Mercurial > hg > orthanc-stl
annotate Sources/Plugin.cpp @ 28:410003c50b17
improved computation of RT-STRUCT geometry
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 04 Apr 2024 10:10:40 +0200 |
parents | 5fc3ea6acbd5 |
children | 62abf3c523f9 |
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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 |
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56 static const char* const STL_SOP_CLASS_UID = "1.2.840.10008.5.1.4.1.1.104.3"; |
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57 |
6 | 58 |
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59 // Forward declaration |
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60 void ReadStaticAsset(std::string& target, |
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61 const std::string& path); |
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62 |
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63 |
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64 /** |
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65 * As the Three.js static assets are gzipped by the |
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66 * "EmbedStaticAssets.py" script, we use a cache to maintain the |
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67 * uncompressed assets in order to avoid multiple gzip decodings. |
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68 **/ |
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69 class ResourcesCache : public boost::noncopyable |
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70 { |
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71 private: |
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72 typedef std::map<std::string, std::string*> Content; |
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73 |
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74 boost::shared_mutex mutex_; |
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75 Content content_; |
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76 |
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77 public: |
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78 ~ResourcesCache() |
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79 { |
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80 for (Content::iterator it = content_.begin(); it != content_.end(); ++it) |
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81 { |
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82 assert(it->second != NULL); |
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83 delete it->second; |
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84 } |
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85 } |
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86 |
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87 void Answer(OrthancPluginRestOutput* output, |
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88 const std::string& path) |
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89 { |
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90 const std::string mime = Orthanc::EnumerationToString(Orthanc::SystemToolbox::AutodetectMimeType(path)); |
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91 |
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92 { |
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93 // Check whether the cache already contains the resource |
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94 boost::shared_lock<boost::shared_mutex> lock(mutex_); |
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95 |
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96 Content::const_iterator found = content_.find(path); |
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97 |
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98 if (found != content_.end()) |
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99 { |
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100 assert(found->second != NULL); |
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101 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, found->second->c_str(), found->second->size(), mime.c_str()); |
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102 return; |
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103 } |
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104 } |
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105 |
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106 // This resource has not been cached yet |
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107 |
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108 std::unique_ptr<std::string> item(new std::string); |
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109 ReadStaticAsset(*item, path); |
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110 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, item->c_str(), item->size(), mime.c_str()); |
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111 |
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112 { |
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113 // Store the resource into the cache |
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114 boost::unique_lock<boost::shared_mutex> lock(mutex_); |
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115 |
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116 if (content_.find(path) == content_.end()) |
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117 { |
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118 content_[path] = item.release(); |
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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 |
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124 |
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125 static ResourcesCache cache_; |
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126 static bool hasCreateDicomStl_; |
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127 |
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128 void ServeFile(OrthancPluginRestOutput* output, |
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129 const char* url, |
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130 const OrthancPluginHttpRequest* request) |
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131 { |
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132 if (request->method != OrthancPluginHttpMethod_Get) |
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133 { |
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134 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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135 return; |
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136 } |
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137 |
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138 std::string file = request->groups[0]; |
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139 |
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140 if (file == "viewer.html") |
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141 { |
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142 std::string s; |
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143 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_HTML); |
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144 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Html)); |
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145 } |
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146 else if (file == "viewer.js") |
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147 { |
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148 std::string s; |
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149 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_JS); |
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150 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_JavaScript)); |
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151 } |
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152 else |
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153 { |
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154 cache_.Answer(output, file); |
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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 |
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160 |
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161 #include <dcmtk/dcmdata/dcdeftag.h> |
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162 #include <dcmtk/dcmdata/dcfilefo.h> |
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163 #include <dcmtk/dcmdata/dcitem.h> |
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164 #include <dcmtk/dcmdata/dcsequen.h> |
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165 |
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166 class Extent2D : public boost::noncopyable |
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167 { |
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168 private: |
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169 bool isEmpty_; |
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170 double x1_; |
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171 double y1_; |
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172 double x2_; |
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173 double y2_; |
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174 |
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175 void CheckNotEmpty() const |
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176 { |
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177 if (isEmpty_) |
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178 { |
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179 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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180 } |
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181 } |
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182 |
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183 public: |
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184 Extent2D() : |
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185 isEmpty_(true), |
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186 x1_(0), |
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187 y1_(0), |
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188 x2_(0), |
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189 y2_(0) |
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190 { |
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191 } |
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192 |
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193 bool IsEmpty() const |
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194 { |
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195 return isEmpty_; |
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196 } |
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197 |
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198 double GetMinX() const |
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199 { |
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200 CheckNotEmpty(); |
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201 return x1_; |
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202 } |
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203 |
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204 double GetMaxX() const |
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205 { |
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206 CheckNotEmpty(); |
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207 return x2_; |
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208 } |
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209 |
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210 double GetMinY() const |
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211 { |
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212 CheckNotEmpty(); |
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213 return y1_; |
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214 } |
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215 |
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216 double GetMaxY() const |
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217 { |
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218 CheckNotEmpty(); |
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219 return y2_; |
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220 } |
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221 |
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222 double GetWidth() const |
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223 { |
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224 CheckNotEmpty(); |
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225 return x2_ - x1_; |
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226 } |
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227 |
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228 double GetHeight() const |
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229 { |
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230 CheckNotEmpty(); |
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231 return y2_ - y1_; |
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232 } |
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233 |
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234 void Add(double x, |
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235 double y) |
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236 { |
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237 if (isEmpty_) |
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238 { |
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239 x1_ = x2_ = x; |
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240 y1_ = y2_ = y; |
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241 isEmpty_ = false; |
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242 } |
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243 else |
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244 { |
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245 x1_ = std::min(x1_, x); |
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246 x2_ = std::max(x2_, x); |
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247 y1_ = std::min(y1_, y); |
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248 y2_ = std::max(y2_, y); |
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249 } |
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250 } |
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251 }; |
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252 |
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253 static std::string GetStringValue(DcmItem& item, |
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254 const DcmTagKey& key) |
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255 { |
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256 const char* s = NULL; |
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257 if (!item.findAndGetString(key, s).good() || |
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258 s == NULL) |
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259 { |
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260 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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261 } |
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262 else |
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263 { |
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264 return Orthanc::Toolbox::StripSpaces(s); |
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265 } |
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266 } |
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267 |
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268 |
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269 static void ListStructuresNames(std::set<std::string>& target, |
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270 Orthanc::ParsedDicomFile& source) |
