Mercurial > hg > orthanc-stl
annotate Sources/Plugin.cpp @ 32:976da5476810
reorganization
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 04 Apr 2024 18:35:54 +0200 |
parents | ab231760799d |
children | 2460b376d3f7 |
rev | line source |
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1 /** |
24 | 2 * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
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3 * SPDX-License-Identifier: GPL-3.0-or-later |
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4 */ |
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5 |
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6 /** |
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7 * STL plugin for Orthanc |
24 | 8 * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
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9 * |
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10 * This program is free software: you can redistribute it and/or |
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11 * modify it under the terms of the GNU General Public License as |
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12 * published by the Free Software Foundation, either version 3 of the |
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13 * License, or (at your option) any later version. |
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14 * |
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15 * This program is distributed in the hope that it will be useful, but |
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16 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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18 * General Public License for more details. |
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19 * |
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20 * You should have received a copy of the GNU General Public License |
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21 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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22 **/ |
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23 |
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24 |
32 | 25 #include "VTKToolbox.h" |
26 #include "Vector3D.h" | |
27 #include "Toolbox.h" | |
28 #include "Extent2D.h" | |
29 | |
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30 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
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31 |
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32 #include <EmbeddedResources.h> |
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33 |
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34 #include <DicomFormat/DicomInstanceHasher.h> |
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35 #include <DicomParsing/FromDcmtkBridge.h> |
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36 #include <DicomParsing/ParsedDicomFile.h> |
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37 #include <Images/ImageProcessing.h> |
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38 #include <Logging.h> |
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39 #include <OrthancFramework.h> |
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40 #include <SerializationToolbox.h> |
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41 #include <SystemToolbox.h> |
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42 |
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43 #include <boost/thread/shared_mutex.hpp> |
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44 |
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45 #define ORTHANC_PLUGIN_NAME "stl" |
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46 |
6 | 47 |
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48 // Forward declaration |
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49 void ReadStaticAsset(std::string& target, |
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50 const std::string& path); |
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51 |
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52 |
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53 /** |
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54 * As the Three.js static assets are gzipped by the |
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55 * "EmbedStaticAssets.py" script, we use a cache to maintain the |
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56 * uncompressed assets in order to avoid multiple gzip decodings. |
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57 **/ |
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58 class ResourcesCache : public boost::noncopyable |
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59 { |
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60 private: |
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61 typedef std::map<std::string, std::string*> Content; |
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62 |
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63 boost::shared_mutex mutex_; |
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64 Content content_; |
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65 |
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66 public: |
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67 ~ResourcesCache() |
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68 { |
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69 for (Content::iterator it = content_.begin(); it != content_.end(); ++it) |
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70 { |
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71 assert(it->second != NULL); |
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72 delete it->second; |
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73 } |
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74 } |
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75 |
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76 void Answer(OrthancPluginRestOutput* output, |
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77 const std::string& path) |
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78 { |
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79 const std::string mime = Orthanc::EnumerationToString(Orthanc::SystemToolbox::AutodetectMimeType(path)); |
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80 |
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81 { |
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82 // Check whether the cache already contains the resource |
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83 boost::shared_lock<boost::shared_mutex> lock(mutex_); |
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84 |
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85 Content::const_iterator found = content_.find(path); |
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86 |
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87 if (found != content_.end()) |
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88 { |
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89 assert(found->second != NULL); |
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90 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, found->second->c_str(), found->second->size(), mime.c_str()); |
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91 return; |
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92 } |
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93 } |
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94 |
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95 // This resource has not been cached yet |
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96 |
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97 std::unique_ptr<std::string> item(new std::string); |
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98 ReadStaticAsset(*item, path); |
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99 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, item->c_str(), item->size(), mime.c_str()); |
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100 |
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101 { |
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102 // Store the resource into the cache |
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103 boost::unique_lock<boost::shared_mutex> lock(mutex_); |
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104 |
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105 if (content_.find(path) == content_.end()) |
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106 { |
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107 content_[path] = item.release(); |
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108 } |
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109 } |
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110 } |
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111 }; |
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112 |
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113 |
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114 static ResourcesCache cache_; |
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115 static bool hasCreateDicomStl_; |
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116 |
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117 void ServeFile(OrthancPluginRestOutput* output, |
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118 const char* url, |
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119 const OrthancPluginHttpRequest* request) |
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120 { |
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121 if (request->method != OrthancPluginHttpMethod_Get) |
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122 { |
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123 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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124 return; |
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125 } |
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126 |
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127 std::string file = request->groups[0]; |
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128 |
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129 if (file == "viewer.html") |
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130 { |
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131 std::string s; |
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132 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_HTML); |
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133 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Html)); |
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134 } |
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135 else if (file == "viewer.js") |
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136 { |
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137 std::string s; |
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138 Orthanc::EmbeddedResources::GetFileResource(s, Orthanc::EmbeddedResources::VIEWER_JS); |
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139 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(Orthanc::MimeType_JavaScript)); |
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140 } |
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141 else |
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142 { |
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143 cache_.Answer(output, file); |
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144 } |
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145 } |
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146 |
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147 |
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148 |
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149 |
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150 #include <dcmtk/dcmdata/dcdeftag.h> |
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151 #include <dcmtk/dcmdata/dcfilefo.h> |
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152 #include <dcmtk/dcmdata/dcitem.h> |
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153 #include <dcmtk/dcmdata/dcsequen.h> |
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154 #include <dcmtk/dcmdata/dcuid.h> |
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155 |
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156 |
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157 static std::string GetStringValue(DcmItem& item, |
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158 const DcmTagKey& key) |
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159 { |
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160 const char* s = NULL; |
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161 if (!item.findAndGetString(key, s).good() || |
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162 s == NULL) |
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163 { |
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164 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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165 } |
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166 else |
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167 { |
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168 return Orthanc::Toolbox::StripSpaces(s); |
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169 } |
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170 } |
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171 |
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172 |
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173 static void ListStructuresNames(std::set<std::string>& target, |
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174 Orthanc::ParsedDicomFile& source) |
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175 { |
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176 target.clear(); |
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177 |
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178 DcmSequenceOfItems* sequence = NULL; |
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179 if (!source.GetDcmtkObject().getDataset()->findAndGetSequence(DCM_StructureSetROISequence, sequence).good() || |
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180 sequence == NULL) |
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181 { |
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182 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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183 } |
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184 |
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185 for (unsigned long i = 0; i < sequence->card(); i++) |
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186 { |
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187 DcmItem* item = sequence->getItem(i); |
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188 if (item == NULL) |
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189 { |
