Mercurial > hg > orthanc-stl
annotate Sources/Plugin.cpp @ 38:970994058acd
building O3DV
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 05 Apr 2024 08:19:54 +0200 |
parents | 13698d34e059 |
children | 8a1daa321afe |
rev | line source |
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1 /** |
24 | 2 * SPDX-FileCopyrightText: 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
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3 * SPDX-License-Identifier: GPL-3.0-or-later |
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4 */ |
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5 |
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6 /** |
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7 * STL plugin for Orthanc |
24 | 8 * Copyright (C) 2023-2024 Sebastien Jodogne, UCLouvain, Belgium |
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9 * |
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10 * This program is free software: you can redistribute it and/or |
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11 * modify it under the terms of the GNU General Public License as |
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12 * published by the Free Software Foundation, either version 3 of the |
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13 * License, or (at your option) any later version. |
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14 * |
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15 * This program is distributed in the hope that it will be useful, but |
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16 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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18 * General Public License for more details. |
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19 * |
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20 * You should have received a copy of the GNU General Public License |
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21 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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22 **/ |
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23 |
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24 |
35 | 25 #include "StructureSetGeometry.h" |
26 #include "StructureSet.h" | |
34 | 27 #include "STLToolbox.h" |
33 | 28 #include "StructurePolygon.h" |
32 | 29 #include "VTKToolbox.h" |
30 #include "Vector3D.h" | |
31 #include "Toolbox.h" | |
32 #include "Extent2D.h" | |
33 | |
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34 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
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35 |
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36 #include <EmbeddedResources.h> |
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37 |
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38 #include <DicomFormat/DicomInstanceHasher.h> |
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39 #include <DicomParsing/FromDcmtkBridge.h> |
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40 #include <DicomParsing/ParsedDicomFile.h> |
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41 #include <Images/ImageProcessing.h> |
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42 #include <Logging.h> |
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43 #include <OrthancFramework.h> |
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44 #include <SerializationToolbox.h> |
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45 #include <SystemToolbox.h> |
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46 |
33 | 47 #include <vtkNew.h> |
48 | |
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49 #include <boost/algorithm/string.hpp> |
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50 #include <boost/thread/shared_mutex.hpp> |
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51 |
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52 #define ORTHANC_PLUGIN_NAME "stl" |
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53 |
6 | 54 |
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55 // Forward declaration |
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56 void ReadStaticAsset(std::string& target, |
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57 const std::string& path); |
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58 |
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59 |
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60 /** |
38 | 61 * As the static assets are gzipped by the "EmbedStaticAssets.py" |
62 * script, we use a cache to maintain the uncompressed assets in order | |
63 * to avoid multiple gzip decodings. | |
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64 **/ |
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65 class ResourcesCache : public boost::noncopyable |
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66 { |
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67 private: |
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68 typedef std::map<std::string, std::string*> Content; |
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69 |
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70 boost::shared_mutex mutex_; |
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71 Content content_; |
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72 |
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73 public: |
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74 ~ResourcesCache() |
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75 { |
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76 for (Content::iterator it = content_.begin(); it != content_.end(); ++it) |
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77 { |
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78 assert(it->second != NULL); |
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79 delete it->second; |
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80 } |
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81 } |
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82 |
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83 void Answer(OrthancPluginRestOutput* output, |
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84 const std::string& path) |
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85 { |
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86 const std::string mime = Orthanc::EnumerationToString(Orthanc::SystemToolbox::AutodetectMimeType(path)); |
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87 |
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88 { |
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89 // Check whether the cache already contains the resource |
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90 boost::shared_lock<boost::shared_mutex> lock(mutex_); |
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91 |
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92 Content::const_iterator found = content_.find(path); |