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271 { |
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272 target.clear(); |
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273 |
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274 DcmSequenceOfItems* sequence = NULL; |
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275 if (!source.GetDcmtkObject().getDataset()->findAndGetSequence(DCM_StructureSetROISequence, sequence).good() || |
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276 sequence == NULL) |
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277 { |
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278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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279 } |
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280 |
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281 for (unsigned long i = 0; i < sequence->card(); i++) |
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282 { |
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283 DcmItem* item = sequence->getItem(i); |
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284 if (item == NULL) |
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285 { |
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286 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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287 } |
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288 else |
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289 { |
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290 target.insert(GetStringValue(*item, DCM_ROIName)); |
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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 |
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296 static bool IsNear(double a, |
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297 double b) |
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298 { |
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299 return std::abs(a - b) < 10.0 * std::numeric_limits<double>::epsilon(); |
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300 } |
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301 |
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302 |
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303 class Vector3D |
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304 { |
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305 private: |
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306 double x_; |
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307 double y_; |
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308 double z_; |
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309 |
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310 public: |
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311 Vector3D() : |
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312 x_(0), |
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313 y_(0), |
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314 z_(0) |
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315 { |
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316 } |
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317 |
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318 Vector3D(double x, |
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319 double y, |
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320 double z) : |
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321 x_(x), |
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322 y_(y), |
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323 z_(z) |
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324 { |
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325 } |
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326 |
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327 Vector3D(const Vector3D& from, |
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328 const Vector3D& to) : |
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329 x_(to.x_ - from.x_), |
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330 y_(to.y_ - from.y_), |
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331 z_(to.z_ - from.z_) |
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332 { |
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333 } |
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334 |
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335 double GetX() const |
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336 { |
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337 return x_; |
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338 } |
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339 |
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340 double GetY() const |
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341 { |
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342 return y_; |
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343 } |
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344 |
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345 double GetZ() const |
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346 { |
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347 return z_; |
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348 } |
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349 |
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350 double ComputeNorm() const |
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351 { |
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352 return sqrt(x_ * x_ + y_ * y_ + z_ * z_); |
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353 } |
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354 |
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355 void Normalize() |
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356 { |
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357 double norm = ComputeNorm(); |
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358 if (!IsNear(norm, 0)) |
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359 { |
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360 x_ /= norm; |
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361 y_ /= norm; |
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362 z_ /= norm; |
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363 } |
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364 } |
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365 |
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366 static Vector3D CrossProduct(const Vector3D& u, |
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367 const Vector3D& v) |
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368 { |
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369 return Vector3D(u.GetY() * v.GetZ() - u.GetZ() * v.GetY(), |
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370 u.GetZ() * v.GetX() - u.GetX() * v.GetZ(), |
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371 u.GetX() * v.GetY() - u.GetY() * v.GetX()); |
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372 } |
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373 |
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374 static double DotProduct(const Vector3D& a, |
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375 const Vector3D& b) |
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376 { |
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377 return a.GetX() * b.GetX() + a.GetY() * b.GetY() + a.GetZ() * b.GetZ(); |
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378 } |
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379 }; |
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380 |
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381 |
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382 |
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383 static bool MyParseDouble(double& value, |
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384 const std::string& s) |
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385 { |
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386 #if 1 |
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387 // This version is much faster, as "ParseDouble()" internally uses |
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388 // "boost::lexical_cast<double>()" |
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389 char* end = NULL; |
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390 value = strtod(s.c_str(), &end); |
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391 return (end == s.c_str() + s.size()); |
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392 #else |
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393 return Orthanc::SerializationToolbox::ParseDouble(value, s); |
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394 #endif |
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395 } |
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396 |
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397 |
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398 class StructurePolygon : public boost::noncopyable |
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399 { |
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400 private: |
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401 std::string roiName_; |
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402 std::string referencedSopInstanceUid_; |
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403 uint8_t red_; |
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404 uint8_t green_; |
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405 uint8_t blue_; |
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406 std::vector<Vector3D> points_; |
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407 |
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408 public: |
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409 StructurePolygon(Orthanc::ParsedDicomFile& dicom, |
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410 unsigned long roiIndex, |
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411 unsigned long contourIndex) |
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412 { |
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413 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
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414 |
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415 DcmItem* structure = NULL; |
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416 DcmItem* roi = NULL; |
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417 DcmItem* contour = NULL; |
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418 DcmSequenceOfItems* referenced = NULL; |
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419 |
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420 if (!dataset.findAndGetSequenceItem(DCM_StructureSetROISequence, structure, roiIndex).good() || |
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421 structure == NULL || |
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422 !dataset.findAndGetSequenceItem(DCM_ROIContourSequence, roi, roiIndex).good() || |
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423 roi == NULL || |
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424 !roi->findAndGetSequenceItem(DCM_ContourSequence, contour, contourIndex).good() || |
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425 contour == NULL || |
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426 !contour->findAndGetSequence(DCM_ContourImageSequence, referenced).good() || |
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427 referenced == NULL || |
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428 referenced->card() != 1) |
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429 { |
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430 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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431 } |
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432 |
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433 roiName_ = GetStringValue(*structure, DCM_ROIName); |
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434 referencedSopInstanceUid_ = GetStringValue(*referenced->getItem(0), DCM_ReferencedSOPInstanceUID); |
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435 |
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436 if (GetStringValue(*contour, DCM_ContourGeometricType) != "CLOSED_PLANAR") |
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437 { |
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438 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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439 } |
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440 |
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441 { |
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442 std::vector<std::string> tokens; |
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443 Orthanc::Toolbox::TokenizeString(tokens, GetStringValue(*roi, DCM_ROIDisplayColor), '\\'); |
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444 |
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445 uint32_t r, g, b; |
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446 if (tokens.size() != 3 || |
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447 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(r, tokens[0]) || |
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448 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(g, tokens[1]) || |
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449 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(b, tokens[2]) || |
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450 r > 255 || |
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451 g > 255 || |
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452 b > 255) |
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453 { |
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454 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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455 } |
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456 |
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457 red_ = r; |
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458 green_ = g; |
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459 blue_ = b; |
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460 } |
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461 |
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462 { |
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463 std::vector<std::string> tokens; |
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464 Orthanc::Toolbox::TokenizeString(tokens, GetStringValue(*contour, DCM_ContourData), '\\'); |
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465 |
3
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466 const std::string s = GetStringValue(*contour, DCM_NumberOfContourPoints); |
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467 |
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468 uint32_t countPoints; |
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469 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(countPoints, s) || |
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470 tokens.size() != 3 * countPoints) |
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471 { |
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472 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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473 } |
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474 |
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475 points_.reserve(countPoints); |
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476 |
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477 for (size_t i = 0; i < tokens.size(); i += 3) |
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478 { |
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479 double x, y, z; |
