoints); |
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510 } |
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511 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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|
512 |
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encoding of RT-STRUCT as STL
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|
513 const std::string& GetRoiName() const |
0f03a8a0bd6f
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parents:
0
diff
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|
514 { |
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parents:
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|
515 return roiName_; |
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516 } |
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encoding of RT-STRUCT as STL
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517 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
518 const std::string& GetReferencedSopInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
519 { |
0f03a8a0bd6f
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parents:
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diff
changeset
|
520 return referencedSopInstanceUid_; |
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encoding of RT-STRUCT as STL
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521 } |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
522 |
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encoding of RT-STRUCT as STL
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|
523 size_t GetPointsCount() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
524 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
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|
525 return points_.size(); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
526 } |
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encoding of RT-STRUCT as STL
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parents:
0
diff
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|
527 |
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encoding of RT-STRUCT as STL
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parents:
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|
528 const Vector3D& GetPoint(size_t i) const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
529 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
530 if (i >= points_.size()) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
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|
531 { |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
532 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
533 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
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|
534 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
535 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
536 return points_[i]; |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
537 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
538 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
539 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
540 bool IsCoplanar(Vector3D& normal) const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
541 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
542 if (points_.size() < 3) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
543 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
544 return false; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
545 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
546 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
547 bool hasNormal = false; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
548 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
549 for (size_t i = 0; i < points_.size(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
550 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
551 normal = Vector3D::CrossProduct(Vector3D(points_[1], points_[0]), |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
552 Vector3D(points_[2], points_[0])); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
553 if (!IsNear(normal.ComputeNorm(), 0)) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
554 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
555 normal.Normalize(); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
556 hasNormal = true; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
557 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
558 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
559 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
560 if (!hasNormal) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
561 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
562 return false; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
563 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
564 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
565 double a = Vector3D::DotProduct(points_[0], normal); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
566 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
567 for (size_t i = 1; i < points_.size(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
568 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
569 double b = Vector3D::DotProduct(points_[i], normal); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
570 if (!IsNear(a, b)) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
571 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
572 return false; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
573 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
574 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
575 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
576 return true; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
577 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
578 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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579 void Add(Extent2D& extent, |
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580 const Vector3D& axisX, |
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581 const Vector3D& axisY) const |
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582 { |
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583 assert(IsNear(1, axisX.ComputeNorm())); |
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584 assert(IsNear(1, axisY.ComputeNorm())); |
0f03a8a0bd6f
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585 |
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586 for (size_t i = 0; i < points_.size(); i++) |
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587 { |
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588 extent.Add(Vector3D::DotProduct(axisX, points_[i]), |
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589 Vector3D::DotProduct(axisY, points_[i])); |
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590 } |
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591 } |
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592 }; |
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593 |
0f03a8a0bd6f
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diff
changeset
|
594 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
595 |
0f03a8a0bd6f
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596 struct IsNearPredicate |
0f03a8a0bd6f
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597 { |
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598 bool operator() (const double& a, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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599 const double& b) |
0f03a8a0bd6f
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|
600 { |
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601 return IsNear(a, b); |
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602 } |
0f03a8a0bd6f
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603 }; |
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diff
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|
604 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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605 static void RemoveDuplicateValues(std::vector<double>& v) |
0f03a8a0bd6f
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606 { |
0f03a8a0bd6f
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diff
changeset
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607 IsNearPredicate predicate; |
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608 std::vector<double>::iterator last = std::unique(v.begin(), v.end(), predicate); |
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609 v.erase(last, v.end()); |
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610 } |
0f03a8a0bd6f
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611 |
0f03a8a0bd6f
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|
612 |
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encoding of RT-STRUCT as STL
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613 class StructureSet : public boost::noncopyable |
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614 { |
0f03a8a0bd6f
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615 private: |
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616 std::vector<StructurePolygon*> polygons_; |
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617 std::string patientId_; |
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encoding of RT-STRUCT as STL
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618 std::string studyInstanceUid_; |
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619 std::string seriesInstanceUid_; |
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620 std::string sopInstanceUid_; |
4
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621 bool hasFrameOfReferenceUid_; |
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622 std::string frameOfReferenceUid_; |
1
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623 |
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624 public: |
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625 explicit StructureSet(Orthanc::ParsedDicomFile& dicom) : |
4
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626 hasFrameOfReferenceUid_(false) |
1
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627 { |
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628 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
3
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629 patientId_ = GetStringValue(dataset, DCM_PatientID); |
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630 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID); |
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631 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID); |
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632 sopInstanceUid_ = GetStringValue(dataset, DCM_SOPInstanceUID); |
1
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633 |
4
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634 DcmSequenceOfItems* frame = NULL; |
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635 if (!dataset.findAndGetSequence(DCM_ReferencedFrameOfReferenceSequence, frame).good() || |
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636 frame == NULL) |
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637 { |
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638 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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|
639 } |
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|
640 |
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641 if (frame->card() == 1) |
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|
642 { |
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643 const char* v = NULL; |
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644 if (frame->getItem(0)->findAndGetString(DCM_FrameOfReferenceUID, v).good() && |
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645 v != NULL) |
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|
646 { |
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647 hasFrameOfReferenceUid_ = true; |
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648 frameOfReferenceUid_.assign(v); |
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|
649 } |
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changeset
|
650 } |
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generated STL pass dciodvfy
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changeset
|
651 |
1
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652 DcmSequenceOfItems* rois = NULL; |
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653 if (!dataset.findAndGetSequence(DCM_ROIContourSequence, rois).good() || |
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654 rois == NULL) |
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655 { |
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656 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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|
657 } |
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|
658 |
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659 std::vector<DcmSequenceOfItems*> contours(rois->card()); |
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660 size_t countPolygons = 0; |
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|
661 |
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|
662 for (unsigned long i = 0; i < rois->card(); i++) |
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changeset
|
663 { |
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|
664 DcmSequenceOfItems* contour = NULL; |