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93 |
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94 if (found != content_.end()) |
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95 { |
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96 assert(found->second != NULL); |
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97 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, found->second->c_str(), found->second->size(), mime.c_str()); |
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98 return; |
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99 } |
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100 } |
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101 |
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102 // This resource has not been cached yet |
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103 |
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104 std::unique_ptr<std::string> item(new std::string); |
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105 ReadStaticAsset(*item, path); |
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106 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, item->c_str(), item->size(), mime.c_str()); |
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107 |
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108 { |
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109 // Store the resource into the cache |
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110 boost::unique_lock<boost::shared_mutex> lock(mutex_); |
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111 |
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112 if (content_.find(path) == content_.end()) |
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113 { |
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114 content_[path] = item.release(); |
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115 } |
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116 } |
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117 } |
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118 }; |
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119 |
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120 |
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121 static ResourcesCache cache_; |
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122 static bool hasCreateDicomStl_; |
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123 |
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124 void ServeFile(OrthancPluginRestOutput* output, |
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125 const char* url, |
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126 const OrthancPluginHttpRequest* request) |
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127 { |
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128 if (request->method != OrthancPluginHttpMethod_Get) |
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129 { |
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130 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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131 return; |
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132 } |
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133 |
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134 std::string file = request->groups[0]; |
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135 |
38 | 136 if (boost::starts_with(file, "libs/")) |
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137 { |
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138 cache_.Answer(output, file.substr(5)); |
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139 } |
38 | 140 else |
141 { | |
142 Orthanc::EmbeddedResources::FileResourceId resourceId; | |
143 Orthanc::MimeType mimeType; | |
144 | |
145 if (file == "three.html") | |
146 { | |
147 resourceId = Orthanc::EmbeddedResources::THREE_HTML; | |
148 mimeType = Orthanc::MimeType_Html; | |
149 } | |
150 else if (file == "three.js") | |
151 { | |
152 resourceId = Orthanc::EmbeddedResources::THREE_JS; | |
153 mimeType = Orthanc::MimeType_JavaScript; | |
154 } | |
155 else if (file == "o3dv.html") | |
156 { | |
157 resourceId = Orthanc::EmbeddedResources::O3DV_HTML; | |
158 mimeType = Orthanc::MimeType_Html; | |
159 } | |
160 else if (file == "o3dv.js") | |
161 { | |
162 resourceId = Orthanc::EmbeddedResources::O3DV_JS; | |
163 mimeType = Orthanc::MimeType_JavaScript; | |
164 } | |
165 else | |
166 { | |
167 OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 404); | |
168 return; | |
169 } | |
170 | |
171 std::string s; | |
172 Orthanc::EmbeddedResources::GetFileResource(s, resourceId); | |
173 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::EnumerationToString(mimeType)); | |
174 } | |
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175 } |
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176 |
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177 |
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178 |
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179 |
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180 #include <dcmtk/dcmdata/dcfilefo.h> |
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181 #include <dcmtk/dcmdata/dcsequen.h> |
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182 #include <dcmtk/dcmdata/dcuid.h> |
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183 |
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184 |
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185 class XorFiller : public Orthanc::ImageProcessing::IPolygonFiller |
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186 { |
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187 private: |
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188 Orthanc::ImageAccessor& target_; |
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189 |
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190 public: |
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191 XorFiller(Orthanc::ImageAccessor& target) : |
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192 target_(target) |
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193 { |
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194 } |
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195 |
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196 virtual void Fill(int y, |
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197 int x1, |
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198 int x2) ORTHANC_OVERRIDE |
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199 { |
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200 assert(x1 <= x2); |
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201 |
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202 if (y >= 0 && |
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203 y < static_cast<int>(target_.GetHeight())) |
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204 { |