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480 if (!MyParseDouble(x, tokens[i]) || |
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481 !MyParseDouble(y, tokens[i + 1]) || |
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482 !MyParseDouble(z, tokens[i + 2])) |
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483 { |
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484 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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485 } |
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486 |
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487 points_.push_back(Vector3D(x, y, z)); |
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488 } |
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489 |
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490 assert(points_.size() == countPoints); |
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491 } |
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492 } |
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493 |
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494 const std::string& GetRoiName() const |
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495 { |
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496 return roiName_; |
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497 } |
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498 |
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499 const std::string& GetReferencedSopInstanceUid() const |
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500 { |
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501 return referencedSopInstanceUid_; |
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502 } |
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503 |
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504 size_t GetPointsCount() const |
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505 { |
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506 return points_.size(); |
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507 } |
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508 |
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509 const Vector3D& GetPoint(size_t i) const |
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510 { |
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511 if (i >= points_.size()) |
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512 { |
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513 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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514 } |
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515 else |
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516 { |
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517 return points_[i]; |
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518 } |
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519 } |
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520 |
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521 bool IsCoplanar(Vector3D& normal) const |
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522 { |
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523 if (points_.size() < 3) |
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524 { |
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525 return false; |
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526 } |
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527 |
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528 bool hasNormal = false; |
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529 |
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530 for (size_t i = 0; i < points_.size(); i++) |
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531 { |
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532 normal = Vector3D::CrossProduct(Vector3D(points_[1], points_[0]), |
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533 Vector3D(points_[2], points_[0])); |
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534 if (!IsNear(normal.ComputeNorm(), 0)) |
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535 { |
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536 normal.Normalize(); |
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537 hasNormal = true; |
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538 } |
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539 } |
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540 |
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541 if (!hasNormal) |
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542 { |
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543 return false; |
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544 } |
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545 |
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546 double a = Vector3D::DotProduct(points_[0], normal); |
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547 |
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548 for (size_t i = 1; i < points_.size(); i++) |
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549 { |
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550 double b = Vector3D::DotProduct(points_[i], normal); |
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551 if (!IsNear(a, b)) |
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552 { |
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553 return false; |
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554 } |
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555 } |
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556 |
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557 return true; |
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558 } |
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559 |
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560 void Add(Extent2D& extent, |
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561 const Vector3D& axisX, |
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562 const Vector3D& axisY) const |
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563 { |
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564 assert(IsNear(1, axisX.ComputeNorm())); |
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565 assert(IsNear(1, axisY.ComputeNorm())); |
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566 |
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567 for (size_t i = 0; i < points_.size(); i++) |
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568 { |
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569 extent.Add(Vector3D::DotProduct(axisX, points_[i]), |
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570 Vector3D::DotProduct(axisY, points_[i])); |
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571 } |
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572 } |
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573 }; |
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574 |
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changeset
|
575 |
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576 |
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577 struct IsNearPredicate |
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578 { |
0f03a8a0bd6f
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parents:
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diff
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|
579 bool operator() (const double& a, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
580 const double& b) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
581 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
582 return IsNear(a, b); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
583 } |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
584 }; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
585 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
586 static void RemoveDuplicateValues(std::vector<double>& v) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
587 { |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
588 IsNearPredicate predicate; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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589 std::vector<double>::iterator last = std::unique(v.begin(), v.end(), predicate); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
590 v.erase(last, v.end()); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
591 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
592 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
593 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
594 class StructureSet : public boost::noncopyable |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
595 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
596 private: |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
597 std::vector<StructurePolygon*> polygons_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
598 std::string patientId_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
599 std::string studyInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
600 std::string seriesInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
601 std::string sopInstanceUid_; |
4
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generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
602 bool hasFrameOfReferenceUid_; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
603 std::string frameOfReferenceUid_; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
604 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
605 public: |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
606 explicit StructureSet(Orthanc::ParsedDicomFile& dicom) : |
4
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generated STL pass dciodvfy
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changeset
|
607 hasFrameOfReferenceUid_(false) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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608 { |
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encoding of RT-STRUCT as STL
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609 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
3
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added route "/instances/{id}/stl"
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|
610 patientId_ = GetStringValue(dataset, DCM_PatientID); |
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added route "/instances/{id}/stl"
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changeset
|
611 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID); |
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added route "/instances/{id}/stl"
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|
612 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID); |
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added route "/instances/{id}/stl"
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613 sopInstanceUid_ = GetStringValue(dataset, DCM_SOPInstanceUID); |
1
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|
614 |
4
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changeset
|
615 DcmSequenceOfItems* frame = NULL; |
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616 if (!dataset.findAndGetSequence(DCM_ReferencedFrameOfReferenceSequence, frame).good() || |
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diff
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|
617 frame == NULL) |
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|
618 { |
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|
619 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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|
620 } |
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changeset
|
621 |
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changeset
|
622 if (frame->card() == 1) |
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generated STL pass dciodvfy
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diff
changeset
|
623 { |
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|
624 const char* v = NULL; |
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|
625 if (frame->getItem(0)->findAndGetString(DCM_FrameOfReferenceUID, v).good() && |
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generated STL pass dciodvfy
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|
626 v != NULL) |
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changeset
|
627 { |
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changeset
|
628 hasFrameOfReferenceUid_ = true; |
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changeset
|
629 frameOfReferenceUid_.assign(v); |
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changeset
|
630 } |
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diff
changeset
|
631 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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3
diff
changeset
|
632 |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
633 DcmSequenceOfItems* rois = NULL; |
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634 if (!dataset.findAndGetSequence(DCM_ROIContourSequence, rois).good() || |
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encoding of RT-STRUCT as STL
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changeset
|
635 rois == NULL) |
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|
636 { |
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|
637 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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changeset
|
638 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
639 |
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|
640 std::vector<DcmSequenceOfItems*> contours(rois->card()); |
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|
641 size_t countPolygons = 0; |
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encoding of RT-STRUCT as STL
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|
642 |
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|
643 for (unsigned long i = 0; i < rois->card(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
644 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
645 DcmSequenceOfItems* contour = NULL; |
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646 if (!rois->getItem(i)->findAndGetSequence(DCM_ContourSequence, contour).good() || |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
647 contour == NULL) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
648 { |
0f03a8a0bd6f
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changeset
|
649 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
650 } |
0f03a8a0bd6f
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changeset
|
651 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
652 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
653 contours[i] = contour; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
654 countPolygons += contour->card(); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
655 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
656 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
657 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
658 polygons_.resize(countPolygons); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
659 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
660 size_t pos = 0; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
661 for (unsigned long i = 0; i < contours.size(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
662 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
663 for (unsigned long j = 0; j < contours[i]->card(); j++, pos++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
664 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
665 polygons_[pos] = new StructurePolygon(dicom, i, j); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
666 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
667 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
668 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
669 assert(pos == countPolygons); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