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190 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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191 } |
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192 else |
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193 { |
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194 target.insert(GetStringValue(*item, DCM_ROIName)); |
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195 } |
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196 } |
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197 } |
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198 |
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199 |
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200 class StructurePolygon : public boost::noncopyable |
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201 { |
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202 private: |
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203 std::string roiName_; |
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204 std::string referencedSopInstanceUid_; |
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205 uint8_t red_; |
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206 uint8_t green_; |
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207 uint8_t blue_; |
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208 std::vector<Vector3D> points_; |
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209 |
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210 public: |
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211 StructurePolygon(Orthanc::ParsedDicomFile& dicom, |
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212 unsigned long roiIndex, |
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213 unsigned long contourIndex) |
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214 { |
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215 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
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216 |
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217 DcmItem* structure = NULL; |
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218 DcmItem* roi = NULL; |
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219 DcmItem* contour = NULL; |
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220 DcmSequenceOfItems* referenced = NULL; |
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221 |
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222 if (!dataset.findAndGetSequenceItem(DCM_StructureSetROISequence, structure, roiIndex).good() || |
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223 structure == NULL || |
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224 !dataset.findAndGetSequenceItem(DCM_ROIContourSequence, roi, roiIndex).good() || |
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225 roi == NULL || |
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226 !roi->findAndGetSequenceItem(DCM_ContourSequence, contour, contourIndex).good() || |
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227 contour == NULL || |
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228 !contour->findAndGetSequence(DCM_ContourImageSequence, referenced).good() || |
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229 referenced == NULL || |
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230 referenced->card() != 1) |
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231 { |
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232 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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233 } |
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234 |
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235 roiName_ = GetStringValue(*structure, DCM_ROIName); |
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236 referencedSopInstanceUid_ = GetStringValue(*referenced->getItem(0), DCM_ReferencedSOPInstanceUID); |
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237 |
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238 if (GetStringValue(*contour, DCM_ContourGeometricType) != "CLOSED_PLANAR") |
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239 { |
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240 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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241 } |
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242 |
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243 { |
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244 std::vector<std::string> tokens; |
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245 Orthanc::Toolbox::TokenizeString(tokens, GetStringValue(*roi, DCM_ROIDisplayColor), '\\'); |
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246 |
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247 uint32_t r, g, b; |
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248 if (tokens.size() != 3 || |
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249 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(r, tokens[0]) || |
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250 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(g, tokens[1]) || |
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251 !Orthanc::SerializationToolbox::ParseFirstUnsignedInteger32(b, tokens[2]) || |
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252 r > 255 || |
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253 g > 255 || |
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254 b > 255) |
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255 { |
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256 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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257 } |
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258 |
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259 red_ = r; |
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260 green_ = g; |
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261 blue_ = b; |
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262 } |
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263 |
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264 { |
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265 std::vector<std::string> tokens; |
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266 Orthanc::Toolbox::TokenizeString(tokens, GetStringValue(*contour, DCM_ContourData), '\\'); |
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267 |
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268 const std::string s = GetStringValue(*contour, DCM_NumberOfContourPoints); |
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269 |
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270 uint32_t countPoints; |
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271 if (!Orthanc::SerializationToolbox::ParseUnsignedInteger32(countPoints, s) || |
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272 tokens.size() != 3 * countPoints) |
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273 { |
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274 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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275 } |
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276 |
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277 points_.reserve(countPoints); |
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278 |
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279 for (size_t i = 0; i < tokens.size(); i += 3) |
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280 { |
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281 double x, y, z; |
32 | 282 if (!Toolbox::MyParseDouble(x, tokens[i]) || |
283 !Toolbox::MyParseDouble(y, tokens[i + 1]) || | |
284 !Toolbox::MyParseDouble(z, tokens[i + 2])) | |
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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 |
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289 points_.push_back(Vector3D(x, y, z)); |
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290 } |
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291 |
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292 assert(points_.size() == countPoints); |
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293 } |
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294 } |
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295 |
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296 const std::string& GetRoiName() const |
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297 { |
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298 return roiName_; |
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299 } |
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300 |
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301 const std::string& GetReferencedSopInstanceUid() const |
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302 { |
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303 return referencedSopInstanceUid_; |
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304 } |
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305 |
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306 size_t GetPointsCount() const |
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307 { |
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308 return points_.size(); |
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309 } |
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310 |
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311 const Vector3D& GetPoint(size_t i) const |
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312 { |
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313 if (i >= points_.size()) |
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314 { |
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315 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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316 } |
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317 else |
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318 { |
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319 return points_[i]; |
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320 } |
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321 } |
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322 |
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323 bool IsCoplanar(Vector3D& normal) const |
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324 { |
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325 if (points_.size() < 3) |
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326 { |
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327 return false; |
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328 } |
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329 |
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330 bool hasNormal = false; |
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331 |
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332 for (size_t i = 0; i < points_.size(); i++) |
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333 { |
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334 normal = Vector3D::CrossProduct(Vector3D(points_[1], points_[0]), |
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335 Vector3D(points_[2], points_[0])); |
32 | 336 if (!Toolbox::IsNear(normal.ComputeNorm(), 0)) |
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337 { |
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338 normal.Normalize(); |
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339 hasNormal = true; |
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340 } |
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341 } |
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342 |
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343 if (!hasNormal) |
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344 { |
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345 return false; |
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346 } |
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347 |
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348 double a = Vector3D::DotProduct(points_[0], normal); |
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349 |
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350 for (size_t i = 1; i < points_.size(); i++) |
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351 { |
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352 double b = Vector3D::DotProduct(points_[i], normal); |
32 | 353 if (!Toolbox::IsNear(a, b)) |
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354 { |
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355 return false; |
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356 } |
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357 } |
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358 |
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359 return true; |
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360 } |
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361 |
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362 void Add(Extent2D& extent, |
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363 const Vector3D& axisX, |
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364 const Vector3D& axisY) const |
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365 { |
32 | 366 assert(Toolbox::IsNear(1, axisX.ComputeNorm())); |
367 assert(Toolbox::IsNear(1, axisY.ComputeNorm())); | |
1
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368 |
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369 for (size_t i = 0; i < points_.size(); i++) |
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370 { |
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371 extent.Add(Vector3D::DotProduct(axisX, points_[i]), |
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372 Vector3D::DotProduct(axisY, points_[i])); |
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373 } |
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374 } |
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375 }; |
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376 |
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377 |
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378 |
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379 class StructureSet : public boost::noncopyable |
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380 { |
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381 private: |
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382 std::vector<StructurePolygon*> polygons_; |
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383 std::string patientId_; |
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384 std::string studyInstanceUid_; |
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385 std::string seriesInstanceUid_; |
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386 std::string sopInstanceUid_; |
4