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205 x1 = std::max(x1, 0); |
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206 x2 = std::min(x2, static_cast<int>(target_.GetWidth()) - 1); |
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207 |
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208 uint8_t* p = reinterpret_cast<uint8_t*>(target_.GetRow(y)) + x1; |
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209 |
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210 for (int i = x1; i <= x2; i++, p++) |
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211 { |
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212 *p = (*p ^ 0xff); |
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213 } |
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214 } |
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215 } |
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216 }; |
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217 |
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218 |
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219 static Orthanc::ParsedDicomFile* LoadInstance(const std::string& instanceId) |
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220 { |
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221 std::string dicom; |
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222 |
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223 if (!OrthancPlugins::RestApiGetString(dicom, "/instances/" + instanceId + "/file", false)) |
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224 { |
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225 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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226 } |
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227 else |
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228 { |
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229 return new Orthanc::ParsedDicomFile(dicom); |
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230 } |
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231 } |
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232 |
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233 |
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234 static void GetReferencedVolumeAxes(Vector3D& axisX, |
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235 Vector3D& axisY, |
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236 const StructureSet& structureSet) |
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237 { |
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238 // This is a rough guess for the X/Y axes |
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239 axisX = Vector3D(1, 0, 0); |
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240 axisY = Vector3D(0, 1, 0); |
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241 |
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242 // Look for one instance from the referenced volume |
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243 const std::string& sopInstanceUid = structureSet.GetPolygon(0).GetReferencedSopInstanceUid(); |
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244 |
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245 Json::Value response; |
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246 if (OrthancPlugins::RestApiPost(response, "/tools/lookup", sopInstanceUid, false)) |
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247 { |
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248 if (response.type() != Json::arrayValue) |
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249 { |
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250 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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251 } |
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252 |
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253 bool first = true; |
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254 |
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255 for (Json::Value::ArrayIndex i = 0; i < response.size(); i++) |
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256 { |
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257 if (response[i].type() != Json::objectValue) |
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258 { |
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259 throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); |
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260 } |
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261 |
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262 if (Orthanc::SerializationToolbox::ReadString(response[i], "Type") == "Instance") |
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263 { |
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264 if (first) |
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265 { |
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266 const std::string& instanceId = Orthanc::SerializationToolbox::ReadString(response[i], "ID"); |
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267 std::unique_ptr<Orthanc::ParsedDicomFile> reference(LoadInstance(instanceId)); |
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268 |
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269 std::string imageOrientation; |
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270 if (reference->GetTagValue(imageOrientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT)) |
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271 { |
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272 std::vector<std::string> items; |
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273 Orthanc::Toolbox::TokenizeString(items, imageOrientation, '\\'); |
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274 |
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275 double x1, x2, x3, y1, y2, y3; |
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276 |
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277 if (items.size() == 6 && |
33 | 278 STLToolbox::MyParseDouble(x1, items[0]) && |
279 STLToolbox::MyParseDouble(x2, items[1]) && | |
280 STLToolbox::MyParseDouble(x3, items[2]) && | |
281 STLToolbox::MyParseDouble(y1, items[3]) && | |
282 STLToolbox::MyParseDouble(y2, items[4]) && | |
283 STLToolbox::MyParseDouble(y3, items[5])) | |
29
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284 { |
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285 axisX = Vector3D(x1, x2, x3); |
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286 axisY = Vector3D(y1, y2, y3); |
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287 } |
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288 } |
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289 } |
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290 else |
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291 { |
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292 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, |