670 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
671 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
672 ~StructureSet() |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
673 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
674 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
|
675 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
676 assert(polygons_[i] != NULL); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
677 delete polygons_[i]; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
678 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
679 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
680 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
681 const std::string& GetPatient() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
682 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
683 return patientId_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
684 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
685 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
686 const std::string& GetStudyInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
687 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
688 return studyInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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 const std::string& GetSeriesInstanceUid() const |
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 return seriesInstanceUid_; |
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 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
696 const std::string& GetSopInstanceUid() const |
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 return sopInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
699 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
700 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
701 std::string HashStudy() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
702 { |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
703 Orthanc::DicomInstanceHasher hasher(patientId_, studyInstanceUid_, seriesInstanceUid_, sopInstanceUid_); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
704 return hasher.HashStudy(); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
705 } |
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 size_t GetPolygonsCount() const |
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 return polygons_.size(); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
710 } |
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 const StructurePolygon& GetPolygon(size_t i) const |
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 if (i >= polygons_.size()) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
715 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
716 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
717 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
718 else |
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 assert(polygons_[i] != NULL); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
721 return *polygons_[i]; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
722 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
723 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
724 |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
725 bool HasFrameOfReferenceUid() const |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
726 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
727 return hasFrameOfReferenceUid_; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
728 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
729 |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
730 const std::string& GetFrameOfReferenceUid() const |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
731 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
732 if (hasFrameOfReferenceUid_) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
733 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
734 return frameOfReferenceUid_; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
735 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
736 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
737 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
738 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
739 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
740 } |
1
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 |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
744 class StructureSetGeometry : public boost::noncopyable |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
745 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
746 private: |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
747 bool strict_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
748 Vector3D slicesNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
749 double slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
750 double minProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
751 double maxProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
752 size_t slicesCount_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
753 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
754 static bool AreNormalsParallel(const Vector3D& a, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
755 const Vector3D& b) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
756 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
757 return IsNear(std::abs(Vector3D::DotProduct(a, b)), 1); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
758 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
759 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
760 bool LookupProjectionIndex(size_t& index, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
761 double z) const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
762 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
763 if (slicesCount_ == 0) |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
766 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
767 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
768 if (z < minProjectionAlongNormal_ || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
769 z > maxProjectionAlongNormal_) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
770 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
771 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
774 assert(slicesSpacing_ > 0 && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
775 minProjectionAlongNormal_ < maxProjectionAlongNormal_); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
776 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
777 double d = (z - minProjectionAlongNormal_) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
778 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
779 if (IsNear(d, round(d))) |
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 (d < 0.0 || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
782 d > static_cast<double>(slicesCount_) - 1.0) |
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_InternalError); |
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 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
787 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
788 index = static_cast<size_t>(round(d)); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
789 return true; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
790 } |
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 else |
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 return false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
795 } |
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 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
798 public: |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
799 StructureSetGeometry(const StructureSet& structures, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
800 bool strict) : |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
801 strict_(strict) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
802 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
803 bool isValid = false; |
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 std::vector<double> projections; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
806 projections.reserve(structures.GetPolygonsCount()); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
807 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
808 for (size_t i = 0; i < structures.GetPolygonsCount(); i++) |
410003c50b17
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
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|
810 Vector3D normal; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
811 if (structures.GetPolygon(i).IsCoplanar(normal)) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
812 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
813 // 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
|
814 if (!isValid) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
815 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
816 isValid = true; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
817 slicesNormal_ = normal; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
818 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
819 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
820 if (AreNormalsParallel(normal, slicesNormal_)) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
821 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
822 // This is a valid slice (it is parallel to the normal) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
823 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
|
824 projections.push_back(Vector3D::DotProduct(point, slicesNormal_)); |
410003c50b17
improved computation of RT-STRUCT geometry
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 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
827 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
828 // RT-STRUCT with non-parallel slices |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
829 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
830 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
831 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
832 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
833 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
834 // Ignore slices that are not coplanar |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
835 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
836 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
837 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
838 if (projections.empty()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
839 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
840 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
841 "Structure set without a valid geometry"); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
842 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
843 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
844 // Only keep unique projections |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
845 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
846 std::sort(projections.begin(), projections.end()); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
847 RemoveDuplicateValues(projections); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
848 assert(!projections.empty()); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
849 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
850 if (projections.size() == 1) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
851 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
852 // Volume with one single slice |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
853 minProjectionAlongNormal_ = projections[0]; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
854 maxProjectionAlongNormal_ = projections[0]; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
855 slicesSpacing_ = 1; // Arbitrary value |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
856 slicesCount_ = 1; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
857 return; |
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 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
860 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
861 // Compute the most probable spacing between the slices |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
862 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
863 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
864 std::vector<double> spacings; |
410003c50b17
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parents:
25
diff
changeset
|
865 spacings.resize(projections.size() - 1); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
866 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
867 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
|
868 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
869 spacings[i] = projections[i + 1] - projections[i]; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
870 assert(spacings[i] > 0); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
871 } |
410003c50b17
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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 std::sort(spacings.begin(), spacings.end()); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
874 RemoveDuplicateValues(spacings); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
875 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
876 if (spacings.empty()) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
877 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
878 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
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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 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
881 slicesSpacing_ = spacings[spacings.size() / 10]; // Take the 90% percentile of smallest spacings |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
882 assert(slicesSpacing_ > 0); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
883 } |
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 // 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
|
887 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
888 bool first = true; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
889 size_t bestSupport; |
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improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
890 double bestProjection; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
891 |
410003c50b17
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parents:
25
diff
changeset
|
892 std::list<size_t> candidates; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
893 for (size_t i = 0; i < projections.size(); i++) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
894 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
895 candidates.push_back(i); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
896 } |
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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 while (!candidates.empty()) |
410003c50b17
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parents:
25
diff
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|
899 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
900 std::list<size_t> next; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
901 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
902 size_t countSupport = 0; |
410003c50b17
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parents:
25
diff
changeset
|
903 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
904 std::list<size_t>::const_iterator it = candidates.begin(); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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|
905 size_t reference = *it; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
906 it++; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
907 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
908 while (it != candidates.end()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
909 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
910 double d = (projections[*it] - projections[reference]) / slicesSpacing_; |