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665 if (!rois->getItem(i)->findAndGetSequence(DCM_ContourSequence, contour).good() || |
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|
666 contour == NULL) |
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|
667 { |
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|
668 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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changeset
|
669 } |
0f03a8a0bd6f
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|
670 else |
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changeset
|
671 { |
0f03a8a0bd6f
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|
672 contours[i] = contour; |
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673 countPolygons += contour->card(); |
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encoding of RT-STRUCT as STL
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changeset
|
674 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
675 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
676 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
677 polygons_.resize(countPolygons); |
0f03a8a0bd6f
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diff
changeset
|
678 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
679 size_t pos = 0; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
680 for (unsigned long i = 0; i < contours.size(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
681 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
682 for (unsigned long j = 0; j < contours[i]->card(); j++, pos++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
683 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
684 polygons_[pos] = new StructurePolygon(dicom, i, j); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
685 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
686 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
687 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
688 assert(pos == countPolygons); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
689 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
690 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
691 ~StructureSet() |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
692 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
693 for (size_t i = 0; i < polygons_.size(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
694 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
695 assert(polygons_[i] != NULL); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
696 delete polygons_[i]; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
697 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
698 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
699 |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
28
diff
changeset
|
700 const std::string& GetPatientId() const |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
701 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
702 return patientId_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
703 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
704 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
705 const std::string& GetStudyInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
706 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
707 return studyInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
708 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
709 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
710 const std::string& GetSeriesInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
711 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
712 return seriesInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
713 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
714 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
715 const std::string& GetSopInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
716 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
717 return sopInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
718 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
719 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
720 std::string HashStudy() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
721 { |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
722 Orthanc::DicomInstanceHasher hasher(patientId_, studyInstanceUid_, seriesInstanceUid_, sopInstanceUid_); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
723 return hasher.HashStudy(); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
724 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
725 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
726 size_t GetPolygonsCount() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
727 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
728 return polygons_.size(); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
729 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
730 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
731 const StructurePolygon& GetPolygon(size_t i) const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
732 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
733 if (i >= polygons_.size()) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
734 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
735 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
736 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
737 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
738 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
739 assert(polygons_[i] != NULL); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
740 return *polygons_[i]; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
741 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
742 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
743 |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
744 bool HasFrameOfReferenceUid() const |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
745 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
746 return hasFrameOfReferenceUid_; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
747 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
748 |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
749 const std::string& GetFrameOfReferenceUid() const |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
750 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
751 if (hasFrameOfReferenceUid_) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
752 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
753 return frameOfReferenceUid_; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
754 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
755 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
756 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
757 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
758 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
759 } |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
760 }; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
761 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
762 |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
763 class StructureSetGeometry : public boost::noncopyable |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
764 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
765 private: |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
766 bool strict_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
767 Vector3D slicesNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
768 double slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
769 double minProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
770 double maxProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
771 size_t slicesCount_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
772 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
773 bool LookupProjectionIndex(size_t& index, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
774 double z) const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
775 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
776 if (slicesCount_ == 0) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
777 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
778 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
779 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
780 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
781 if (z < minProjectionAlongNormal_ || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
782 z > maxProjectionAlongNormal_) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
783 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
784 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
785 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
786 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
787 assert(slicesSpacing_ > 0 && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
788 minProjectionAlongNormal_ < maxProjectionAlongNormal_); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
789 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
790 double d = (z - minProjectionAlongNormal_) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
791 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
792 if (IsNear(d, round(d))) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
793 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
794 if (d < 0.0 || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
795 d > static_cast<double>(slicesCount_) - 1.0) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
796 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
797 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
798 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
799 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
800 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
801 index = static_cast<size_t>(round(d)); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
802 return true; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
803 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
804 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
805 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
806 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
807 return false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
808 } |
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improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
809 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
810 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
811 public: |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
812 StructureSetGeometry(const StructureSet& structures, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
813 bool strict) : |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
814 strict_(strict) |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
815 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
816 bool isValid = false; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
817 |
410003c50b17
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25
diff
changeset
|
818 std::vector<double> projections; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
819 projections.reserve(structures.GetPolygonsCount()); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
820 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
821 for (size_t i = 0; i < structures.GetPolygonsCount(); i++) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
822 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
823 Vector3D normal; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
824 if (structures.GetPolygon(i).IsCoplanar(normal)) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
825 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
826 // Initialize the normal of the whole volume, if need be |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
827 if (!isValid) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
828 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
829 isValid = true; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
830 slicesNormal_ = normal; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
831 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
832 |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
28
diff
changeset
|
833 if (Vector3D::AreParallel(normal, slicesNormal_)) |
28
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
834 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
835 // This is a valid slice (it is parallel to the normal) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
836 const Vector3D& point = structures.GetPolygon(i).GetPoint(0); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
837 projections.push_back(Vector3D::DotProduct(point, slicesNormal_)); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
838 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
839 else |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
840 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
841 // RT-STRUCT with non-parallel slices |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
842 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
410003c50b17
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25
diff
changeset
|
843 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
844 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
845 else |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
846 { |
410003c50b17
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parents:
25
diff
changeset
|
847 // Ignore slices that are not coplanar |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
848 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
849 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
850 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