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293 "Multiple instances with the same SOP Instance UID"); |
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294 } |
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295 } |
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296 } |
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297 } |
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298 } |
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299 |
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300 |
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301 static bool EncodeStructureSetMesh(std::string& stl, |
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302 const StructureSet& structureSet, |
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303 const StructureSetGeometry& geometry, |
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304 const std::set<std::string>& roiNames, |
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305 unsigned int resolution, |
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306 bool smooth) |
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307 { |
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308 if (resolution < 1 || |
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309 structureSet.GetPolygonsCount() < 1) |
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310 { |
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311 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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312 } |
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313 |
33 | 314 if (!STLToolbox::IsNear(1, geometry.GetSlicesNormal().ComputeNorm())) |
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315 { |
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316 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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317 } |
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318 |
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319 Vector3D axisX, axisY; |
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320 GetReferencedVolumeAxes(axisX, axisY, structureSet); |
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321 |
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322 Vector3D axisZ = Vector3D::CrossProduct(axisX, axisY); |
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323 |
33 | 324 if (!STLToolbox::IsNear(1, axisX.ComputeNorm()) || |
325 !STLToolbox::IsNear(1, axisY.ComputeNorm()) || | |
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326 !Vector3D::AreParallel(axisZ, geometry.GetSlicesNormal())) |
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327 { |
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328 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
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329 } |
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330 |
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331 Extent2D extent; |
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332 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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333 { |
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334 structureSet.GetPolygon(i).Add(extent, axisX, axisY); |
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335 } |
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336 |
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337 const int depth = geometry.GetSlicesCount(); |
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338 |
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339 vtkNew<vtkImageData> volume; |
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340 volume->SetDimensions(resolution, resolution, depth); |
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341 volume->AllocateScalars(VTK_UNSIGNED_CHAR, 1); |
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342 |
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343 assert(sizeof(unsigned char) == 1); |
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344 memset(volume->GetScalarPointer(), 0, resolution * resolution * depth); |
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345 |
30 | 346 const double pixelSpacingX = extent.GetWidth() / static_cast<double>(resolution); |
347 const double pixelSpacingY = extent.GetHeight() / static_cast<double>(resolution); | |
348 const double pixelSpacingZ = geometry.GetSlicesSpacing(); | |
349 | |
350 bool first = true; | |
351 | |
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352 for (size_t i = 0; i < structureSet.GetPolygonsCount(); i++) |
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353 { |
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354 const StructurePolygon& polygon = structureSet.GetPolygon(i); |
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355 if (roiNames.find(polygon.GetRoiName()) != roiNames.end()) |
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356 { |
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357 // This polygon corresponds to a ROI of interest |
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358 |
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359 size_t z; |
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360 if (geometry.LookupSliceIndex(z, polygon)) |
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361 { |
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362 std::vector<Orthanc::ImageProcessing::ImagePoint> points; |
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363 points.reserve(polygon.GetPointsCount()); |
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364 |
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365 for (size_t j = 0; j < polygon.GetPointsCount(); j++) |
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366 { |
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367 const Vector3D& point = polygon.GetPoint(j); |
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368 double x = (Vector3D::DotProduct(point, axisX) - extent.GetMinX()) / extent.GetWidth() * static_cast<double>(resolution); |
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369 double y = (Vector3D::DotProduct(point, axisY) - extent.GetMinY()) / extent.GetHeight() * static_cast<double>(resolution); |
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370 points.push_back(Orthanc::ImageProcessing::ImagePoint(static_cast<int32_t>(std::floor(x)), |
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371 static_cast<int32_t>(std::floor(y)))); |
30 | 372 |
373 if (first) | |
374 { | |
375 first = false; | |
376 volume->SetOrigin(point.GetX() - x * pixelSpacingX, | |
377 point.GetY() - y * pixelSpacingY, | |
378 point.GetZ() - z * pixelSpacingZ); | |
379 } | |
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380 } |
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381 |
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382 Orthanc::ImageAccessor slice; |