410003c50b17
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parents:
25
diff
changeset
|
911 if (IsNear(d, round(d))) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
912 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
913 countSupport ++; |
410003c50b17
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25
diff
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|
914 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
915 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
916 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
917 next.push_back(*it); |
410003c50b17
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25
diff
changeset
|
918 } |
410003c50b17
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parents:
25
diff
changeset
|
919 |
410003c50b17
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parents:
25
diff
changeset
|
920 it++; |
410003c50b17
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parents:
25
diff
changeset
|
921 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
922 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
923 if (first || |
410003c50b17
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parents:
25
diff
changeset
|
924 countSupport > bestSupport) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
925 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
926 first = false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
927 bestSupport = countSupport; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
928 bestProjection = projections[reference]; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
929 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
930 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
931 if (strict && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
932 !next.empty()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
933 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
934 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
935 "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
|
936 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
937 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
938 candidates.swap(next); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
939 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
940 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
941 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
942 // Compute the range of the projections |
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 minProjectionAlongNormal_ = bestProjection; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
945 maxProjectionAlongNormal_ = bestProjection; |
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 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
|
948 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
949 double d = (projections[i] - bestProjection) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
950 if (IsNear(d, round(d))) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
951 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
952 minProjectionAlongNormal_ = std::min(minProjectionAlongNormal_, projections[i]); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
953 maxProjectionAlongNormal_ = std::max(maxProjectionAlongNormal_, projections[i]); |
410003c50b17
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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 } |
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 double d = (maxProjectionAlongNormal_ - minProjectionAlongNormal_) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
958 if (IsNear(d, round(d))) |
410003c50b17
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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 slicesCount_ = static_cast<size_t>(round(d)) + 1; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
961 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
962 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
963 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
964 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
965 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
966 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
967 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
968 // Sanity check |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
969 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
970 size_t a, b; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
971 if (!LookupProjectionIndex(a, minProjectionAlongNormal_) || |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
972 !LookupProjectionIndex(b, maxProjectionAlongNormal_) || |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
973 a != 0 || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
974 b + 1 != slicesCount_) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
975 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
976 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
977 } |
410003c50b17
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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
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25
diff
changeset
|
980 const Vector3D& GetSlicesNormal() const |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
981 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
982 return slicesNormal_; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
983 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
984 |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
985 double GetSlicesSpacing() const |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
986 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
987 return slicesSpacing_; |
410003c50b17
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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 |
410003c50b17
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parents:
25
diff
changeset
|
990 double GetMinProjectionAlongNormal() const |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
991 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
992 return minProjectionAlongNormal_; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
993 } |
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 double GetMaxProjectionAlongNormal() const |
410003c50b17
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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 return maxProjectionAlongNormal_; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
998 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
999 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1000 bool ProjectAlongNormal(double& z, |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
1001 const StructurePolygon& polygon) const |
410003c50b17
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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 Vector3D normal; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1004 if (polygon.IsCoplanar(normal) && |
410003c50b17
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parents:
25
diff
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|
1005 AreNormalsParallel(normal, slicesNormal_)) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1006 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1007 z = Vector3D::DotProduct(polygon.GetPoint(0), slicesNormal_); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
1008 return true; |
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parents:
25
diff
changeset
|
1009 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1010 else |
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>
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25
diff
changeset
|
1012 return false; |
410003c50b17
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25
diff
changeset
|
1013 } |
410003c50b17
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25
diff
changeset
|
1014 } |
410003c50b17
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25
diff
changeset
|
1015 |
410003c50b17
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25
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|
1016 size_t GetSlicesCount() const |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
1017 { |
410003c50b17
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25
diff
changeset
|
1018 return slicesCount_; |
410003c50b17
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25
diff
changeset
|
1019 } |
410003c50b17
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25
diff
changeset
|
1020 |
410003c50b17
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25
diff
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|
1021 bool LookupSliceIndex(size_t& slice, |
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25
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|
1022 const StructurePolygon& polygon) const |
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25
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|
1023 { |
410003c50b17
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25
diff
changeset
|
1024 double z; |
410003c50b17
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|
1025 return (ProjectAlongNormal(z, polygon) && |
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25
diff
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|
1026 LookupProjectionIndex(slice, z)); |
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25
diff
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|
1027 } |
410003c50b17
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25
diff
changeset
|
1028 }; |
410003c50b17
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25
diff
changeset
|
1029 |
410003c50b17
improved computation of RT-STRUCT geometry
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25
diff
changeset
|
1030 |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1031 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1032 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1033 class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1034 { |
0f03a8a0bd6f
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parents:
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diff
changeset
|
1035 private: |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1036 Orthanc::ImageAccessor& target_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1037 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1038 public: |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1039 XorFiller(Orthanc::ImageAccessor& target) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1040 target_(target) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1041 { |
0f03a8a0bd6f
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parents:
0
diff
changeset
|
1042 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1043 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1044 virtual void Fill(int y, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1045 int x1, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1046 int x2) ORTHANC_OVERRIDE |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
1047 { |
0f03a8a0bd6f
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0
diff
changeset
|
1048 assert(x1 <= x2); |
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1049 |
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1050 if (y >= 0 && |
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1051 y < static_cast<int>(target_.GetHeight())) |
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1052 { |
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1053 x1 = std::max(x1, 0); |
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1054 x2 = std::min(x2, static_cast<int>(target_.GetWidth()) - 1); |
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1055 |
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1056 uint8_t* p = reinterpret_cast<uint8_t*>(target_.GetRow(y)) + x1; |
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1057 |
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1058 for (int i = x1; i <= x2; i++, p++) |
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1059 { |
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1060 *p = (*p ^ 0xff); |
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1061 } |
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1062 } |
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1063 } |
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1064 }; |
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1065 |
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1066 |
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1067 static void EncodeSTL(std::string& target /* out */, |
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1068 vtkPolyData& mesh /* in */) |
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1069 { |
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1070 // TODO - Conversion to little endian on big endian |
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1071 |
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1072 Orthanc::ChunkedBuffer buffer; |
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1073 |
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1074 uint8_t header[80]; |
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1075 memset(header, 0, sizeof(header)); |
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1076 buffer.AddChunk(header, sizeof(header)); |
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1077 |
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1078 uint32_t n = mesh.GetNumberOfCells(); |
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1079 buffer.AddChunk(&n, sizeof(n)); |
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1080 |
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1081 for (vtkIdType i = 0; i < mesh.GetNumberOfCells(); i++) |
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1082 { |
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1083 vtkCell* cell = mesh.GetCell(i); |
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1084 vtkTriangle* triangle = dynamic_cast<vtkTriangle*>(cell); |
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1085 |
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1086 double p0[3]; |
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1087 double p1[3]; |
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1088 double p2[3]; |
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1089 triangle->GetPoints()->GetPoint(0, p0); |
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1090 triangle->GetPoints()->GetPoint(1, p1); |
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1091 triangle->GetPoints()->GetPoint(2, p2); |
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1092 |
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1093 double normal[3]; |
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1094 vtkTriangle::ComputeNormal(p0, p1, p2, normal); |
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1095 |
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1096 float d[4 * 3] = { |
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1097 static_cast<float>(normal[0]), static_cast<float>(normal[1]), static_cast<float>(normal[2]), |
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1098 static_cast<float>(p0[0]), static_cast<float>(p0[1]), static_cast<float>(p0[2]), |
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1099 static_cast<float>(p1[0]), static_cast<float>(p1[1]), static_cast<float>(p1[2]), |
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1100 static_cast<float>(p2[0]), static_cast<float>(p2[1]), static_cast<float>(p2[2]) }; |
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1101 buffer.AddChunk(d, sizeof(d)); |
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1102 |
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1103 uint16_t a = 0; |
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1104 buffer.AddChunk(&a, sizeof(a)); |
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1105 } |
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1106 |
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1107 buffer.Flatten(target); |
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1108 } |
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1109 |