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387 bool hasFrameOfReferenceUid_; |
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|
388 std::string frameOfReferenceUid_; |
1
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389 |
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390 public: |
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391 explicit StructureSet(Orthanc::ParsedDicomFile& dicom) : |
4
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392 hasFrameOfReferenceUid_(false) |
1
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393 { |
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394 DcmDataset& dataset = *dicom.GetDcmtkObject().getDataset(); |
3
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395 patientId_ = GetStringValue(dataset, DCM_PatientID); |
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396 studyInstanceUid_ = GetStringValue(dataset, DCM_StudyInstanceUID); |
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397 seriesInstanceUid_ = GetStringValue(dataset, DCM_SeriesInstanceUID); |
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398 sopInstanceUid_ = GetStringValue(dataset, DCM_SOPInstanceUID); |
1
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399 |
4
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400 DcmSequenceOfItems* frame = NULL; |
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401 if (!dataset.findAndGetSequence(DCM_ReferencedFrameOfReferenceSequence, frame).good() || |
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402 frame == NULL) |
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403 { |
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404 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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405 } |
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|
406 |
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407 if (frame->card() == 1) |
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408 { |
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409 const char* v = NULL; |
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410 if (frame->getItem(0)->findAndGetString(DCM_FrameOfReferenceUID, v).good() && |
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411 v != NULL) |
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|
412 { |
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413 hasFrameOfReferenceUid_ = true; |
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414 frameOfReferenceUid_.assign(v); |
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changeset
|
415 } |
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changeset
|
416 } |
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changeset
|
417 |
1
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418 DcmSequenceOfItems* rois = NULL; |
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419 if (!dataset.findAndGetSequence(DCM_ROIContourSequence, rois).good() || |
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420 rois == NULL) |
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421 { |
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422 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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423 } |
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|
424 |
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425 std::vector<DcmSequenceOfItems*> contours(rois->card()); |
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426 size_t countPolygons = 0; |
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|
427 |
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428 for (unsigned long i = 0; i < rois->card(); i++) |
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|
429 { |
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|
430 DcmSequenceOfItems* contour = NULL; |
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431 if (!rois->getItem(i)->findAndGetSequence(DCM_ContourSequence, contour).good() || |
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|
432 contour == NULL) |
0f03a8a0bd6f
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|
433 { |
0f03a8a0bd6f
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|
434 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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changeset
|
435 } |
0f03a8a0bd6f
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changeset
|
436 else |
0f03a8a0bd6f
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changeset
|
437 { |
0f03a8a0bd6f
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diff
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|
438 contours[i] = contour; |
0f03a8a0bd6f
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|
439 countPolygons += contour->card(); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
440 } |
0f03a8a0bd6f
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diff
changeset
|
441 } |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
442 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
443 polygons_.resize(countPolygons); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
444 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
445 size_t pos = 0; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
446 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
|
447 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
448 for (unsigned long j = 0; j < contours[i]->card(); j++, pos++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
449 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
450 polygons_[pos] = new StructurePolygon(dicom, i, j); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
451 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
452 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
453 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
454 assert(pos == countPolygons); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
455 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
456 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
457 ~StructureSet() |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
458 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
459 for (size_t i = 0; i < polygons_.size(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
460 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
461 assert(polygons_[i] != NULL); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
462 delete polygons_[i]; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
463 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
464 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
465 |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
changeset
|
466 const std::string& GetPatientId() const |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
467 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
468 return patientId_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
469 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
470 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
471 const std::string& GetStudyInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
472 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
473 return studyInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
474 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
475 |
0f03a8a0bd6f
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diff
changeset
|
476 const std::string& GetSeriesInstanceUid() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
477 { |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
478 return seriesInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
479 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
480 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
481 const std::string& GetSopInstanceUid() const |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
482 { |
0f03a8a0bd6f
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diff
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|
483 return sopInstanceUid_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
484 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
485 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
486 std::string HashStudy() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
487 { |
28
410003c50b17
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diff
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|
488 Orthanc::DicomInstanceHasher hasher(patientId_, studyInstanceUid_, seriesInstanceUid_, sopInstanceUid_); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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489 return hasher.HashStudy(); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
490 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
491 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
492 size_t GetPolygonsCount() const |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
493 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
494 return polygons_.size(); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
495 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
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diff
changeset
|
496 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
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|
497 const StructurePolygon& GetPolygon(size_t i) const |
0f03a8a0bd6f
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|
498 { |
0f03a8a0bd6f
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|
499 if (i >= polygons_.size()) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
500 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
501 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
502 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
503 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
504 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
505 assert(polygons_[i] != NULL); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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506 return *polygons_[i]; |
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encoding of RT-STRUCT as STL
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changeset
|
507 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
508 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
509 |
4
5ee4448a8ff8
generated STL pass dciodvfy
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diff
changeset
|
510 bool HasFrameOfReferenceUid() const |
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generated STL pass dciodvfy
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diff
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|
511 { |
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diff
changeset
|
512 return hasFrameOfReferenceUid_; |
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generated STL pass dciodvfy
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diff
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|
513 } |
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generated STL pass dciodvfy
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diff
changeset
|
514 |
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generated STL pass dciodvfy
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diff
changeset
|
515 const std::string& GetFrameOfReferenceUid() const |
5ee4448a8ff8
generated STL pass dciodvfy
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|
516 { |
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generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
517 if (hasFrameOfReferenceUid_) |
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generated STL pass dciodvfy
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diff
changeset
|
518 { |
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generated STL pass dciodvfy
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diff
changeset
|
519 return frameOfReferenceUid_; |
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generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
520 } |
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generated STL pass dciodvfy
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parents:
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diff
changeset
|
521 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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3
diff
changeset
|
522 { |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
523 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
524 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
525 } |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
526 }; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
527 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
528 |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
529 class StructureSetGeometry : public boost::noncopyable |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
530 { |
410003c50b17
improved computation of RT-STRUCT geometry
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diff
changeset
|
531 private: |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
532 bool strict_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
533 Vector3D slicesNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
534 double slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
535 double minProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
536 double maxProjectionAlongNormal_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
537 size_t slicesCount_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
538 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
539 bool LookupProjectionIndex(size_t& index, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
540 double z) const |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
541 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
542 if (slicesCount_ == 0) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
543 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
544 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
545 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
546 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
547 if (z < minProjectionAlongNormal_ || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
548 z > maxProjectionAlongNormal_) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
549 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
550 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
551 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
552 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
553 assert(slicesSpacing_ > 0 && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
554 minProjectionAlongNormal_ < maxProjectionAlongNormal_); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
555 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
556 double d = (z - minProjectionAlongNormal_) / slicesSpacing_; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
557 |
32 | 558 if (Toolbox::IsNear(d, round(d))) |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
559 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
560 if (d < 0.0 || |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