851 if (projections.empty()) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
852 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
853 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
854 "Structure set without a valid geometry"); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
855 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
856 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
857 // Only keep unique projections |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
858 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
859 std::sort(projections.begin(), projections.end()); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
860 RemoveDuplicateValues(projections); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
861 assert(!projections.empty()); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
862 |
410003c50b17
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parents:
25
diff
changeset
|
863 if (projections.size() == 1) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
864 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
865 // Volume with one single slice |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
866 minProjectionAlongNormal_ = projections[0]; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
867 maxProjectionAlongNormal_ = projections[0]; |
410003c50b17
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25
diff
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|
868 slicesSpacing_ = 1; // Arbitrary value |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
869 slicesCount_ = 1; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
870 return; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
871 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
872 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
873 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
874 // Compute the most probable spacing between the slices |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
875 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
876 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
877 std::vector<double> spacings; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
878 spacings.resize(projections.size() - 1); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
879 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
880 for (size_t i = 0; i < spacings.size(); i++) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
881 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
882 spacings[i] = projections[i + 1] - projections[i]; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
883 assert(spacings[i] > 0); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
884 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
885 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
886 std::sort(spacings.begin(), spacings.end()); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
887 RemoveDuplicateValues(spacings); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
888 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
889 if (spacings.empty()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
890 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
891 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
892 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
893 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
894 slicesSpacing_ = spacings[spacings.size() / 10]; // Take the 90% percentile of smallest spacings |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
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|
895 assert(slicesSpacing_ > 0); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
896 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
897 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
898 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
899 // Find the projection along the normal with the largest support |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
900 |
410003c50b17
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parents:
25
diff
changeset
|
901 bool first = true; |
410003c50b17
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25
diff
changeset
|
902 size_t bestSupport; |
410003c50b17
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parents:
25
diff
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|
903 double bestProjection; |
410003c50b17
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25
diff
changeset
|
904 |
410003c50b17
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parents:
25
diff
changeset
|
905 std::list<size_t> candidates; |
410003c50b17
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25
diff
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|
906 for (size_t i = 0; i < projections.size(); i++) |
410003c50b17
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parents:
25
diff
changeset
|
907 { |
410003c50b17
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parents:
25
diff
changeset
|
908 candidates.push_back(i); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
909 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
910 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
911 while (!candidates.empty()) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
912 { |
410003c50b17
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parents:
25
diff
changeset
|
913 std::list<size_t> next; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
914 |
410003c50b17
improved computation of RT-STRUCT geometry
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25
diff
changeset
|
915 size_t countSupport = 0; |
410003c50b17
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25
diff
changeset
|
916 |
410003c50b17
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25
diff
changeset
|
917 std::list<size_t>::const_iterator it = candidates.begin(); |
410003c50b17
improved computation of RT-STRUCT geometry
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25
diff
changeset
|
918 size_t reference = *it; |
410003c50b17
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25
diff
changeset
|
919 it++; |
410003c50b17
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parents:
25
diff
changeset
|
920 |
410003c50b17
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parents:
25
diff
changeset
|
921 while (it != candidates.end()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
922 { |
410003c50b17
improved computation of RT-STRUCT geometry
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25
diff
changeset
|
923 double d = (projections[*it] - projections[reference]) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
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25
diff
changeset
|
924 if (IsNear(d, round(d))) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
925 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
926 countSupport ++; |
410003c50b17
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25
diff
changeset
|
927 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
928 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
929 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
930 next.push_back(*it); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
931 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
932 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
933 it++; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
934 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
935 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
936 if (first || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
937 countSupport > bestSupport) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
938 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
939 first = false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
940 bestSupport = countSupport; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
941 bestProjection = projections[reference]; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
942 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
943 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
944 if (strict && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
945 !next.empty()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
946 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
947 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
948 "Structure set with multiple support, which is not allowed in Strict mode"); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
949 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
950 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
951 candidates.swap(next); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
952 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
953 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
954 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
955 // Compute the range of the projections |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
956 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
957 minProjectionAlongNormal_ = bestProjection; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
958 maxProjectionAlongNormal_ = bestProjection; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
959 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
960 for (size_t i = 0; i < projections.size(); i++) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
961 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
962 double d = (projections[i] - bestProjection) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
963 if (IsNear(d, round(d))) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
964 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
965 minProjectionAlongNormal_ = std::min(minProjectionAlongNormal_, projections[i]); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
966 maxProjectionAlongNormal_ = std::max(maxProjectionAlongNormal_, projections[i]); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
967 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
968 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
969 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
970 double d = (maxProjectionAlongNormal_ - minProjectionAlongNormal_) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
971 if (IsNear(d, round(d))) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
972 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
973 slicesCount_ = static_cast<size_t>(round(d)) + 1; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
974 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
975 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
976 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
977 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
978 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
979 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
980 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
981 // Sanity check |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
982 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
983 size_t a, b; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
984 if (!LookupProjectionIndex(a, minProjectionAlongNormal_) || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
985 !LookupProjectionIndex(b, maxProjectionAlongNormal_) || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
986 a != 0 || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
987 b + 1 != slicesCount_) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
988 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
989 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
990 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
991 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
992 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
993 const Vector3D& GetSlicesNormal() const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
994 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
995 return slicesNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
996 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
997 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
998 double GetSlicesSpacing() const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
999 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1000 return slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1001 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1002 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1003 double GetMinProjectionAlongNormal() const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1004 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1005 return minProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1006 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1007 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1008 double GetMaxProjectionAlongNormal() const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1009 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1010 return maxProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1011 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1012 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1013 bool ProjectAlongNormal(double& z, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1014 const StructurePolygon& polygon) const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1015 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1016 Vector3D normal; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1017 if (polygon.IsCoplanar(normal) && |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
28
diff
changeset
|