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1110 |
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1111 bool EncodeVolume(std::string& stl, |
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1112 vtkImageData* volume, |
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1113 unsigned int resolution, |
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1114 bool smooth) |
7 | 1115 { |
1116 if (volume == NULL) | |
1117 { | |
1118 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
1119 } | |
1120 | |
1121 vtkNew<vtkImageResize> resize; | |
1122 resize->SetOutputDimensions(resolution, resolution, resolution); | |
1123 resize->SetInputData(volume); | |
1124 resize->Update(); | |
1125 | |
1126 vtkNew<vtkImageConstantPad> padding; | |
1127 padding->SetConstant(0); | |
1128 padding->SetOutputNumberOfScalarComponents(1); | |
1129 padding->SetOutputWholeExtent(-1, resolution, -1, resolution, -1, resolution); | |
1130 padding->SetInputData(resize->GetOutput()); | |
1131 padding->Update(); | |
1132 | |
1133 double range[2]; | |
1134 padding->GetOutput()->GetScalarRange(range); | |
1135 | |
1136 const double isoValue = (range[0] + range[1]) / 2.0; | |
1137 | |
1138 vtkNew<vtkMarchingCubes> surface; | |
1139 surface->SetInputData(padding->GetOutput()); | |
1140 surface->ComputeNormalsOn(); | |
1141 surface->SetValue(0, isoValue); | |
1142 surface->Update(); | |
1143 | |
1144 if (smooth) | |
1145 { | |
1146 vtkNew<vtkSmoothPolyDataFilter> smoothFilter; | |
1147 // Apply volume smoothing | |
1148 // https://examples.vtk.org/site/Cxx/PolyData/SmoothPolyDataFilter/ | |
1149 smoothFilter->SetInputConnection(surface->GetOutputPort()); | |
1150 smoothFilter->SetNumberOfIterations(15); | |
1151 smoothFilter->SetRelaxationFactor(0.1); | |
1152 smoothFilter->FeatureEdgeSmoothingOff(); | |
1153 smoothFilter->BoundarySmoothingOn(); | |
1154 smoothFilter->Update(); | |
1155 | |
1156 vtkNew<vtkPolyDataNormals> normalGenerator; | |
1157 normalGenerator->SetInputConnection(smoothFilter->GetOutputPort()); | |
1158 normalGenerator->ComputePointNormalsOn(); | |
1159 normalGenerator->ComputeCellNormalsOn(); | |
1160 normalGenerator->Update(); | |
1161 | |
1162 EncodeSTL(stl, *normalGenerator->GetOutput()); | |
1163 } | |
1164 else | |
1165 { | |
1166 EncodeSTL(stl, *surface->GetOutput()); | |
1167 } | |
1168 | |
1169 return true; | |
1170 } | |
1171 | |
1172 | |
1173 bool EncodeStructureSetMesh(std::string& stl, | |
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1174 const StructureSet& structureSet, |
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1175 const StructureSetGeometry& geometry, |
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1176 const std::set<std::string>& roiNames, |
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1177 unsigned int resolution, |
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1178 bool smooth) |
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1179 { |
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1180 if (resolution < 1) |
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1181 { |
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1182 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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1183 } |
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1184 |
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1185 if (!IsNear(1, geometry.GetSlicesNormal().ComputeNorm())) |
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1186 { |
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1187 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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1188 } |
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1189 |
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1190 // TODO - Axes could be retrieved from the referenced CT volume |
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1191 Vector3D axisX(1, 0, 0); |
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1192 Vector3D axisY = Vector3D::CrossProduct(geometry.GetSlicesNormal(), axisX); |
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1193 |
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1194 if (!IsNear(1, axisX.ComputeNorm()) || |
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1195 !IsNear(1, axisY.ComputeNorm())) |
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1196 { |
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1197 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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1198 } |
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1199 |
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1200 Extent2D extent; |
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1201 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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1202 { |
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1203 structureSet.GetPolygon(i).Add(extent, axisX, axisY); |
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1204 } |
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1205 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
1206 const int depth = geometry.GetSlicesCount(); |
1
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1207 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1208 vtkNew<vtkImageData> volume; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1209 volume->SetDimensions(resolution, resolution, depth); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1210 volume->AllocateScalars(VTK_UNSIGNED_CHAR, 1); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1211 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1212 assert(sizeof(unsigned char) == 1); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1213 memset(volume->GetScalarPointer(), 0, resolution * resolution * depth); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1214 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1215 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1216 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1217 const StructurePolygon& polygon = structureSet.GetPolygon(i); |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1218 if (roiNames.find(polygon.GetRoiName()) == roiNames.end()) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1219 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1220 // This polygon doesn't correspond to a ROI of interest |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1221 continue; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1222 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1223 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1224 size_t j; |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1225 if (!geometry.LookupSliceIndex(j, polygon)) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1226 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1227 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1228 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1229 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1230 std::vector<Orthanc::ImageProcessing::ImagePoint> points; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1231 points.reserve(polygon.GetPointsCount()); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1232 for (size_t j = 0; j < polygon.GetPointsCount(); j++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1233 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1234 const Vector3D& point = polygon.GetPoint(j); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1235 double x = (Vector3D::DotProduct(point, axisX) - extent.GetMinX()) / extent.GetWidth() * static_cast<double>(resolution); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1236 double y = (Vector3D::DotProduct(point, axisY) - extent.GetMinY()) / extent.GetHeight() * static_cast<double>(resolution); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1237 points.push_back(Orthanc::ImageProcessing::ImagePoint(static_cast<int32_t>(std::floor(x)), |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1238 static_cast<int32_t>(std::floor(y)))); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1239 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1240 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1241 Orthanc::ImageAccessor slice; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1242 slice.AssignWritable(Orthanc::PixelFormat_Grayscale8, resolution, resolution, resolution /* pitch */, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1243 reinterpret_cast<uint8_t*>(volume->GetScalarPointer()) + j * resolution * resolution); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1244 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1245 XorFiller filler(slice); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1246 Orthanc::ImageProcessing::FillPolygon(filler, points); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1247 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1248 |
7 | 1249 volume->SetSpacing( |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1250 extent.GetWidth() / static_cast<double>(resolution), |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1251 extent.GetHeight() / static_cast<double>(resolution), |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1252 (geometry.GetMaxProjectionAlongNormal() - geometry.GetMinProjectionAlongNormal()) / static_cast<double>(depth)); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1253 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1254 // TODO |
7 | 1255 // volume->SetOrigin() |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1256 |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1257 return EncodeVolume(stl, volume.Get(), resolution, smooth); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1258 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1259 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1260 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1261 static Orthanc::ParsedDicomFile* LoadInstance(const std::string& instanceId) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1262 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1263 std::string dicom; |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1264 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1265 if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false)) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1266 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1267 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1268 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1269 else |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1270 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1271 return new Orthanc::ParsedDicomFile(dicom); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1272 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1273 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1274 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1275 |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1276 void ListStructures(OrthancPluginRestOutput* output, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1277 const char* url, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1278 const OrthancPluginHttpRequest* request) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1279 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1280 if (request->method != OrthancPluginHttpMethod_Get) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1281 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1282 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1283 return; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1284 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1285 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1286 const std::string instanceId(request->groups[0]); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1287 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1288 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1289 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1290 std::set<std::string> names; |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1291 ListStructuresNames(names, *dicom); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1292 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1293 Json::Value answer = Json::arrayValue; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1294 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1295 for (std::set<std::string>::const_iterator it = names.begin(); it != names.end(); ++it) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1296 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1297 answer.append(*it); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1298 } |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1299 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1300 std::string s = answer.toStyledString(); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1301 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
|
1302 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1303 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1304 |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1305 static void AddDefaultTagValue(Json::Value& target, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1306 const Orthanc::DicomTag& tag, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1307 const std::string& value) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1308 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1309 if (!target.isMember(tag.Format())) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1310 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1311 target[tag.Format()] = value; |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1312 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1313 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1314 |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1315 |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1316 static void AddDefaultTagValue(Json::Value& target, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1317 const DcmTagKey& tag, |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1318 const std::string& value) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1319 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1320 AddDefaultTagValue(target, Orthanc::DicomTag(tag.getGroup(), tag.getElement()), value); |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1321 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1322 |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1323 |
7 | 1324 static void CallCreateDicom(Json::Value& answer, |
1325 const std::string& stl, | |
1326 const Json::Value& body, | |
1327 const std::string& parentStudy, | |
1328 const std::string& defaultSeriesDescription, | |
1329 const std::string& defaultFrameOfReferenceUid, | |
1330 const std::string& defaultTitle) | |
1331 { | |
1332 static const char* const KEY_TAGS = "Tags"; | |
1333 | |
1334 Json::Value normalized = Json::objectValue; | |
1335 | |
1336 if (body.isMember(KEY_TAGS)) | |
1337 { | |
1338 const Json::Value& tags = body[KEY_TAGS]; | |
1339 | |
1340 if (tags.type() != Json::objectValue) | |
1341 { | |
1342 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Tags must be provided as a JSON object"); | |
1343 } | |
1344 | |
1345 std::vector<std::string> keys = tags.getMemberNames(); | |
1346 for (size_t i = 0; i < keys.size(); i++) | |
1347 { | |
1348 const Orthanc::DicomTag tag = Orthanc::FromDcmtkBridge::ParseTag(keys[i]); | |
1349 normalized[tag.Format()] = tags[keys[i]]; | |
1350 } | |
1351 } | |
1352 | |
1353 if (!normalized.isMember(Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format())) | |
1354 { | |
1355 normalized[Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format()] = defaultSeriesDescription; | |
1356 } | |
1357 | |
1358 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_SERIES_NUMBER, "1"); | |
1359 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, defaultFrameOfReferenceUid); | |
1360 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_INSTANCE_NUMBER, "1"); | |
1361 | |
1362 AddDefaultTagValue(normalized, DCM_BurnedInAnnotation, "NO"); | |