561 d > static_cast<double>(slicesCount_) - 1.0) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
562 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
563 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
564 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
565 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
566 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
567 index = static_cast<size_t>(round(d)); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
568 return true; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
569 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
570 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
571 else |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
572 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
573 return false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
574 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
575 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
576 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
577 public: |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
578 StructureSetGeometry(const StructureSet& structures, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
579 bool strict) : |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
580 strict_(strict) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
581 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
582 bool isValid = false; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
583 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
584 std::vector<double> projections; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
585 projections.reserve(structures.GetPolygonsCount()); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
586 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
587 for (size_t i = 0; i < structures.GetPolygonsCount(); i++) |
410003c50b17
improved computation of RT-STRUCT geometry
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588 { |
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589 Vector3D normal; |
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590 if (structures.GetPolygon(i).IsCoplanar(normal)) |
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591 { |
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592 // Initialize the normal of the whole volume, if need be |
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593 if (!isValid) |
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594 { |
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595 isValid = true; |
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596 slicesNormal_ = normal; |
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597 } |
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598 |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
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28
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599 if (Vector3D::AreParallel(normal, slicesNormal_)) |
28
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600 { |
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601 // This is a valid slice (it is parallel to the normal) |
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602 const Vector3D& point = structures.GetPolygon(i).GetPoint(0); |
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603 projections.push_back(Vector3D::DotProduct(point, slicesNormal_)); |
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604 } |
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25
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605 else |
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606 { |
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25
diff
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|
607 // RT-STRUCT with non-parallel slices |
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608 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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609 } |
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610 } |
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611 else |
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|
612 { |
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613 // Ignore slices that are not coplanar |
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|
614 } |
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diff
changeset
|
615 } |
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improved computation of RT-STRUCT geometry
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25
diff
changeset
|
616 |
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617 if (projections.empty()) |
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25
diff
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618 { |
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diff
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619 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
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620 "Structure set without a valid geometry"); |
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|
621 } |
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|
622 |
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diff
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|
623 // Only keep unique projections |
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624 |
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625 std::sort(projections.begin(), projections.end()); |
32 | 626 Toolbox::RemoveDuplicateValues(projections); |
28
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627 assert(!projections.empty()); |
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|
628 |
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629 if (projections.size() == 1) |
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630 { |
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|
631 // Volume with one single slice |
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632 minProjectionAlongNormal_ = projections[0]; |
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633 maxProjectionAlongNormal_ = projections[0]; |
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634 slicesSpacing_ = 1; // Arbitrary value |
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diff
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635 slicesCount_ = 1; |
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636 return; |
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|
637 } |
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diff
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|
638 |
410003c50b17
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25
diff
changeset
|
639 |
410003c50b17
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diff
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|
640 // Compute the most probable spacing between the slices |
410003c50b17
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25
diff
changeset
|
641 |
410003c50b17
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25
diff
changeset
|
642 { |
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parents:
25
diff
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|
643 std::vector<double> spacings; |
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diff
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|
644 spacings.resize(projections.size() - 1); |
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parents:
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|
645 |
410003c50b17
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parents:
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diff
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|
646 for (size_t i = 0; i < spacings.size(); i++) |
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|
647 { |
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parents:
25
diff
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|
648 spacings[i] = projections[i + 1] - projections[i]; |
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diff
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|
649 assert(spacings[i] > 0); |
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parents:
25
diff
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|
650 } |
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parents:
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diff
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|
651 |
410003c50b17
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parents:
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diff
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|
652 std::sort(spacings.begin(), spacings.end()); |
32 | 653 Toolbox::RemoveDuplicateValues(spacings); |
28
410003c50b17
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25
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|
654 |
410003c50b17
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parents:
25
diff
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|
655 if (spacings.empty()) |
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25
diff
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|
656 { |
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parents:
25
diff
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657 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
658 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
659 |
410003c50b17
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660 slicesSpacing_ = spacings[spacings.size() / 10]; // Take the 90% percentile of smallest spacings |
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661 assert(slicesSpacing_ > 0); |
410003c50b17
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|
662 } |
410003c50b17
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|
663 |
410003c50b17
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|
664 |
410003c50b17
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|
665 // Find the projection along the normal with the largest support |
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|
666 |
410003c50b17
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|
667 bool first = true; |
410003c50b17
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|
668 size_t bestSupport; |
410003c50b17
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|
669 double bestProjection; |
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|
670 |
410003c50b17
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|
671 std::list<size_t> candidates; |
410003c50b17
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672 for (size_t i = 0; i < projections.size(); i++) |
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|
673 { |
410003c50b17
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|
674 candidates.push_back(i); |
410003c50b17
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parents:
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diff
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|
675 } |
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parents:
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diff
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|
676 |
410003c50b17
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diff
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|
677 while (!candidates.empty()) |
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|
678 { |
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|
679 std::list<size_t> next; |
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25
diff
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|
680 |
410003c50b17
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|
681 size_t countSupport = 0; |
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|
682 |
410003c50b17
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diff
changeset
|
683 std::list<size_t>::const_iterator it = candidates.begin(); |
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684 size_t reference = *it; |
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25
diff
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|
685 it++; |
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changeset
|
686 |
410003c50b17
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|
687 while (it != candidates.end()) |
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|
688 { |
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|
689 double d = (projections[*it] - projections[reference]) / slicesSpacing_; |
32 | 690 if (Toolbox::IsNear(d, round(d))) |
28
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
691 { |
410003c50b17
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|
692 countSupport ++; |
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|
693 } |
410003c50b17
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25
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changeset
|
694 else |
410003c50b17
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25
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changeset
|
695 { |
410003c50b17
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25
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changeset
|
696 next.push_back(*it); |
410003c50b17
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25
diff
changeset
|
697 } |
410003c50b17
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25
diff
changeset
|
698 |
410003c50b17
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25
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changeset
|
699 it++; |
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25
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changeset
|
700 } |
410003c50b17
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25
diff
changeset
|
701 |
410003c50b17
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25
diff
changeset
|
702 if (first || |
410003c50b17
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diff
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|
703 countSupport > bestSupport) |
410003c50b17
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25
diff
changeset
|
704 { |
410003c50b17
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25
diff
changeset
|
705 first = false; |
410003c50b17
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|
706 bestSupport = countSupport; |
410003c50b17
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|
707 bestProjection = projections[reference]; |
410003c50b17
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25
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|
708 } |
410003c50b17
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25
diff
changeset
|
709 |
410003c50b17
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25
diff
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|
710 if (strict && |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
711 !next.empty()) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
712 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
713 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
714 "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
|
715 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