1018 Vector3D::AreParallel(normal, slicesNormal_)) |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1019 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1020 z = Vector3D::DotProduct(polygon.GetPoint(0), slicesNormal_); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1021 return true; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1022 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1023 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1024 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1025 return false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1026 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1027 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1028 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1029 size_t GetSlicesCount() const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1030 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1031 return slicesCount_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1032 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1033 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1034 bool LookupSliceIndex(size_t& slice, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1035 const StructurePolygon& polygon) const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1036 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1037 double z; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1038 return (ProjectAlongNormal(z, polygon) && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1039 LookupProjectionIndex(slice, z)); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1040 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1041 }; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1042 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1043 |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1044 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1045 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1046 class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1047 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1048 private: |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1049 Orthanc::ImageAccessor& target_; |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1050 |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
1051 public: |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
1052 XorFiller(Orthanc::ImageAccessor& target) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1053 target_(target) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1054 { |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1055 } |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1056 |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
1057 virtual void Fill(int y, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1058 int x1, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
1059 int x2) ORTHANC_OVERRIDE |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
1060 { |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1061 assert(x1 <= x2); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
1062 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1063 if (y >= 0 && |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1064 y < static_cast<int>(target_.GetHeight())) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1065 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1066 x1 = std::max(x1, 0); |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1067 x2 = std::min(x2, static_cast<int>(target_.GetWidth()) - 1); |
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encoding of RT-STRUCT as STL
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|
1068 |
0f03a8a0bd6f
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0
diff
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|
1069 uint8_t* p = reinterpret_cast<uint8_t*>(target_.GetRow(y)) + x1; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1070 |
0f03a8a0bd6f
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0
diff
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|
1071 for (int i = x1; i <= x2; i++, p++) |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1072 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1073 *p = (*p ^ 0xff); |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
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|
1074 } |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1075 } |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1076 } |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1077 }; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1078 |
0f03a8a0bd6f
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diff
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|
1079 |
29
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|
1080 static void WriteFloat(Orthanc::ChunkedBuffer& buffer, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1081 float value, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1082 Orthanc::Endianness endianness) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1083 { |
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28
diff
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|
1084 switch (endianness) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1085 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1086 case Orthanc::Endianness_Little: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1087 buffer.AddChunk(&value, sizeof(float)); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1088 break; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1089 |
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28
diff
changeset
|
1090 case Orthanc::Endianness_Big: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1091 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1092 uint8_t tmp[4]; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1093 tmp[0] = reinterpret_cast<uint8_t*>(&value) [3]; |
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diff
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|
1094 tmp[1] = reinterpret_cast<uint8_t*>(&value) [2]; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1095 tmp[2] = reinterpret_cast<uint8_t*>(&value) [1]; |
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|
1096 tmp[3] = reinterpret_cast<uint8_t*>(&value) [0]; |
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diff
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|
1097 buffer.AddChunk(&tmp, sizeof(float)); |
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diff
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|
1098 break; |
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|
1099 } |
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|
1100 |
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|
1101 default: |
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|
1102 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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diff
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|
1103 } |
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|
1104 } |
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|
1105 |
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|
1106 |
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|
1107 static void WriteInteger(Orthanc::ChunkedBuffer& buffer, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1108 uint32_t value, |
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28
diff
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|
1109 Orthanc::Endianness endianness) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1110 { |
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28
diff
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|
1111 switch (endianness) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1112 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1113 case Orthanc::Endianness_Little: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1114 buffer.AddChunk(&value, sizeof(uint32_t)); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1115 break; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1116 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1117 case Orthanc::Endianness_Big: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1118 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
1119 uint8_t tmp[4]; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1120 tmp[0] = reinterpret_cast<uint8_t*>(&value) [3]; |
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diff
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|
1121 tmp[1] = reinterpret_cast<uint8_t*>(&value) [2]; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1122 tmp[2] = reinterpret_cast<uint8_t*>(&value) [1]; |
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diff
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|
1123 tmp[3] = reinterpret_cast<uint8_t*>(&value) [0]; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1124 buffer.AddChunk(&tmp, sizeof(uint32_t)); |
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diff
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|
1125 break; |
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diff
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|
1126 } |
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diff
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|
1127 |
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diff
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|
1128 default: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1129 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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1130 } |
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|
1131 } |
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|
1132 |
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|
1133 |
1
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diff
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|
1134 static void EncodeSTL(std::string& target /* out */, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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1135 vtkPolyData& mesh /* in */) |
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1136 { |
29
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|
1137 const Orthanc::Endianness endianness = Orthanc::Toolbox::DetectEndianness(); |
1
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1138 |
0f03a8a0bd6f
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1139 Orthanc::ChunkedBuffer buffer; |
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1140 |
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|
1141 uint8_t header[80]; |
0f03a8a0bd6f
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|
1142 memset(header, 0, sizeof(header)); |
29
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|
1143 buffer.AddChunk(header, sizeof(header)); // This doesn't depend on endianness |
1
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1144 |
29
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|
1145 WriteInteger(buffer, mesh.GetNumberOfCells(), endianness); |
1
0f03a8a0bd6f
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|
1146 |
0f03a8a0bd6f
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1147 for (vtkIdType i = 0; i < mesh.GetNumberOfCells(); i++) |
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encoding of RT-STRUCT as STL
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|
1148 { |
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|
1149 vtkCell* cell = mesh.GetCell(i); |
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|
1150 vtkTriangle* triangle = dynamic_cast<vtkTriangle*>(cell); |
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|
1151 |
0f03a8a0bd6f
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|
1152 double p0[3]; |
0f03a8a0bd6f
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|
1153 double p1[3]; |
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|
1154 double p2[3]; |
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|
1155 triangle->GetPoints()->GetPoint(0, p0); |
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encoding of RT-STRUCT as STL
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|
1156 triangle->GetPoints()->GetPoint(1, p1); |
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|
1157 triangle->GetPoints()->GetPoint(2, p2); |
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|
1158 |
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1159 double normal[3]; |
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1160 vtkTriangle::ComputeNormal(p0, p1, p2, normal); |
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1161 |
29
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1162 WriteFloat(buffer, normal[0], endianness); |
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1163 WriteFloat(buffer, normal[1], endianness); |
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1164 WriteFloat(buffer, normal[2], endianness); |
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1165 WriteFloat(buffer, p0[0], endianness); |
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1166 WriteFloat(buffer, p0[1], endianness); |
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1167 WriteFloat(buffer, p0[2], endianness); |
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1168 WriteFloat(buffer, p1[0], endianness); |
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1169 WriteFloat(buffer, p1[1], endianness); |
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1170 WriteFloat(buffer, p1[2], endianness); |
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1171 WriteFloat(buffer, p2[0], endianness); |
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1172 WriteFloat(buffer, p2[1], endianness); |
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1173 WriteFloat(buffer, p2[2], endianness); |
1
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1174 |
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1175 uint16_t a = 0; |