1363 AddDefaultTagValue(normalized, DCM_DeviceSerialNumber, ORTHANC_STL_VERSION); | |
1364 AddDefaultTagValue(normalized, DCM_DocumentTitle, defaultTitle); | |
1365 AddDefaultTagValue(normalized, DCM_Manufacturer, "Orthanc STL plugin"); | |
1366 AddDefaultTagValue(normalized, DCM_ManufacturerModelName, "Orthanc STL plugin"); | |
1367 AddDefaultTagValue(normalized, DCM_PositionReferenceIndicator, ""); | |
1368 AddDefaultTagValue(normalized, DCM_SoftwareVersions, ORTHANC_STL_VERSION); | |
1369 AddDefaultTagValue(normalized, DCM_ConceptNameCodeSequence, ""); | |
1370 | |
1371 std::string date, time; | |
1372 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); | |
1373 AddDefaultTagValue(normalized, DCM_AcquisitionDateTime, date + time); | |
1374 | |
1375 const Orthanc::DicomTag MEASUREMENT_UNITS_CODE_SEQUENCE(DCM_MeasurementUnitsCodeSequence.getGroup(), | |
1376 DCM_MeasurementUnitsCodeSequence.getElement()); | |
1377 | |
1378 if (!normalized.isMember(MEASUREMENT_UNITS_CODE_SEQUENCE.Format())) | |
1379 { | |
1380 Json::Value item; | |
1381 item["CodeValue"] = "mm"; | |
1382 item["CodingSchemeDesignator"] = "UCUM"; | |
1383 item["CodeMeaning"] = defaultTitle; | |
1384 | |
1385 normalized[MEASUREMENT_UNITS_CODE_SEQUENCE.Format()].append(item); | |
1386 } | |
1387 | |
1388 std::string content; | |
1389 Orthanc::Toolbox::EncodeDataUriScheme(content, Orthanc::MIME_STL, stl); | |
1390 | |
1391 Json::Value create; | |
1392 create["Content"] = content; | |
1393 create["Parent"] = parentStudy; | |
1394 create["Tags"] = normalized; | |
1395 | |
1396 if (!OrthancPlugins::RestApiPost(answer, "/tools/create-dicom", create.toStyledString(), false)) | |
1397 { | |
1398 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Cannot create DICOM from STL"); | |
1399 } | |
1400 } | |
1401 | |
1402 | |
1403 void EncodeStructureSet(OrthancPluginRestOutput* output, | |
1404 const char* url, | |
1405 const OrthancPluginHttpRequest* request) | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1406 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1407 static const char* const KEY_INSTANCE = "Instance"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1408 static const char* const KEY_RESOLUTION = "Resolution"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1409 static const char* const KEY_ROI_NAMES = "RoiNames"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1410 static const char* const KEY_SMOOTH = "Smooth"; |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1411 static const char* const KEY_STRICT = "Strict"; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1412 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1413 if (request->method != OrthancPluginHttpMethod_Post) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1414 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1415 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1416 return; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1417 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1418 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1419 Json::Value body; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1420 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
|
1421 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1422 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1423 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1424 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1425 const std::string instanceId = Orthanc::SerializationToolbox::ReadString(body, KEY_INSTANCE); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1426 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1427 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1428 true /* smooth by default */); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1429 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1430 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1431 256 /* default value */); |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1432 const bool strict = (body.isMember(KEY_STRICT) ? |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1433 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_STRICT) : |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1434 true /* strict by default */); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1435 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1436 std::set<std::string> roiNames; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1437 Orthanc::SerializationToolbox::ReadSetOfStrings(roiNames, body, KEY_ROI_NAMES); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1438 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1439 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1440 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1441 StructureSet structureSet(*dicom); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1442 |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1443 StructureSetGeometry geometry(structureSet, strict); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1444 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1445 std::string stl; |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1446 if (!EncodeStructureSetMesh(stl, structureSet, geometry, roiNames, resolution, smooth)) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1447 { |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1448 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from RT-STRUCT"); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1449 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1450 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1451 { |
7 | 1452 std::string seriesDescription; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1453 |
7 | 1454 if (dicom->GetTagValue(seriesDescription, Orthanc::DICOM_TAG_SERIES_DESCRIPTION)) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1455 { |
7 | 1456 seriesDescription += ": "; |
1457 } | |
1458 else | |
1459 { | |
1460 seriesDescription.clear(); | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1461 } |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1462 |
7 | 1463 bool first = true; |
1464 for (std::set<std::string>::const_iterator it = roiNames.begin(); it != roiNames.end(); ++it) | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1465 { |
7 | 1466 if (first) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1467 { |
7 | 1468 first = false; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1469 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1470 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1471 { |
7 | 1472 seriesDescription += ", "; |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1473 } |
2
2bdb9acb7dcf
added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1474 |
7 | 1475 seriesDescription += *it; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1476 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1477 |
7 | 1478 std::string frameOfReferenceUid; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1479 if (structureSet.HasFrameOfReferenceUid()) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1480 { |
7 | 1481 frameOfReferenceUid = structureSet.GetFrameOfReferenceUid(); |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1482 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1483 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1484 { |
7 | 1485 frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1486 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1487 |
7 | 1488 Json::Value answer; |
1489 CallCreateDicom(answer, stl, body, structureSet.HashStudy(), seriesDescription, | |
1490 frameOfReferenceUid, "STL model generated from DICOM RT-STRUCT"); | |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1491 |
7 | 1492 std::string s = answer.toStyledString(); |
1493 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
|
1494 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1495 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1496 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1497 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1498 void ExtractStl(OrthancPluginRestOutput* output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1499 const char* url, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1500 const OrthancPluginHttpRequest* request) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1501 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1502 if (request->method != OrthancPluginHttpMethod_Get) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1503 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1504 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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diff
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|
1505 return; |
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diff
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|
1506 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1507 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1508 const std::string instanceId(request->groups[0]); |
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diff
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|
1509 |
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diff
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|
1510 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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diff
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|
1511 DcmDataset& dataset = *dicom->GetDcmtkObject().getDataset(); |
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diff
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|
1512 |
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2
diff
changeset
|
1513 std::string stl; |
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diff
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|
1514 if (GetStringValue(dataset, DCM_MIMETypeOfEncapsulatedDocument) != Orthanc::MIME_STL || |
28
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
1515 GetStringValue(dataset, DCM_SOPClassUID) != STL_SOP_CLASS_UID || |
3
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diff
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|
1516 !dicom->GetTagValue(stl, Orthanc::DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1517 { |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1518 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "DICOM instance not encapsulating a STL model: " + instanceId); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1519 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1520 else |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1521 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1522 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1523 stl.empty() ? NULL : stl.c_str(), stl.size(), Orthanc::MIME_STL); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1524 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1525 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1526 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1527 |
6 | 1528 |
1529 class NiftiHeader : public boost::noncopyable | |
1530 { | |
1531 private: | |
1532 nifti_image* image_; | |
1533 | |
1534 public: | |
1535 NiftiHeader(const std::string& nifti) | |
1536 { | |
1537 nifti_1_header header; | |
1538 if (nifti.size() < sizeof(header)) | |
1539 { | |
1540 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1541 } | |
1542 | |
1543 memcpy(&header, nifti.c_str(), sizeof(header)); | |
1544 if (!nifti_hdr_looks_good(&header)) | |
1545 { | |
1546 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1547 } | |
1548 | |
1549 image_ = nifti_convert_nhdr2nim(header, "dummy_filename"); | |
1550 if (image_ == NULL) | |
1551 { | |
1552 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1553 } | |
1554 } | |
1555 | |
1556 ~NiftiHeader() | |
1557 { | |
1558 nifti_image_free(image_); | |
1559 } | |
1560 | |
1561 const nifti_image& GetInfo() const | |
1562 { | |
1563 assert(image_ != NULL); | |
1564 return *image_; | |
1565 } | |
1566 }; | |
1567 | |
1568 | |
1569 static void LoadNifti(vtkImageData* volume, | |
1570 std::string& nifti) | |
1571 { | |
1572 if (volume == NULL) | |
1573 { | |
1574 throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); | |
1575 } | |
1576 | |
1577 const uint8_t* p = reinterpret_cast<const uint8_t*>(nifti.c_str()); | |
1578 | |
1579 if (nifti.size() >= 2 && | |
1580 p[0] == 0x1f && | |
1581 p[1] == 0x8b) | |
1582 { | |
1583 Orthanc::GzipCompressor compressor; | |
1584 std::string uncompressed; | |
1585 Orthanc::IBufferCompressor::Uncompress(uncompressed, compressor, nifti); | |
1586 nifti.swap(uncompressed); | |
1587 } | |
1588 | |
1589 NiftiHeader header(nifti); | |
1590 | |
1591 if (header.GetInfo().ndim != 3) | |
1592 { | |
1593 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, | |
1594 "Only 3D NIfTI volumes are allowed"); | |
1595 } | |
1596 | |
8
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diff
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1597 size_t itemSize; |
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diff
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1598 int vtkType; |
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diff
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|
1599 |
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diff
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|
1600 switch (header.GetInfo().datatype) |
6 | 1601 { |
8
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|
1602 case DT_UNSIGNED_CHAR: |
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diff
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|
1603 itemSize = 1; |
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diff
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|
1604 vtkType = VTK_UNSIGNED_CHAR; |
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diff
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|
1605 break; |
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diff
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1606 |
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diff
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|
1607 case DT_FLOAT: |
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diff
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|
1608 itemSize = sizeof(float); |
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1609 vtkType = VTK_FLOAT; |
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diff
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|
1610 break; |
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diff
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1611 |
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diff
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|
1612 case DT_DOUBLE: |
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diff
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1613 itemSize = sizeof(double); |
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diff
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1614 vtkType = VTK_DOUBLE; |
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diff
changeset
|
1615 break; |
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diff
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1616 |
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diff
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1617 default: |
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|
1618 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
6 | 1619 } |
1620 | |
1621 assert(static_cast<int>(header.GetInfo().nvox) == header.GetInfo().nx * header.GetInfo().ny * header.GetInfo().nz); | |
1622 | |
1623 const size_t pixelDataOffset = sizeof(nifti_1_header) + 4 /* extension */; | |
1624 | |
8
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diff
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|
1625 if (nifti.size() != pixelDataOffset + header.GetInfo().nvox * itemSize) |
6 | 1626 { |
1627 throw Orthanc::OrthancException(Orthanc::ErrorCode_CorruptedFile); | |
1628 } | |
1629 | |
1630 volume->SetDimensions(header.GetInfo().nx, header.GetInfo().ny, header.GetInfo().nz); | |
8