716 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
717 candidates.swap(next); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
718 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
719 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
720 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
721 // Compute the range of the projections |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
722 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
723 minProjectionAlongNormal_ = bestProjection; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
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|
724 maxProjectionAlongNormal_ = bestProjection; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
725 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
726 for (size_t i = 0; i < projections.size(); i++) |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
727 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
728 double d = (projections[i] - bestProjection) / slicesSpacing_; |
32 | 729 if (Toolbox::IsNear(d, round(d))) |
28
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
730 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
731 minProjectionAlongNormal_ = std::min(minProjectionAlongNormal_, projections[i]); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
732 maxProjectionAlongNormal_ = std::max(maxProjectionAlongNormal_, projections[i]); |
410003c50b17
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25
diff
changeset
|
733 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
734 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
735 |
410003c50b17
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25
diff
changeset
|
736 double d = (maxProjectionAlongNormal_ - minProjectionAlongNormal_) / slicesSpacing_; |
32 | 737 if (Toolbox::IsNear(d, round(d))) |
28
410003c50b17
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25
diff
changeset
|
738 { |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
739 slicesCount_ = static_cast<size_t>(round(d)) + 1; |
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25
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|
740 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
741 else |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
742 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
743 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
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25
diff
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|
744 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
745 |
410003c50b17
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25
diff
changeset
|
746 |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
747 // Sanity check |
410003c50b17
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25
diff
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|
748 |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
749 size_t a, b; |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
750 if (!LookupProjectionIndex(a, minProjectionAlongNormal_) || |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
751 !LookupProjectionIndex(b, maxProjectionAlongNormal_) || |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
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|
752 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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|
753 b + 1 != slicesCount_) |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
754 { |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
755 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
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25
diff
changeset
|
756 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
757 } |
410003c50b17
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25
diff
changeset
|
758 |
410003c50b17
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diff
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|
759 const Vector3D& GetSlicesNormal() const |
410003c50b17
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|
760 { |
410003c50b17
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25
diff
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|
761 return slicesNormal_; |
410003c50b17
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25
diff
changeset
|
762 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
763 |
410003c50b17
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25
diff
changeset
|
764 double GetSlicesSpacing() const |
410003c50b17
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25
diff
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|
765 { |
410003c50b17
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25
diff
changeset
|
766 return slicesSpacing_; |
410003c50b17
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25
diff
changeset
|
767 } |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
768 |
410003c50b17
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parents:
25
diff
changeset
|
769 double GetMinProjectionAlongNormal() const |
410003c50b17
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25
diff
changeset
|
770 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
771 return minProjectionAlongNormal_; |
410003c50b17
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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
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parents:
25
diff
changeset
|
774 double GetMaxProjectionAlongNormal() const |
410003c50b17
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25
diff
changeset
|
775 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
776 return maxProjectionAlongNormal_; |
410003c50b17
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parents:
25
diff
changeset
|
777 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
778 |
410003c50b17
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25
diff
changeset
|
779 bool ProjectAlongNormal(double& z, |
410003c50b17
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25
diff
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|
780 const StructurePolygon& polygon) const |
410003c50b17
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25
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|
781 { |
410003c50b17
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25
diff
changeset
|
782 Vector3D normal; |
410003c50b17
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parents:
25
diff
changeset
|
783 if (polygon.IsCoplanar(normal) && |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
28
diff
changeset
|
784 Vector3D::AreParallel(normal, slicesNormal_)) |
28
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
785 { |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
786 z = Vector3D::DotProduct(polygon.GetPoint(0), slicesNormal_); |
410003c50b17
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25
diff
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|
787 return true; |
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25
diff
changeset
|
788 } |
410003c50b17
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25
diff
changeset
|
789 else |
410003c50b17
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parents:
25
diff
changeset
|
790 { |
410003c50b17
improved computation of RT-STRUCT geometry
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25
diff
changeset
|
791 return false; |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
792 } |
410003c50b17
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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 |
410003c50b17
improved computation of RT-STRUCT geometry
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parents:
25
diff
changeset
|
795 size_t GetSlicesCount() const |
410003c50b17
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25
diff
changeset
|
796 { |
410003c50b17
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25
diff
changeset
|
797 return slicesCount_; |
410003c50b17
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25
diff
changeset
|
798 } |
410003c50b17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
799 |
410003c50b17
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25
diff
changeset
|
800 bool LookupSliceIndex(size_t& slice, |
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|
801 const StructurePolygon& polygon) const |
410003c50b17
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25
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changeset
|
802 { |
410003c50b17
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25
diff
changeset
|
803 double z; |
410003c50b17
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25
diff
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|
804 return (ProjectAlongNormal(z, polygon) && |
410003c50b17
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25
diff
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|
805 LookupProjectionIndex(slice, z)); |
410003c50b17
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25
diff
changeset
|
806 } |
410003c50b17
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25
diff
changeset
|
807 }; |
410003c50b17
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25
diff
changeset
|
808 |
410003c50b17
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parents:
25
diff
changeset
|
809 |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
810 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
811 |
0f03a8a0bd6f
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0
diff
changeset
|
812 class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
813 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
814 private: |
0f03a8a0bd6f
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parents:
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diff
changeset
|
815 Orthanc::ImageAccessor& target_; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
816 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
817 public: |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
818 XorFiller(Orthanc::ImageAccessor& target) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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diff
changeset
|
819 target_(target) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
820 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
821 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
822 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
823 virtual void Fill(int y, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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0
diff
changeset
|
824 int x1, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
825 int x2) ORTHANC_OVERRIDE |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
826 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
827 assert(x1 <= x2); |
0f03a8a0bd6f
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parents:
0
diff
changeset
|
828 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
829 if (y >= 0 && |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
830 y < static_cast<int>(target_.GetHeight())) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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parents:
0
diff
changeset
|
831 { |
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832 x1 = std::max(x1, 0); |
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833 x2 = std::min(x2, static_cast<int>(target_.GetWidth()) - 1); |
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834 |
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835 uint8_t* p = reinterpret_cast<uint8_t*>(target_.GetRow(y)) + x1; |
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836 |
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837 for (int i = x1; i <= x2; i++, p++) |
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838 { |
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839 *p = (*p ^ 0xff); |
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840 } |
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|
841 } |
0f03a8a0bd6f
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842 } |
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843 }; |
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844 |
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|
845 |
29
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846 static Orthanc::ParsedDicomFile* LoadInstance(const std::string& instanceId) |
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847 { |
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|
848 std::string dicom; |
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849 |
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850 if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false)) |
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851 { |
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|
852 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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|
853 } |
62abf3c523f9
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|
854 else |
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diff
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|
855 { |
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|
856 return new Orthanc::ParsedDicomFile(dicom); |
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857 } |
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858 } |
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|
859 |
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|
860 |
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861 static void GetReferencedVolumeAxes(Vector3D& axisX, |
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862 Vector3D& axisY, |
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|
863 const StructureSet& structureSet) |
1
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864 { |
29
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865 // This is a rough guess for the X/Y axes |
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866 axisX = Vector3D(1, 0, 0); |
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867 axisY = Vector3D(0, 1, 0); |
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868 |
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869 // Look for one instance from the referenced volume |
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870 const std::string& sopInstanceUid = structureSet.GetPolygon(0).GetReferencedSopInstanceUid(); |
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871 |
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872 Json::Value response; |
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873 if (OrthancPlugins::RestApiPost(response, "/tools/lookup", sopInstanceUid, false)) |
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874 { |
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|
875 if (response.type() != Json::arrayValue) |
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876 { |
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|
877 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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878 } |
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|
879 |
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|