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383 slice.AssignWritable(Orthanc::PixelFormat_Grayscale8, resolution, resolution, resolution /* pitch */, |
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384 reinterpret_cast<uint8_t*>(volume->GetScalarPointer()) + z * resolution * resolution); |
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385 |
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386 XorFiller filler(slice); |
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387 Orthanc::ImageProcessing::FillPolygon(filler, points); |
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388 } |
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389 } |
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390 } |
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391 |
30 | 392 volume->SetSpacing(pixelSpacingX, pixelSpacingY, pixelSpacingZ); |
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393 |
32 | 394 return VTKToolbox::EncodeVolume(stl, volume.Get(), resolution, smooth); |
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395 } |
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396 |
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397 |
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398 void ListStructures(OrthancPluginRestOutput* output, |
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399 const char* url, |
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400 const OrthancPluginHttpRequest* request) |
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401 { |
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402 if (request->method != OrthancPluginHttpMethod_Get) |
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403 { |
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404 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
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405 return; |
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406 } |
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407 |
3
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408 const std::string instanceId(request->groups[0]); |
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409 |
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410 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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411 |
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412 std::set<std::string> names; |
33 | 413 StructureSet::ListStructuresNames(names, *dicom); |
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414 |
3
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415 Json::Value answer = Json::arrayValue; |
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416 |
3
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417 for (std::set<std::string>::const_iterator it = names.begin(); it != names.end(); ++it) |
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418 { |
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419 answer.append(*it); |
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420 } |
1
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421 |
3
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422 std::string s = answer.toStyledString(); |
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423 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
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424 } |
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425 |
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426 |
4
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427 static void AddDefaultTagValue(Json::Value& target, |
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428 const Orthanc::DicomTag& tag, |
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429 const std::string& value) |
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430 { |
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431 if (!target.isMember(tag.Format())) |
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432 { |
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433 target[tag.Format()] = value; |
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434 } |
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435 } |
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436 |
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437 |
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438 static void AddDefaultTagValue(Json::Value& target, |
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439 const DcmTagKey& tag, |
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440 const std::string& value) |
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441 { |
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442 AddDefaultTagValue(target, Orthanc::DicomTag(tag.getGroup(), tag.getElement()), value); |
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443 } |
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444 |
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445 |
7 | 446 static void CallCreateDicom(Json::Value& answer, |
447 const std::string& stl, | |
448 const Json::Value& body, | |
449 const std::string& parentStudy, | |
450 const std::string& defaultSeriesDescription, | |
451 const std::string& defaultFrameOfReferenceUid, | |
452 const std::string& defaultTitle) | |
453 { | |
454 static const char* const KEY_TAGS = "Tags"; | |
455 | |
456 Json::Value normalized = Json::objectValue; | |
457 | |
458 if (body.isMember(KEY_TAGS)) | |
459 { | |
460 const Json::Value& tags = body[KEY_TAGS]; | |
461 | |
462 if (tags.type() != Json::objectValue) | |
463 { | |
464 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Tags must be provided as a JSON object"); | |
465 } | |
466 | |
467 std::vector<std::string> keys = tags.getMemberNames(); | |
468 for (size_t i = 0; i < keys.size(); i++) | |
469 { | |
470 const Orthanc::DicomTag tag = Orthanc::FromDcmtkBridge::ParseTag(keys[i]); | |
471 normalized[tag.Format()] = tags[keys[i]]; | |
472 } | |
473 } | |
474 | |
475 if (!normalized.isMember(Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format())) | |
476 { | |
477 normalized[Orthanc::DICOM_TAG_SERIES_DESCRIPTION.Format()] = defaultSeriesDescription; | |
478 } | |
479 | |
480 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_SERIES_NUMBER, "1"); | |
481 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, defaultFrameOfReferenceUid); | |
482 AddDefaultTagValue(normalized, Orthanc::DICOM_TAG_INSTANCE_NUMBER, "1"); | |
483 | |
484 AddDefaultTagValue(normalized, DCM_BurnedInAnnotation, "NO"); | |
485 AddDefaultTagValue(normalized, DCM_DeviceSerialNumber, ORTHANC_STL_VERSION); | |
486 AddDefaultTagValue(normalized, DCM_DocumentTitle, defaultTitle); | |
487 AddDefaultTagValue(normalized, DCM_Manufacturer, "Orthanc STL plugin"); | |
488 AddDefaultTagValue(normalized, DCM_ManufacturerModelName, "Orthanc STL plugin"); | |
489 AddDefaultTagValue(normalized, DCM_PositionReferenceIndicator, ""); | |