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diff
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|
1631 volume->AllocateScalars(vtkType, 1); |
6 | 1632 volume->SetSpacing(header.GetInfo().dx, header.GetInfo().dy, header.GetInfo().dz); |
8
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|
1633 memcpy(volume->GetScalarPointer(), &nifti[pixelDataOffset], header.GetInfo().nvox * itemSize); |
6 | 1634 } |
1635 | |
8
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diff
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1636 |
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diff
changeset
|
1637 void EncodeNifti(OrthancPluginRestOutput* output, |
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diff
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|
1638 const char* url, |
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diff
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|
1639 const OrthancPluginHttpRequest* request) |
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diff
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1640 { |
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diff
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|
1641 static const char* const KEY_NIFTI = "Nifti"; |
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|
1642 static const char* const KEY_RESOLUTION = "Resolution"; |
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diff
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1643 static const char* const KEY_PARENT_STUDY = "ParentStudy"; |
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diff
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1644 static const char* const KEY_SMOOTH = "Smooth"; |
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1645 |
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1646 if (request->method != OrthancPluginHttpMethod_Post) |
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1647 { |
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|
1648 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
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1649 return; |
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1650 } |
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1651 |
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1652 Json::Value body; |
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1653 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
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1654 { |
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1655 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
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1656 } |
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1657 |
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changeset
|
1658 std::string mime, nifti; |
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1659 if (!Orthanc::Toolbox::DecodeDataUriScheme(mime, nifti, Orthanc::SerializationToolbox::ReadString(body, KEY_NIFTI))) |
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1660 { |
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|
1661 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Missing the \"Nifti\" argument containing the NIfTI file"); |
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1662 } |
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1663 |
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1664 const std::string parentStudy = Orthanc::SerializationToolbox::ReadString(body, KEY_PARENT_STUDY); |
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1665 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
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1666 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
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1667 true /* smooth by default */); |
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1668 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
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1669 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
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|
1670 256 /* default value */); |
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1671 |
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1672 vtkNew<vtkImageData> volume; |
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|
1673 LoadNifti(volume.Get(), nifti); |
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1674 |
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|
1675 std::string stl; |
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1676 if (!EncodeVolume(stl, volume.Get(), resolution, smooth)) |
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1677 { |
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changeset
|
1678 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from NIfTI"); |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1679 } |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1680 else |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1681 { |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1682 const std::string title = "STL model generated from NIfTI"; |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1683 |
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added route /stl/encode-nifti
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parents:
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diff
changeset
|
1684 const std::string frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1685 |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1686 Json::Value answer; |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1687 CallCreateDicom(answer, stl, body, parentStudy, title, frameOfReferenceUid, title); |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1688 |
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added route /stl/encode-nifti
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parents:
7
diff
changeset
|
1689 std::string s = answer.toStyledString(); |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1690 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1691 } |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1692 } |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1693 |
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added route /stl/encode-nifti
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parents:
7
diff
changeset
|
1694 |
0
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1695 extern "C" |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1696 { |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1697 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1698 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1699 OrthancPlugins::SetGlobalContext(context); |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1700 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1701 /* Check the version of the Orthanc core */ |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
1702 if (OrthancPluginCheckVersion(OrthancPlugins::GetGlobalContext()) == 0) |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
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|
1703 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1704 char info[1024]; |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1705 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1706 OrthancPlugins::GetGlobalContext()->orthancVersion, |
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initial commit of the viewer plugin
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parents:
diff
changeset
|
1707 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
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initial commit of the viewer plugin
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parents:
diff
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|
1708 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, |
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parents:
diff
changeset
|
1709 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); |
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initial commit of the viewer plugin
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parents:
diff
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|
1710 OrthancPluginLogError(OrthancPlugins::GetGlobalContext(), info); |
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initial commit of the viewer plugin
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parents:
diff
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|
1711 return -1; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1712 } |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1713 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1714 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1715 Orthanc::Logging::InitializePluginContext(context); |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1716 #else |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1717 Orthanc::Logging::Initialize(context); |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1718 #endif |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1719 |
1
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encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1720 Orthanc::InitializeFramework("", false); |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1721 |
0
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parents:
diff
changeset
|
1722 hasCreateDicomStl_ = OrthancPlugins::CheckMinimalOrthancVersion(1, 12, 1); |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1723 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1724 if (!hasCreateDicomStl_) |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1725 { |
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parents:
diff
changeset
|
1726 LOG(WARNING) << "Your version of Orthanc (" << std::string(context->orthancVersion) |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1727 << ") is insufficient to create DICOM STL, it should be above 1.12.1"; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1728 } |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1729 |
25
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fix deprecated calls
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parents:
24
diff
changeset
|
1730 OrthancPlugins::SetDescription(ORTHANC_PLUGIN_NAME, "STL plugin for Orthanc."); |
0
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1731 |
1
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encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1732 OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/app/(.*)", true); |
3
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added route "/instances/{id}/stl"
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parents:
2
diff
changeset
|
1733 OrthancPlugins::RegisterRestCallback<ExtractStl>("/instances/([0-9a-f-]+)/stl", true); |
1
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1734 OrthancPlugins::RegisterRestCallback<ListStructures>("/stl/rt-struct/([0-9a-f-]+)", true); |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1735 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1736 if (hasCreateDicomStl_) |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1737 { |
8
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1738 OrthancPlugins::RegisterRestCallback<EncodeStructureSet>("/stl/encode-rtstruct", true); |
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added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1739 OrthancPlugins::RegisterRestCallback<EncodeNifti>("/stl/encode-nifti", true); |
1
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1740 } |
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1741 |
2
2bdb9acb7dcf
added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1742 // Extend the default Orthanc Explorer with custom JavaScript for STL |
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added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1743 std::string explorer; |
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added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1744 |
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added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1745 { |
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added STL viewer button at instance level too
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parents:
1
diff
changeset
|
1746 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); |
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added STL viewer button at instance level too
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parents:
1
diff
changeset
|
1747 |
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added STL viewer button at instance level too
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parents:
1
diff
changeset
|
1748 std::map<std::string, std::string> dictionary; |
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added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1749 dictionary["HAS_CREATE_DICOM_STL"] = (hasCreateDicomStl_ ? "true" : "false"); |
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added STL viewer button at instance level too
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parents:
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diff
changeset
|
1750 explorer = Orthanc::Toolbox::SubstituteVariables(explorer, dictionary); |
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added STL viewer button at instance level too
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parents:
1
diff
changeset
|
1751 |
25
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fix deprecated calls
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parents:
24
diff
changeset
|
1752 OrthancPlugins::ExtendOrthancExplorer(ORTHANC_PLUGIN_NAME, explorer); |
2
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added STL viewer button at instance level too
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parents:
1
diff
changeset
|
1753 } |
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added STL viewer button at instance level too
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parents:
1
diff
changeset
|
1754 |
0
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diff
changeset
|
1755 return 0; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1756 } |
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parents:
diff
changeset
|
1757 |
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parents:
diff
changeset
|
1758 |
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parents:
diff
changeset
|
1759 ORTHANC_PLUGINS_API void OrthancPluginFinalize() |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1760 { |
1
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encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
1761 Orthanc::FinalizeFramework(); |
0
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parents:
diff
changeset
|
1762 } |
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parents:
diff
changeset
|
1763 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1764 |
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parents:
diff
changeset
|
1765 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1766 { |
25
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fix deprecated calls
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24
diff
changeset
|
1767 return ORTHANC_PLUGIN_NAME; |
0
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parents:
diff
changeset
|
1768 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1769 |
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initial commit of the viewer plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
1770 |
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parents:
diff
changeset
|
1771 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() |
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changeset
|
1772 { |
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diff
changeset
|
1773 return ORTHANC_STL_VERSION; |
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parents:
diff
changeset
|
1774 } |
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parents:
diff
changeset
|
1775 } |