880 bool first = true; |
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|
881 |
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882 for (Json::Value::ArrayIndex i = 0; i < response.size(); i++) |
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|
883 { |
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diff
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|
884 if (response[i].type() != Json::objectValue) |
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diff
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885 { |
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|
886 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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diff
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|
887 } |
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diff
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|
888 |
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diff
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|
889 if (Orthanc::SerializationToolbox::ReadString(response[i], "Type") == "Instance") |
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diff
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|
890 { |
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diff
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|
891 if (first) |
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diff
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|
892 { |
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|
893 const std::string& instanceId = Orthanc::SerializationToolbox::ReadString(response[i], "ID"); |
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|
894 std::unique_ptr<Orthanc::ParsedDicomFile> reference(LoadInstance(instanceId)); |
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diff
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|
895 |
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|
896 std::string imageOrientation; |
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diff
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|
897 if (reference->GetTagValue(imageOrientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT)) |
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diff
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|
898 { |
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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28
diff
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|
899 std::vector<std::string> items; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
900 Orthanc::Toolbox::TokenizeString(items, imageOrientation, '\\'); |
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diff
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|
901 |
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diff
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|
902 double x1, x2, x3, y1, y2, y3; |
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diff
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|
903 |
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diff
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|
904 if (items.size() == 6 && |
32 | 905 Toolbox::MyParseDouble(x1, items[0]) && |
906 Toolbox::MyParseDouble(x2, items[1]) && | |
907 Toolbox::MyParseDouble(x3, items[2]) && | |
908 Toolbox::MyParseDouble(y1, items[3]) && | |
909 Toolbox::MyParseDouble(y2, items[4]) && | |
910 Toolbox::MyParseDouble(y3, items[5])) | |
29
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|
911 { |
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|
912 axisX = Vector3D(x1, x2, x3); |
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|
913 axisY = Vector3D(y1, y2, y3); |
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diff
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|
914 } |
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diff
changeset
|
915 } |
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|
916 } |
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|
917 else |
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|
918 { |
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|
919 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, |
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920 "Multiple instances with the same SOP Instance UID"); |
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|
921 } |
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changeset
|
922 } |
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|
923 } |
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diff
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|
924 } |
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diff
changeset
|
925 } |
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diff
changeset
|
926 |
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diff
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|
927 |
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|
928 static bool EncodeStructureSetMesh(std::string& stl, |
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|
929 const StructureSet& structureSet, |
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|
930 const StructureSetGeometry& geometry, |
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931 const std::set<std::string>& roiNames, |
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932 unsigned int resolution, |
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|
933 bool smooth) |
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|
934 { |
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|
935 if (resolution < 1 || |
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|
936 structureSet.GetPolygonsCount() < 1) |
1
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|
937 { |
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|
938 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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|
939 } |
0f03a8a0bd6f
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|
940 |
32 | 941 if (!Toolbox::IsNear(1, geometry.GetSlicesNormal().ComputeNorm())) |
1
0f03a8a0bd6f
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|
942 { |
0f03a8a0bd6f
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|
943 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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|
944 } |
0f03a8a0bd6f
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diff
changeset
|
945 |
29
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|
946 Vector3D axisX, axisY; |
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|
947 GetReferencedVolumeAxes(axisX, axisY, structureSet); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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948 |
62abf3c523f9
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diff
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|
949 Vector3D axisZ = Vector3D::CrossProduct(axisX, axisY); |
1
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|
950 |
32 | 951 if (!Toolbox::IsNear(1, axisX.ComputeNorm()) || |
952 !Toolbox::IsNear(1, axisY.ComputeNorm()) || | |
29
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953 !Vector3D::AreParallel(axisZ, geometry.GetSlicesNormal())) |
1
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954 { |
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|
955 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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|
956 } |
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|
957 |
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|
958 Extent2D extent; |
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959 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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960 { |
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|
961 structureSet.GetPolygon(i).Add(extent, axisX, axisY); |
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|
962 } |
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|
963 |
28
410003c50b17
improved computation of RT-STRUCT geometry
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diff
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|
964 const int depth = geometry.GetSlicesCount(); |
1
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|
965 |
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|
966 vtkNew<vtkImageData> volume; |
0f03a8a0bd6f
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|
967 volume->SetDimensions(resolution, resolution, depth); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
968 volume->AllocateScalars(VTK_UNSIGNED_CHAR, 1); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
969 |
0f03a8a0bd6f
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|
970 assert(sizeof(unsigned char) == 1); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
971 memset(volume->GetScalarPointer(), 0, resolution * resolution * depth); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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|
972 |
30 | 973 const double pixelSpacingX = extent.GetWidth() / static_cast<double>(resolution); |
974 const double pixelSpacingY = extent.GetHeight() / static_cast<double>(resolution); | |
975 const double pixelSpacingZ = geometry.GetSlicesSpacing(); | |
976 | |
977 bool first = true; | |
978 | |
1
0f03a8a0bd6f
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|
979 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
980 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
981 const StructurePolygon& polygon = structureSet.GetPolygon(i); |
29
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
982 if (roiNames.find(polygon.GetRoiName()) != roiNames.end()) |
1
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encoding of RT-STRUCT as STL
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|
983 { |
29
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
984 // This polygon corresponds to a ROI of interest |
1
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encoding of RT-STRUCT as STL
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diff
changeset
|
985 |
29
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
986 size_t z; |
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
987 if (geometry.LookupSliceIndex(z, polygon)) |
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
988 { |
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diff
changeset
|
989 std::vector<Orthanc::ImageProcessing::ImagePoint> points; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
990 points.reserve(polygon.GetPointsCount()); |
1
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encoding of RT-STRUCT as STL
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|
991 |
29
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
992 for (size_t j = 0; j < polygon.GetPointsCount(); j++) |
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
993 { |
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
994 const Vector3D& point = polygon.GetPoint(j); |
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big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
995 double x = (Vector3D::DotProduct(point, axisX) - extent.GetMinX()) / extent.GetWidth() * static_cast<double>(resolution); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
996 double y = (Vector3D::DotProduct(point, axisY) - extent.GetMinY()) / extent.GetHeight() * static_cast<double>(resolution); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
997 points.push_back(Orthanc::ImageProcessing::ImagePoint(static_cast<int32_t>(std::floor(x)), |
62abf3c523f9
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diff
changeset
|
998 static_cast<int32_t>(std::floor(y)))); |
30 | 999 |
1000 if (first) | |
1001 { | |
1002 first = false; | |
1003 volume->SetOrigin(point.GetX() - x * pixelSpacingX, | |
1004 point.GetY() - y * pixelSpacingY, | |
1005 point.GetZ() - z * pixelSpacingZ); | |
1006 } | |
29
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1007 } |
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big endian support, retrieve axes from referenced volume
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|
1008 |
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big endian support, retrieve axes from referenced volume
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diff
changeset
|
1009 Orthanc::ImageAccessor slice; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1010 slice.AssignWritable(Orthanc::PixelFormat_Grayscale8, resolution, resolution, resolution /* pitch */, |
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diff
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|
1011 reinterpret_cast<uint8_t*>(volume->GetScalarPointer()) + z * resolution * resolution); |
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diff
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|
1012 |
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diff
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|
1013 XorFiller filler(slice); |
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|
1014 Orthanc::ImageProcessing::FillPolygon(filler, points); |
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|
1015 } |
1
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|
1016 } |
0f03a8a0bd6f
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|
1017 } |
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|
1018 |
30 | 1019 volume->SetSpacing(pixelSpacingX, pixelSpacingY, pixelSpacingZ); |
1
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|
1020 |
32 | 1021 return VTKToolbox::EncodeVolume(stl, volume.Get(), resolution, smooth); |
1
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|
1022 } |
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changeset
|
1023 |
0f03a8a0bd6f
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changeset
|
1024 |
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|
1025 void ListStructures(OrthancPluginRestOutput* output, |
0f03a8a0bd6f
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|
1026 const char* url, |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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changeset
|
1027 const OrthancPluginHttpRequest* request) |
0f03a8a0bd6f
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changeset
|
1028 { |
0f03a8a0bd6f
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diff
changeset
|
1029 if (request->method != OrthancPluginHttpMethod_Get) |
0f03a8a0bd6f
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1030 { |
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|
1031 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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encoding of RT-STRUCT as STL
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diff
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|
1032 return; |
0f03a8a0bd6f
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|
1033 } |
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|
1034 |
3
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added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1035 const std::string instanceId(request->groups[0]); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1036 |