29
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1176 buffer.AddChunk(&a, sizeof(a)); // This doesn't depend on endianness |
1
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1177 } |
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1178 |
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1179 buffer.Flatten(target); |
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1180 } |
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1181 |
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1182 |
8
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1183 bool EncodeVolume(std::string& stl, |
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1184 vtkImageData* volume, |
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1185 unsigned int resolution, |
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1186 bool smooth) |
7 | 1187 { |
1188 if (volume == NULL) | |
1189 { | |
1190 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
1191 } | |
1192 | |
1193 vtkNew<vtkImageResize> resize; | |
1194 resize->SetOutputDimensions(resolution, resolution, resolution); | |
1195 resize->SetInputData(volume); | |
1196 resize->Update(); | |
1197 | |
1198 vtkNew<vtkImageConstantPad> padding; | |
1199 padding->SetConstant(0); | |
1200 padding->SetOutputNumberOfScalarComponents(1); | |
1201 padding->SetOutputWholeExtent(-1, resolution, -1, resolution, -1, resolution); | |
1202 padding->SetInputData(resize->GetOutput()); | |
1203 padding->Update(); | |
1204 | |
1205 double range[2]; | |
1206 padding->GetOutput()->GetScalarRange(range); | |
1207 | |
1208 const double isoValue = (range[0] + range[1]) / 2.0; | |
1209 | |
1210 vtkNew<vtkMarchingCubes> surface; | |
1211 surface->SetInputData(padding->GetOutput()); | |
1212 surface->ComputeNormalsOn(); | |
1213 surface->SetValue(0, isoValue); | |
1214 surface->Update(); | |
1215 | |
1216 if (smooth) | |
1217 { | |
1218 vtkNew<vtkSmoothPolyDataFilter> smoothFilter; | |
1219 // Apply volume smoothing | |
1220 // https://examples.vtk.org/site/Cxx/PolyData/SmoothPolyDataFilter/ | |
1221 smoothFilter->SetInputConnection(surface->GetOutputPort()); | |
1222 smoothFilter->SetNumberOfIterations(15); | |
1223 smoothFilter->SetRelaxationFactor(0.1); | |
1224 smoothFilter->FeatureEdgeSmoothingOff(); | |
1225 smoothFilter->BoundarySmoothingOn(); | |
1226 smoothFilter->Update(); | |
1227 | |
1228 vtkNew<vtkPolyDataNormals> normalGenerator; | |
1229 normalGenerator->SetInputConnection(smoothFilter->GetOutputPort()); | |
1230 normalGenerator->ComputePointNormalsOn(); | |
1231 normalGenerator->ComputeCellNormalsOn(); | |
1232 normalGenerator->Update(); | |
1233 | |
1234 EncodeSTL(stl, *normalGenerator->GetOutput()); | |
1235 } | |
1236 else | |
1237 { | |
1238 EncodeSTL(stl, *surface->GetOutput()); | |
1239 } | |
1240 | |
1241 return true; | |
1242 } | |
1243 | |
1244 | |
29
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1245 static Orthanc::ParsedDicomFile* LoadInstance(const std::string& instanceId) |
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1246 { |
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1247 std::string dicom; |
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1248 |
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1249 if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false)) |
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1250 { |
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1251 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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1252 } |
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1253 else |
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1254 { |
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1255 return new Orthanc::ParsedDicomFile(dicom); |
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1256 } |
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1257 } |
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1258 |
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1259 |
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1260 static void GetReferencedVolumeAxes(Vector3D& axisX, |
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1261 Vector3D& axisY, |
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1262 const StructureSet& structureSet) |
1
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1263 { |
29
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1264 // This is a rough guess for the X/Y axes |
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1265 axisX = Vector3D(1, 0, 0); |
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1266 axisY = Vector3D(0, 1, 0); |
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1267 |
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1268 // Look for one instance from the referenced volume |
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1269 const std::string& sopInstanceUid = structureSet.GetPolygon(0).GetReferencedSopInstanceUid(); |
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1270 |
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1271 Json::Value response; |
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1272 if (OrthancPlugins::RestApiPost(response, "/tools/lookup", sopInstanceUid, false)) |
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1273 { |
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1274 if (response.type() != Json::arrayValue) |
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1275 { |
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1276 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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1277 } |
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1278 |
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1279 bool first = true; |
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1280 |
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1281 for (Json::Value::ArrayIndex i = 0; i < response.size(); i++) |
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1282 { |
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1283 if (response[i].type() != Json::objectValue) |
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1284 { |
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1285 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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1286 } |
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1287 |
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1288 if (Orthanc::SerializationToolbox::ReadString(response[i], "Type") == "Instance") |
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1289 { |
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1290 if (first) |
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1291 { |
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1292 const std::string& instanceId = Orthanc::SerializationToolbox::ReadString(response[i], "ID"); |
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1293 std::unique_ptr<Orthanc::ParsedDicomFile> reference(LoadInstance(instanceId)); |
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1294 |
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1295 std::string imageOrientation; |
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1296 if (reference->GetTagValue(imageOrientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT)) |
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1297 { |
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1298 std::vector<std::string> items; |
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1299 Orthanc::Toolbox::TokenizeString(items, imageOrientation, '\\'); |
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1300 |
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1301 double x1, x2, x3, y1, y2, y3; |
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1302 |
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1303 if (items.size() == 6 && |
30 | 1304 MyParseDouble(x1, items[0]) && |
1305 MyParseDouble(x2, items[1]) && | |
1306 MyParseDouble(x3, items[2]) && | |
1307 MyParseDouble(y1, items[3]) && | |
1308 MyParseDouble(y2, items[4]) && | |
1309 MyParseDouble(y3, items[5])) | |
29
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1310 { |
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1311 axisX = Vector3D(x1, x2, x3); |
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1312 axisY = Vector3D(y1, y2, y3); |
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1313 } |
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1314 } |
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1315 } |
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1316 else |
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1317 { |
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1318 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, |
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1319 "Multiple instances with the same SOP Instance UID"); |
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1320 } |
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1321 } |
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1322 } |
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1323 } |
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1324 } |
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1325 |
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1326 |
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1327 static bool EncodeStructureSetMesh(std::string& stl, |
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1328 const StructureSet& structureSet, |
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1329 const StructureSetGeometry& geometry, |
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1330 const std::set<std::string>& roiNames, |
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1331 unsigned int resolution, |
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1332 bool smooth) |
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1333 { |
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1334 if (resolution < 1 || |
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1335 structureSet.GetPolygonsCount() < 1) |
1
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1336 { |
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1337 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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1338 } |
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1339 |
28
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1340 if (!IsNear(1, geometry.GetSlicesNormal().ComputeNorm())) |
1
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1341 { |
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1342 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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1343 } |
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1344 |
29
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1345 Vector3D axisX, axisY; |
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1346 GetReferencedVolumeAxes(axisX, axisY, structureSet); |
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1347 |
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1348 Vector3D axisZ = Vector3D::CrossProduct(axisX, axisY); |
1
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1349 |
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1350 if (!IsNear(1, axisX.ComputeNorm()) || |
29
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1351 !IsNear(1, axisY.ComputeNorm()) || |
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1352 !Vector3D::AreParallel(axisZ, geometry.GetSlicesNormal())) |
1
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1353 { |
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1354 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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1355 } |
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1356 |
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1357 Extent2D extent; |
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1358 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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1359 { |
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1360 structureSet.GetPolygon(i).Add(extent, axisX, axisY); |
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1361 } |
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1362 |
28
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1363 const int depth = geometry.GetSlicesCount(); |
1
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1364 |
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1365 vtkNew<vtkImageData> volume; |
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1366 volume->SetDimensions(resolution, resolution, depth); |
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1367 volume->AllocateScalars(VTK_UNSIGNED_CHAR, 1); |
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1368 |
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1369 assert(sizeof(unsigned char) == 1); |
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1370 memset(volume->GetScalarPointer(), 0, resolution * resolution * depth); |
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1371 |
30 | 1372 const double pixelSpacingX = extent.GetWidth() / static_cast<double>(resolution); |
1373 const double pixelSpacingY = extent.GetHeight() / static_cast<double>(resolution); | |
1374 const double pixelSpacingZ = geometry.GetSlicesSpacing(); | |
1375 | |
1376 bool first = true; | |
1377 | |
1
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1378 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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1379 { |