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|
1037 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1038 |
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|
1039 std::set<std::string> names; |
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|
1040 ListStructuresNames(names, *dicom); |
1
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|
1041 |
3
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diff
changeset
|
1042 Json::Value answer = Json::arrayValue; |
1
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|
1043 |
3
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changeset
|
1044 for (std::set<std::string>::const_iterator it = names.begin(); it != names.end(); ++it) |
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|
1045 { |
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|
1046 answer.append(*it); |
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changeset
|
1047 } |
1
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|
1048 |
3
0fb06c6a6c87
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diff
changeset
|
1049 std::string s = answer.toStyledString(); |
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|
1050 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
1051 } |
0f03a8a0bd6f
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diff
changeset
|
1052 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
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|
1053 |
4
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diff
changeset
|
1054 static void AddDefaultTagValue(Json::Value& target, |
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generated STL pass dciodvfy
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|
1055 const Orthanc::DicomTag& tag, |
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changeset
|
1056 const std::string& value) |
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changeset
|
1057 { |
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|
1058 if (!target.isMember(tag.Format())) |
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|
1059 { |
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changeset
|
1060 target[tag.Format()] = value; |
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|
1061 } |
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changeset
|
1062 } |
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|
1063 |
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changeset
|
1064 |
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diff
changeset
|
1065 static void AddDefaultTagValue(Json::Value& target, |
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|
1066 const DcmTagKey& tag, |
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changeset
|
1067 const std::string& value) |
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changeset
|
1068 { |
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diff
changeset
|
1069 AddDefaultTagValue(target, Orthanc::DicomTag(tag.getGroup(), tag.getElement()), value); |
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diff
changeset
|
1070 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1071 |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1072 |
7 | 1073 static void CallCreateDicom(Json::Value& answer, |
1074 const std::string& stl, | |
1075 const Json::Value& body, | |
1076 const std::string& parentStudy, | |
1077 const std::string& defaultSeriesDescription, | |
1078 const std::string& defaultFrameOfReferenceUid, | |
1079 const std::string& defaultTitle) | |
1080 { | |
1081 static const char* const KEY_TAGS = "Tags"; | |
1082 | |
1083 Json::Value normalized = Json::objectValue; | |
1084 | |
1085 if (body.isMember(KEY_TAGS)) | |
1086 { | |
1087 const Json::Value& tags = body[KEY_TAGS]; | |
1088 | |
1089 if (tags.type() != Json::objectValue) | |
1090 { | |
1091 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Tags must be provided as a JSON object"); | |
1092 } | |
1093 | |
1094 std::vector<std::string> keys = tags.getMemberNames(); | |
1095 for (size_t i = 0; i < keys.size(); i++) | |
1096 { | |
1097 const Orthanc::DicomTag tag = Orthanc::FromDcmtkBridge::ParseTag(keys[i]); | |
1098 normalized[tag.Format()] = tags[keys[i]]; | |
1099 } | |
1100 } | |
1101 | |
1102 if (!normalized.isMember(Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format())) | |
1103 { | |
1104 normalized[Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format()] = defaultSeriesDescription; | |
1105 } | |
1106 | |
1107 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_SERIES_NUMBER, "1"); | |
1108 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, defaultFrameOfReferenceUid); | |
1109 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_INSTANCE_NUMBER, "1"); | |
1110 | |
1111 AddDefaultTagValue(normalized, DCM_BurnedInAnnotation, "NO"); | |
1112 AddDefaultTagValue(normalized, DCM_DeviceSerialNumber, ORTHANC_STL_VERSION); | |
1113 AddDefaultTagValue(normalized, DCM_DocumentTitle, defaultTitle); | |
1114 AddDefaultTagValue(normalized, DCM_Manufacturer, "Orthanc STL plugin"); | |
1115 AddDefaultTagValue(normalized, DCM_ManufacturerModelName, "Orthanc STL plugin"); | |
1116 AddDefaultTagValue(normalized, DCM_PositionReferenceIndicator, ""); | |
1117 AddDefaultTagValue(normalized, DCM_SoftwareVersions, ORTHANC_STL_VERSION); | |
1118 AddDefaultTagValue(normalized, DCM_ConceptNameCodeSequence, ""); | |
1119 | |
1120 std::string date, time; | |
1121 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); | |
1122 AddDefaultTagValue(normalized, DCM_AcquisitionDateTime, date + time); | |
1123 | |
1124 const Orthanc::DicomTag MEASUREMENT_UNITS_CODE_SEQUENCE(DCM_MeasurementUnitsCodeSequence.getGroup(), | |
1125 DCM_MeasurementUnitsCodeSequence.getElement()); | |
1126 | |
1127 if (!normalized.isMember(MEASUREMENT_UNITS_CODE_SEQUENCE.Format())) | |
1128 { | |
1129 Json::Value item; | |
1130 item["CodeValue"] = "mm"; | |
1131 item["CodingSchemeDesignator"] = "UCUM"; | |
1132 item["CodeMeaning"] = defaultTitle; | |
1133 | |
1134 normalized[MEASUREMENT_UNITS_CODE_SEQUENCE.Format()].append(item); | |
1135 } | |
1136 | |
1137 std::string content; | |
1138 Orthanc::Toolbox::EncodeDataUriScheme(content, Orthanc::MIME_STL, stl); | |
1139 | |
1140 Json::Value create; | |
1141 create["Content"] = content; | |
1142 create["Parent"] = parentStudy; | |
1143 create["Tags"] = normalized; | |
1144 | |
1145 if (!OrthancPlugins::RestApiPost(answer, "/tools/create-dicom", create.toStyledString(), false)) | |
1146 { | |
1147 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Cannot create DICOM from STL"); | |
1148 } | |
1149 } | |
1150 | |
1151 | |
1152 void EncodeStructureSet(OrthancPluginRestOutput* output, | |
1153 const char* url, | |
1154 const OrthancPluginHttpRequest* request) | |
1
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encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1155 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1156 static const char* const KEY_INSTANCE = "Instance"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1157 static const char* const KEY_RESOLUTION = "Resolution"; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1158 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
|
1159 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
|
1160 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
|
1161 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1162 if (request->method != OrthancPluginHttpMethod_Post) |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1163 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1164 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1165 return; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1166 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1167 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1168 Json::Value body; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1169 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
|
1170 { |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1171 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1172 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1173 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1174 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
|
1175 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1176 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1177 true /* smooth by default */); |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1178 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
|
1179 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1180 256 /* default value */); |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1181 const bool strict = (body.isMember(KEY_STRICT) ? |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1182 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_STRICT) : |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1183 true /* strict by default */); |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1184 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1185 std::set<std::string> roiNames; |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1186 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
|
1187 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1188 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1189 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1190 StructureSet structureSet(*dicom); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1191 |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1192 StructureSetGeometry geometry(structureSet, strict); |
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1193 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1194 std::string stl; |
28
410003c50b17
improved computation of RT-STRUCT geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
25
diff
changeset
|
1195 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
|
1196 { |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
1197 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
|
1198 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1199 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1200 { |
7 | 1201 std::string seriesDescription; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1202 |
7 | 1203 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
|
1204 { |
7 | 1205 seriesDescription += ": "; |
1206 } | |
1207 else | |
1208 { | |
1209 seriesDescription.clear(); | |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1210 } |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1211 |
7 | 1212 bool first = true; |
1213 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
|
1214 { |
7 | 1215 if (first) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1216 { |
7 | 1217 first = false; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1218 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1219 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1220 { |
7 | 1221 seriesDescription += ", "; |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1222 } |
2
2bdb9acb7dcf
added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
1223 |
7 | 1224 seriesDescription += *it; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1225 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1226 |
7 | 1227 std::string frameOfReferenceUid; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1228 if (structureSet.HasFrameOfReferenceUid()) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1229 { |
7 | 1230 frameOfReferenceUid = structureSet.GetFrameOfReferenceUid(); |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1231 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1232 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1233 { |
7 | 1234 frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1235 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1236 |
7 | 1237 Json::Value answer; |
1238 CallCreateDicom(answer, stl, body, structureSet.HashStudy(), seriesDescription, | |
1239 frameOfReferenceUid, "STL model generated from DICOM RT-STRUCT"); | |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
1240 |
7 | 1241 std::string s = answer.toStyledString(); |
1242 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
|
1243 } |
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 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
1246 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1247 void ExtractStl(OrthancPluginRestOutput* output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1248 const char* url, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1249 const OrthancPluginHttpRequest* request) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1250 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1251 if (request->method != OrthancPluginHttpMethod_Get) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1252 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1253 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1254 return; |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1255 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1256 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1257 const std::string instanceId(request->groups[0]); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1258 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1259 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1260 DcmDataset& dataset = *dicom->GetDcmtkObject().getDataset(); |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1261 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1262 std::string stl; |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
1263 if (GetStringValue(dataset, DCM_MIMETypeOfEncapsulatedDocument) != Orthanc::MIME_STL || |
29
62abf3c523f9
big endian support, retrieve axes from referenced volume
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
28
diff
changeset
|
1264 GetStringValue(dataset, DCM_SOPClassUID) != UID_EncapsulatedSTLStorage || |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
changeset
|
1265 !dicom->GetTagValue(stl, Orthanc::DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1266 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1267 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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|
1268 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1269 else |
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added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1270 { |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1271 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
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|
1272 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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diff
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|
1273 } |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1274 } |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1275 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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2
diff
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|
1276 |
6 | 1277 |
8
d1267c6c33e1
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diff
changeset
|
1278 void EncodeNifti(OrthancPluginRestOutput* output, |
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diff
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|
1279 const char* url, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1280 const OrthancPluginHttpRequest* request) |
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diff
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|
1281 { |
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diff
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|
1282 static const char* const KEY_NIFTI = "Nifti"; |
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diff
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|
1283 static const char* const KEY_RESOLUTION = "Resolution"; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1284 static const char* const KEY_PARENT_STUDY = "ParentStudy"; |
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diff
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|
1285 static const char* const KEY_SMOOTH = "Smooth"; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1286 |
d1267c6c33e1
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diff
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|
1287 if (request->method != OrthancPluginHttpMethod_Post) |
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diff
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|
1288 { |
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diff
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|
1289 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
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diff
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|
1290 return; |
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diff
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|
1291 } |
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diff
changeset
|
1292 |
d1267c6c33e1
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diff
changeset
|
1293 Json::Value body; |
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diff
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|
1294 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
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diff
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|
1295 { |
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diff
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|
1296 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
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diff
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|
1297 } |
d1267c6c33e1
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diff
changeset
|
1298 |
d1267c6c33e1
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diff
changeset
|
1299 std::string mime, nifti; |
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diff
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|
1300 if (!Orthanc::Toolbox::DecodeDataUriScheme(mime, nifti, Orthanc::SerializationToolbox::ReadString(body, KEY_NIFTI))) |
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diff
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|
1301 { |
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diff
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|
1302 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Missing the \"Nifti\" argument containing the NIfTI file"); |
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diff
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|
1303 } |
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diff
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|
1304 |
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diff
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|
1305 const std::string parentStudy = Orthanc::SerializationToolbox::ReadString(body, KEY_PARENT_STUDY); |
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diff
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|
1306 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
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diff
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|
1307 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
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diff
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|
1308 true /* smooth by default */); |
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diff
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|
1309 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1310 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
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diff
changeset
|
1311 256 /* default value */); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1312 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1313 vtkNew<vtkImageData> volume; |
32 | 1314 VTKToolbox::LoadNifti(volume.Get(), nifti); |
8
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diff
changeset
|
1315 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1316 std::string stl; |
32 | 1317 if (!VTKToolbox::EncodeVolume(stl, volume.Get(), resolution, smooth)) |
8
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diff
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|
1318 { |
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diff
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|
1319 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from NIfTI"); |
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diff
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|
1320 } |
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diff
changeset
|
1321 else |
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diff
changeset
|
1322 { |
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diff
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|
1323 const std::string title = "STL model generated from NIfTI"; |
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diff
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|
1324 |
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diff
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|
1325 const std::string frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
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diff
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|
1326 |
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diff
changeset
|
1327 Json::Value answer; |
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diff
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|
1328 CallCreateDicom(answer, stl, body, parentStudy, title, frameOfReferenceUid, title); |
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diff
changeset
|
1329 |
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diff
changeset
|
1330 std::string s = answer.toStyledString(); |
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diff
changeset
|
1331 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
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diff
changeset
|
1332 } |
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diff
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|
1333 } |
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diff
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|
1334 |
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diff
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|
1335 |
0
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initial commit of the viewer plugin
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|
1336 extern "C" |
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|
1337 { |
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|
1338 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) |
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|
1339 { |
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|
1340 OrthancPlugins::SetGlobalContext(context); |
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|
1341 |
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1342 /* Check the version of the Orthanc core */ |
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|
1343 if (OrthancPluginCheckVersion(OrthancPlugins::GetGlobalContext()) == 0) |
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|
1344 { |
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|
1345 char info[1024]; |
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|
1346 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", |
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|
1347 OrthancPlugins::GetGlobalContext()->orthancVersion, |
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|
1348 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
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|
1349 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, |
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|
1350 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); |
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|
1351 OrthancPluginLogError(OrthancPlugins::GetGlobalContext(), info); |
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1352 return -1; |
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|
1353 } |
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|
1354 |
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|
1355 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
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1356 Orthanc::Logging::InitializePluginContext(context); |
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|
1357 #else |
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|
1358 Orthanc::Logging::Initialize(context); |
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|
1359 #endif |
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|
1360 |
1
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diff
changeset
|
1361 Orthanc::InitializeFramework("", false); |
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|
1362 |
0
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|
1363 hasCreateDicomStl_ = OrthancPlugins::CheckMinimalOrthancVersion(1, 12, 1); |
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1364 |
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|
1365 if (!hasCreateDicomStl_) |
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1366 { |
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|
1367 LOG(WARNING) << "Your version of Orthanc (" << std::string(context->orthancVersion) |
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1368 << ") is insufficient to create DICOM STL, it should be above 1.12.1"; |
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1369 } |
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1370 |
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1371 OrthancPlugins::SetDescription(ORTHANC_PLUGIN_NAME, "STL plugin for Orthanc."); |
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1372 |
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1373 OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/app/(.*)", true); |
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1374 OrthancPlugins::RegisterRestCallback<ExtractStl>("/instances/([0-9a-f-]+)/stl", true); |
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1375 OrthancPlugins::RegisterRestCallback<ListStructures>("/stl/rt-struct/([0-9a-f-]+)", true); |
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1376 |
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1377 if (hasCreateDicomStl_) |
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1378 { |
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1379 OrthancPlugins::RegisterRestCallback<EncodeStructureSet>("/stl/encode-rtstruct", true); |
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1380 OrthancPlugins::RegisterRestCallback<EncodeNifti>("/stl/encode-nifti", true); |
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1381 } |
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1382 |
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1383 OrthancPlugins::OrthancConfiguration globalConfiguration; |
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1384 OrthancPlugins::OrthancConfiguration configuration; |
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1385 globalConfiguration.GetSection(configuration, "STL"); |
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1386 |
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1387 // Extend the default Orthanc Explorer with custom JavaScript for STL |
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1388 std::string explorer; |
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1389 |
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1390 { |
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1391 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); |
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1392 |
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1393 std::map<std::string, std::string> dictionary; |
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1394 dictionary["HAS_CREATE_DICOM_STL"] = (hasCreateDicomStl_ ? "true" : "false"); |
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1395 dictionary["SHOW_NIFTI_BUTTON"] = (configuration.GetBooleanValue("NIfTI", false) ? "true" : "false"); |
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1396 explorer = Orthanc::Toolbox::SubstituteVariables(explorer, dictionary); |
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1397 |
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1398 OrthancPlugins::ExtendOrthancExplorer(ORTHANC_PLUGIN_NAME, explorer); |
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1399 } |
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1400 |
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1401 return 0; |
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1402 } |
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1403 |
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1404 |
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1405 ORTHANC_PLUGINS_API void OrthancPluginFinalize() |
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1406 { |
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1407 Orthanc::FinalizeFramework(); |
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1408 } |
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1409 |
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1410 |
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1411 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() |
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1412 { |
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1413 return ORTHANC_PLUGIN_NAME; |
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1414 } |
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1415 |
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1416 |
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1417 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() |
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1418 { |
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1419 return ORTHANC_STL_VERSION; |
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1420 } |
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1421 } |