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1380 const StructurePolygon& polygon = structureSet.GetPolygon(i); |
29
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1381 if (roiNames.find(polygon.GetRoiName()) != roiNames.end()) |
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1382 { |
29
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1383 // This polygon corresponds to a ROI of interest |
1
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1384 |
29
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1385 size_t z; |
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1386 if (geometry.LookupSliceIndex(z, polygon)) |
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1387 { |
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1388 std::vector<Orthanc::ImageProcessing::ImagePoint> points; |
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1389 points.reserve(polygon.GetPointsCount()); |
1
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1390 |
29
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1391 for (size_t j = 0; j < polygon.GetPointsCount(); j++) |
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1392 { |
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1393 const Vector3D& point = polygon.GetPoint(j); |
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1394 double x = (Vector3D::DotProduct(point, axisX) - extent.GetMinX()) / extent.GetWidth() * static_cast<double>(resolution); |
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1395 double y = (Vector3D::DotProduct(point, axisY) - extent.GetMinY()) / extent.GetHeight() * static_cast<double>(resolution); |
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1396 points.push_back(Orthanc::ImageProcessing::ImagePoint(static_cast<int32_t>(std::floor(x)), |
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1397 static_cast<int32_t>(std::floor(y)))); |
30 | 1398 |
1399 if (first) | |
1400 { | |
1401 first = false; | |
1402 volume->SetOrigin(point.GetX() - x * pixelSpacingX, | |
1403 point.GetY() - y * pixelSpacingY, | |
1404 point.GetZ() - z * pixelSpacingZ); | |
1405 } | |
29
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1406 } |
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1407 |
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1408 Orthanc::ImageAccessor slice; |
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1409 slice.AssignWritable(Orthanc::PixelFormat_Grayscale8, resolution, resolution, resolution /* pitch */, |
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1410 reinterpret_cast<uint8_t*>(volume->GetScalarPointer()) + z * resolution * resolution); |
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1411 |
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1412 XorFiller filler(slice); |
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1413 Orthanc::ImageProcessing::FillPolygon(filler, points); |
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1414 } |
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1415 } |
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1416 } |
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1417 |
30 | 1418 volume->SetSpacing(pixelSpacingX, pixelSpacingY, pixelSpacingZ); |
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1419 |
8
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1420 return EncodeVolume(stl, volume.Get(), resolution, smooth); |
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1421 } |
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1422 |
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1423 |
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1424 void ListStructures(OrthancPluginRestOutput* output, |
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1425 const char* url, |
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1426 const OrthancPluginHttpRequest* request) |
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1427 { |
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1428 if (request->method != OrthancPluginHttpMethod_Get) |
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1429 { |
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1430 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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1431 return; |
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1432 } |
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1433 |
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1434 const std::string instanceId(request->groups[0]); |
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1435 |
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1436 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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1437 |
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1438 std::set<std::string> names; |
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1439 ListStructuresNames(names, *dicom); |
1
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diff
changeset
|
1440 |
3
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1441 Json::Value answer = Json::arrayValue; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
1442 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1443 for (std::set<std::string>::const_iterator it = names.begin(); it != names.end(); ++it) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1444 { |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1445 answer.append(*it); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1446 } |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1447 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1448 std::string s = answer.toStyledString(); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1449 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>
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diff
changeset
|
1450 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1451 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
1452 |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1453 static void AddDefaultTagValue(Json::Value& target, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1454 const Orthanc::DicomTag& tag, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1455 const std::string& value) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1456 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1457 if (!target.isMember(tag.Format())) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1458 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1459 target[tag.Format()] = value; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1460 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1461 } |
5ee4448a8ff8
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1462 |
5ee4448a8ff8
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diff
changeset
|
1463 |
5ee4448a8ff8
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1464 static void AddDefaultTagValue(Json::Value& target, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1465 const DcmTagKey& tag, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1466 const std::string& value) |
5ee4448a8ff8
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1467 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1468 AddDefaultTagValue(target, Orthanc::DicomTag(tag.getGroup(), tag.getElement()), value); |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1469 } |
5ee4448a8ff8
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1470 |
5ee4448a8ff8
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1471 |
7 | 1472 static void CallCreateDicom(Json::Value& answer, |
1473 const std::string& stl, | |
1474 const Json::Value& body, | |
1475 const std::string& parentStudy, | |
1476 const std::string& defaultSeriesDescription, | |
1477 const std::string& defaultFrameOfReferenceUid, | |
1478 const std::string& defaultTitle) | |
1479 { | |
1480 static const char* const KEY_TAGS = "Tags"; | |
1481 | |
1482 Json::Value normalized = Json::objectValue; | |
1483 | |
1484 if (body.isMember(KEY_TAGS)) | |
1485 { | |
1486 const Json::Value& tags = body[KEY_TAGS]; | |
1487 | |
1488 if (tags.type() != Json::objectValue) | |
1489 { | |
1490 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Tags must be provided as a JSON object"); | |
1491 } | |
1492 | |
1493 std::vector<std::string> keys = tags.getMemberNames(); | |
1494 for (size_t i = 0; i < keys.size(); i++) | |
1495 { | |
1496 const Orthanc::DicomTag tag = Orthanc::FromDcmtkBridge::ParseTag(keys[i]); | |
1497 normalized[tag.Format()] = tags[keys[i]]; | |
1498 } | |
1499 } | |
1500 | |
1501 if (!normalized.isMember(Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format())) | |
1502 { | |
1503 normalized[Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format()] = defaultSeriesDescription; | |
1504 } | |
1505 | |
1506 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_SERIES_NUMBER, "1"); | |
1507 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, defaultFrameOfReferenceUid); | |
1508 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_INSTANCE_NUMBER, "1"); | |
1509 | |
1510 AddDefaultTagValue(normalized, DCM_BurnedInAnnotation, "NO"); | |
1511 AddDefaultTagValue(normalized, DCM_DeviceSerialNumber, ORTHANC_STL_VERSION); | |
1512 AddDefaultTagValue(normalized, DCM_DocumentTitle, defaultTitle); | |
1513 AddDefaultTagValue(normalized, DCM_Manufacturer, "Orthanc STL plugin"); | |
1514 AddDefaultTagValue(normalized, DCM_ManufacturerModelName, "Orthanc STL plugin"); | |
1515 AddDefaultTagValue(normalized, DCM_PositionReferenceIndicator, ""); | |
1516 AddDefaultTagValue(normalized, DCM_SoftwareVersions, ORTHANC_STL_VERSION); | |
1517 AddDefaultTagValue(normalized, DCM_ConceptNameCodeSequence, ""); | |
1518 | |
1519 std::string date, time; | |
1520 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); | |
1521 AddDefaultTagValue(normalized, DCM_AcquisitionDateTime, date + time); | |
1522 | |
1523 const Orthanc::DicomTag MEASUREMENT_UNITS_CODE_SEQUENCE(DCM_MeasurementUnitsCodeSequence.getGroup(), | |
1524 DCM_MeasurementUnitsCodeSequence.getElement()); | |
1525 | |
1526 if (!normalized.isMember(MEASUREMENT_UNITS_CODE_SEQUENCE.Format())) | |
1527 { | |
1528 Json::Value item; | |
1529 item["CodeValue"] = "mm"; | |
1530 item["CodingSchemeDesignator"] = "UCUM"; | |
1531 item["CodeMeaning"] = defaultTitle; | |
1532 | |
1533 normalized[MEASUREMENT_UNITS_CODE_SEQUENCE.Format()].append(item); | |
1534 } | |
1535 | |
1536 std::string content; | |
1537 Orthanc::Toolbox::EncodeDataUriScheme(content, Orthanc::MIME_STL, stl); | |
1538 | |
1539 Json::Value create; | |
1540 create["Content"] = content; | |
1541 create["Parent"] = parentStudy; | |
1542 create["Tags"] = normalized; | |
1543 | |
1544 if (!OrthancPlugins::RestApiPost(answer, "/tools/create-dicom", create.toStyledString(), false)) | |
1545 { | |
1546 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Cannot create DICOM from STL"); | |
1547 } | |
1548 } | |
1549 | |
1550 | |
1551 void EncodeStructureSet(OrthancPluginRestOutput* output, | |
1552 const char* url, | |
1553 const OrthancPluginHttpRequest* request) | |
1
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1554 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1555 static const char* const KEY_INSTANCE = "Instance"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
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|
1556 static const char* const KEY_RESOLUTION = "Resolution"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1557 static const char* const KEY_ROI_NAMES = "RoiNames"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1558 static const char* const KEY_SMOOTH = "Smooth"; |
28
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
1559 static const char* const KEY_STRICT = "Strict"; |
1
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encoding of RT-STRUCT as STL
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diff
changeset
|
1560 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1561 if (request->method != OrthancPluginHttpMethod_Post) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1562 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1563 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1564 return; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1565 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1566 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1567 Json::Value body; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1568 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1569 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1570 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1571 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1572 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1573 const std::string instanceId = Orthanc::SerializationToolbox::ReadString(body, KEY_INSTANCE); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
1574 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1575 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
1576 true /* smooth by default */); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1577 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
1578 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1579 256 /* default value */); |
28
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
1580 const bool strict = (body.isMember(KEY_STRICT) ? |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
1581 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_STRICT) : |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
1582 true /* strict by default */); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1583 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1584 std::set<std::string> roiNames; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1585 Orthanc::SerializationToolbox::ReadSetOfStrings(roiNames, body, KEY_ROI_NAMES); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1586 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1587 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1588 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1589 StructureSet structureSet(*dicom); |
0fb06c6a6c87
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diff
changeset
|
1590 |
28
410003c50b17
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25
diff
changeset
|
1591 StructureSetGeometry geometry(structureSet, strict); |
410003c50b17
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25
diff
changeset
|
1592 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1593 std::string stl; |
28
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diff
changeset
|
1594 if (!EncodeStructureSetMesh(stl, structureSet, geometry, roiNames, resolution, smooth)) |
1
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encoding of RT-STRUCT as STL
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diff
changeset
|
1595 { |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
1596 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from RT-STRUCT"); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1597 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1598 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1599 { |
7 | 1600 std::string seriesDescription; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1601 |
7 | 1602 if (dicom->GetTagValue(seriesDescription, Orthanc::DICOM_TAG_SERIES_DESCRIPTION)) |
1
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encoding of RT-STRUCT as STL
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diff
changeset
|
1603 { |
7 | 1604 seriesDescription += ": "; |
1605 } | |
1606 else | |
1607 { | |
1608 seriesDescription.clear(); | |
1
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1609 } |
4
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generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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3
diff
changeset
|
1610 |
7 | 1611 bool first = true; |
1612 for (std::set<std::string>::const_iterator it = roiNames.begin(); it != roiNames.end(); ++it) | |
1
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encoding of RT-STRUCT as STL
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diff
changeset
|
1613 { |
7 | 1614 if (first) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1615 { |
7 | 1616 first = false; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1617 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1618 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
1619 { |
7 | 1620 seriesDescription += ", "; |
3
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added route "/instances/{id}/stl"
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parents:
2
diff
changeset
|
1621 } |
2
2bdb9acb7dcf
added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1622 |
7 | 1623 seriesDescription += *it; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1624 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1625 |
7 | 1626 std::string frameOfReferenceUid; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1627 if (structureSet.HasFrameOfReferenceUid()) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1628 { |
7 | 1629 frameOfReferenceUid = structureSet.GetFrameOfReferenceUid(); |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1630 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1631 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1632 { |
7 | 1633 frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1634 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1635 |
7 | 1636 Json::Value answer; |
1637 CallCreateDicom(answer, stl, body, structureSet.HashStudy(), seriesDescription, | |
1638 frameOfReferenceUid, "STL model generated from DICOM RT-STRUCT"); | |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1639 |
7 | 1640 std::string s = answer.toStyledString(); |
1641 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
|
1642 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1643 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1644 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1645 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1646 void ExtractStl(OrthancPluginRestOutput* output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1647 const char* url, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1648 const OrthancPluginHttpRequest* request) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1649 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1650 if (request->method != OrthancPluginHttpMethod_Get) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1651 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1652 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1653 return; |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1654 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1655 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1656 const std::string instanceId(request->groups[0]); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1657 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1658 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1659 DcmDataset& dataset = *dicom->GetDcmtkObject().getDataset(); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1660 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1661 std::string stl; |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1662 if (GetStringValue(dataset, DCM_MIMETypeOfEncapsulatedDocument) != Orthanc::MIME_STL || |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
28
diff
changeset
|
1663 GetStringValue(dataset, DCM_SOPClassUID) != UID_EncapsulatedSTLStorage || |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1664 !dicom->GetTagValue(stl, Orthanc::DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1665 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1666 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
|
1667 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1668 else |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1669 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1670 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1671 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
|
1672 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1673 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1674 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1675 |
6 | 1676 |
1677 class NiftiHeader : public boost::noncopyable | |
1678 { | |
1679 private: | |
1680 nifti_image* image_; | |
1681 | |
1682 public: | |
1683 NiftiHeader(const std::string& nifti) | |
1684 { | |
1685 nifti_1_header header; | |
1686 if (nifti.size() < sizeof(header)) | |
1687 { | |
1688 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1689 } | |
1690 | |
1691 memcpy(&header, nifti.c_str(), sizeof(header)); | |
1692 if (!nifti_hdr_looks_good(&header)) | |
1693 { | |
1694 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1695 } | |
1696 | |
1697 image_ = nifti_convert_nhdr2nim(header, "dummy_filename"); | |
1698 if (image_ == NULL) | |
1699 { | |
1700 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1701 } | |
1702 } | |
1703 | |
1704 ~NiftiHeader() | |
1705 { | |
1706 nifti_image_free(image_); | |
1707 } | |
1708 | |
1709 const nifti_image& GetInfo() const | |
1710 { | |
1711 assert(image_ != NULL); | |
1712 return *image_; | |
1713 } | |
1714 }; | |
1715 | |
1716 | |
1717 static void LoadNifti(vtkImageData* volume, | |
1718 std::string& nifti) | |
1719 { | |
1720 if (volume == NULL) | |
1721 { | |
1722 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
1723 } | |
1724 | |
1725 const uint8_t* p = reinterpret_cast<const uint8_t*>(nifti.c_str()); | |
1726 | |
1727 if (nifti.size() >= 2 && | |
1728 p[0] == 0x1f && | |
1729 p[1] == 0x8b) | |
1730 { | |
1731 Orthanc::GzipCompressor compressor; | |
1732 std::string uncompressed; | |
1733 Orthanc::IBufferCompressor::Uncompress(uncompressed, compressor, nifti); | |
1734 nifti.swap(uncompressed); | |
1735 } | |
1736 | |
1737 NiftiHeader header(nifti); | |
1738 | |
1739 if (header.GetInfo().ndim != 3) | |
1740 { | |
1741 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, | |
1742 "Only 3D NIfTI volumes are allowed"); | |
1743 } | |
1744 | |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1745 size_t itemSize; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1746 int vtkType; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1747 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1748 switch (header.GetInfo().datatype) |
6 | 1749 { |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1750 case DT_UNSIGNED_CHAR: |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1751 itemSize = 1; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1752 vtkType = VTK_UNSIGNED_CHAR; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1753 break; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1754 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1755 case DT_FLOAT: |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1756 itemSize = sizeof(float); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1757 vtkType = VTK_FLOAT; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1758 break; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1759 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1760 case DT_DOUBLE: |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1761 itemSize = sizeof(double); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1762 vtkType = VTK_DOUBLE; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1763 break; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1764 |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1765 default: |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1766 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
6 | 1767 } |
1768 | |
1769 assert(static_cast<int>(header.GetInfo().nvox) == header.GetInfo().nx * header.GetInfo().ny * header.GetInfo().nz); | |
1770 | |
1771 const size_t pixelDataOffset = sizeof(nifti_1_header) + 4 /* extension */; | |
1772 | |
8
d1267c6c33e1
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1773 if (nifti.size() != pixelDataOffset + header.GetInfo().nvox * itemSize) |
6 | 1774 { |
1775 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
1776 } | |
1777 | |
1778 volume->SetDimensions(header.GetInfo().nx, header.GetInfo().ny, header.GetInfo().nz); | |
8
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1779 volume->AllocateScalars(vtkType, 1); |
6 | 1780 volume->SetSpacing(header.GetInfo().dx, header.GetInfo().dy, header.GetInfo().dz); |
8
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1781 memcpy(volume->GetScalarPointer(), &nifti[pixelDataOffset], header.GetInfo().nvox * itemSize); |
6 | 1782 } |
1783 | |
8
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added route /stl/encode-nifti
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diff
changeset
|
1784 |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
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diff
changeset
|
1785 void EncodeNifti(OrthancPluginRestOutput* output, |
d1267c6c33e1
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diff
changeset
|
1786 const char* url, |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
1787 const OrthancPluginHttpRequest* request) |
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diff
changeset
|
1788 { |
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diff
changeset
|
1789 static const char* const KEY_NIFTI = "Nifti"; |
d1267c6c33e1
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1790 static const char* const KEY_RESOLUTION = "Resolution"; |
d1267c6c33e1
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parents:
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diff
changeset
|
1791 static const char* const KEY_PARENT_STUDY = "ParentStudy"; |
d1267c6c33e1
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diff
changeset
|
1792 static const char* const KEY_SMOOTH = "Smooth"; |
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diff
changeset
|
1793 |
d1267c6c33e1
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diff
changeset
|
1794 if (request->method != OrthancPluginHttpMethod_Post) |
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diff
changeset
|
1795 { |
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diff
changeset
|
1796 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
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diff
changeset
|
1797 return; |
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diff
changeset
|
1798 } |
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diff
changeset
|
1799 |
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diff
changeset
|
1800 Json::Value body; |
d1267c6c33e1
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diff
changeset
|
1801 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
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diff
changeset
|
1802 { |
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diff
changeset
|
1803 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
d1267c6c33e1
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diff
changeset
|
1804 } |
d1267c6c33e1
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diff
changeset
|
1805 |
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diff
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|
1806 std::string mime, nifti; |
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diff
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1807 if (!Orthanc::Toolbox::DecodeDataUriScheme(mime, nifti, Orthanc::SerializationToolbox::ReadString(body, KEY_NIFTI))) |
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diff
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|
1808 { |
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diff
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1809 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Missing the \"Nifti\" argument containing the NIfTI file"); |
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diff
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1810 } |
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diff
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|
1811 |
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diff
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1812 const std::string parentStudy = Orthanc::SerializationToolbox::ReadString(body, KEY_PARENT_STUDY); |
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diff
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|
1813 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
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diff
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|
1814 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
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diff
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1815 true /* smooth by default */); |
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diff
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1816 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
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diff
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|
1817 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
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diff
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|
1818 256 /* default value */); |
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diff
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|
1819 |
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diff
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|
1820 vtkNew<vtkImageData> volume; |
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diff
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|
1821 LoadNifti(volume.Get(), nifti); |
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diff
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|
1822 |
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diff
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|
1823 std::string stl; |
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diff
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|
1824 if (!EncodeVolume(stl, volume.Get(), resolution, smooth)) |
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diff
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1825 { |
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diff
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1826 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from NIfTI"); |
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diff
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|
1827 } |
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diff
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|
1828 else |
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diff
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|
1829 { |
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diff
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1830 const std::string title = "STL model generated from NIfTI"; |
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diff
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|
1831 |
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diff
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|
1832 const std::string frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
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diff
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|
1833 |
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diff
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|
1834 Json::Value answer; |
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diff
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1835 CallCreateDicom(answer, stl, body, parentStudy, title, frameOfReferenceUid, title); |
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diff
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|
1836 |
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diff
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1837 std::string s = answer.toStyledString(); |
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diff
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|
1838 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
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diff
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|
1839 } |
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diff
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|
1840 } |
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diff
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|
1841 |
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diff
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|
1842 |
0
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|
1843 extern "C" |
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|
1844 { |
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|
1845 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) |
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1846 { |
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|
1847 OrthancPlugins::SetGlobalContext(context); |
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|
1848 |
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1849 /* Check the version of the Orthanc core */ |
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1850 if (OrthancPluginCheckVersion(OrthancPlugins::GetGlobalContext()) == 0) |
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|
1851 { |
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|
1852 char info[1024]; |
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|
1853 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", |
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|
1854 OrthancPlugins::GetGlobalContext()->orthancVersion, |
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1855 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
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|
1856 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, |
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|
1857 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); |
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|
1858 OrthancPluginLogError(OrthancPlugins::GetGlobalContext(), info); |
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1859 return -1; |
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|
1860 } |
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|
1861 |
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|
1862 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
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|
1863 Orthanc::Logging::InitializePluginContext(context); |
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|
1864 #else |
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|
1865 Orthanc::Logging::Initialize(context); |
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|
1866 #endif |
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|
1867 |
1
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diff
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|
1868 Orthanc::InitializeFramework("", false); |
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|
1869 |
0
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1870 hasCreateDicomStl_ = OrthancPlugins::CheckMinimalOrthancVersion(1, 12, 1); |
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|
1871 |
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1872 if (!hasCreateDicomStl_) |
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|
1873 { |
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|
1874 LOG(WARNING) << "Your version of Orthanc (" << std::string(context->orthancVersion) |
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|
1875 << ") is insufficient to create DICOM STL, it should be above 1.12.1"; |
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1876 } |
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|
1877 |
25
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diff
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|
1878 OrthancPlugins::SetDescription(ORTHANC_PLUGIN_NAME, "STL plugin for Orthanc."); |
0
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|
1879 |
1
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|
1880 OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/app/(.*)", true); |
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diff
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|
1881 OrthancPlugins::RegisterRestCallback<ExtractStl>("/instances/([0-9a-f-]+)/stl", true); |
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|
1882 OrthancPlugins::RegisterRestCallback<ListStructures>("/stl/rt-struct/([0-9a-f-]+)", true); |
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1883 |
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1884 if (hasCreateDicomStl_) |
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1885 { |
8
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diff
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|
1886 OrthancPlugins::RegisterRestCallback<EncodeStructureSet>("/stl/encode-rtstruct", true); |
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diff
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|
1887 OrthancPlugins::RegisterRestCallback<EncodeNifti>("/stl/encode-nifti", true); |
1
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1888 } |
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|
1889 |
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diff
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|
1890 OrthancPlugins::OrthancConfiguration globalConfiguration; |
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diff
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|
1891 OrthancPlugins::OrthancConfiguration configuration; |
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1892 globalConfiguration.GetSection(configuration, "STL"); |
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|
1893 |
2
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1894 // Extend the default Orthanc Explorer with custom JavaScript for STL |
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1895 std::string explorer; |
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1896 |
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|
1897 { |
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|
1898 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); |
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|
1899 |
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|
1900 std::map<std::string, std::string> dictionary; |
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1901 dictionary["HAS_CREATE_DICOM_STL"] = (hasCreateDicomStl_ ? "true" : "false"); |
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|
1902 dictionary["SHOW_NIFTI_BUTTON"] = (configuration.GetBooleanValue("NIfTI", false) ? "true" : "false"); |
2
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|
1903 explorer = Orthanc::Toolbox::SubstituteVariables(explorer, dictionary); |
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|
1904 |
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|
1905 OrthancPlugins::ExtendOrthancExplorer(ORTHANC_PLUGIN_NAME, explorer); |
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|
1906 } |
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|
1907 |
0
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|
1908 return 0; |
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|
1909 } |
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|
1910 |
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|
1911 |
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|
1912 ORTHANC_PLUGINS_API void OrthancPluginFinalize() |
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1913 { |
1
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Sebastien Jodogne <s.jodogne@gmail.com>
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1914 Orthanc::FinalizeFramework(); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1915 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
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1916 |
4e889a8e8be2
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1917 |
4e889a8e8be2
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1918 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() |
4e889a8e8be2
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1919 { |
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fix deprecated calls
Sebastien Jodogne <s.jodogne@gmail.com>
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1920 return ORTHANC_PLUGIN_NAME; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1921 } |
4e889a8e8be2
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
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1922 |
4e889a8e8be2
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1923 |
4e889a8e8be2
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
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1924 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1925 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1926 return ORTHANC_STL_VERSION; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1927 } |
4e889a8e8be2
initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1928 } |