490 AddDefaultTagValue(normalized, DCM_SoftwareVersions, ORTHANC_STL_VERSION); | |
491 AddDefaultTagValue(normalized, DCM_ConceptNameCodeSequence, ""); | |
492 | |
493 std::string date, time; | |
494 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); | |
495 AddDefaultTagValue(normalized, DCM_AcquisitionDateTime, date + time); | |
496 | |
497 const Orthanc::DicomTag MEASUREMENT_UNITS_CODE_SEQUENCE(DCM_MeasurementUnitsCodeSequence.getGroup(), | |
498 DCM_MeasurementUnitsCodeSequence.getElement()); | |
499 | |
500 if (!normalized.isMember(MEASUREMENT_UNITS_CODE_SEQUENCE.Format())) | |
501 { | |
502 Json::Value item; | |
503 item["CodeValue"] = "mm"; | |
504 item["CodingSchemeDesignator"] = "UCUM"; | |
505 item["CodeMeaning"] = defaultTitle; | |
506 | |
507 normalized[MEASUREMENT_UNITS_CODE_SEQUENCE.Format()].append(item); | |
508 } | |
509 | |
510 std::string content; | |
511 Orthanc::Toolbox::EncodeDataUriScheme(content, Orthanc::MIME_STL, stl); | |
512 | |
513 Json::Value create; | |
514 create["Content"] = content; | |
515 create["Parent"] = parentStudy; | |
516 create["Tags"] = normalized; | |
517 | |
518 if (!OrthancPlugins::RestApiPost(answer, "/tools/create-dicom", create.toStyledString(), false)) | |
519 { | |
520 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Cannot create DICOM from STL"); | |
521 } | |
522 } | |
523 | |
524 | |
525 void EncodeStructureSet(OrthancPluginRestOutput* output, | |
526 const char* url, | |
527 const OrthancPluginHttpRequest* request) | |
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528 { |
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529 static const char* const KEY_INSTANCE = "Instance"; |
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530 static const char* const KEY_RESOLUTION = "Resolution"; |
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531 static const char* const KEY_ROI_NAMES = "RoiNames"; |
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532 static const char* const KEY_SMOOTH = "Smooth"; |
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533 static const char* const KEY_STRICT = "Strict"; |
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534 |
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535 if (request->method != OrthancPluginHttpMethod_Post) |
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536 { |
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537 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
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538 return; |
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539 } |
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540 |
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541 Json::Value body; |
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542 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
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543 { |
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544 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
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545 } |
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546 |
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547 const std::string instanceId = Orthanc::SerializationToolbox::ReadString(body, KEY_INSTANCE); |
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548 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
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549 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
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550 true /* smooth by default */); |
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551 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
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552 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
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553 256 /* default value */); |
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554 const bool strict = (body.isMember(KEY_STRICT) ? |
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555 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_STRICT) : |
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556 true /* strict by default */); |
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557 |
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558 std::set<std::string> roiNames; |
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559 Orthanc::SerializationToolbox::ReadSetOfStrings(roiNames, body, KEY_ROI_NAMES); |
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560 |
3
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561 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
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562 |
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563 StructureSet structureSet(*dicom); |
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564 |
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565 StructureSetGeometry geometry(structureSet, strict); |
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|
566 |
3
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567 std::string stl; |
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568 if (!EncodeStructureSetMesh(stl, structureSet, geometry, roiNames, resolution, smooth)) |
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569 { |
8
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570 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from RT-STRUCT"); |
1
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571 } |
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572 else |
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573 { |
7 | 574 std::string seriesDescription; |
1
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575 |
7 | 576 if (dicom->GetTagValue(seriesDescription, Orthanc::DICOM_TAG_SERIES_DESCRIPTION)) |
1
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577 { |
7 | 578 seriesDescription += ": "; |
579 } | |
580 else | |
581 { | |
582 seriesDescription.clear(); | |
1
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583 } |
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|
584 |
7 | 585 bool first = true; |
586 for (std::set<std::string>::const_iterator it = roiNames.begin(); it != roiNames.end(); ++it) | |
1
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0
diff
changeset
|
587 { |
7 | 588 if (first) |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
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0
diff
changeset
|
589 { |
7 | 590 first = false; |
1
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
591 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
592 else |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
593 { |
7 | 594 seriesDescription += ", "; |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
595 } |
2
2bdb9acb7dcf
added STL viewer button at instance level too
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1
diff
changeset
|
596 |
7 | 597 seriesDescription += *it; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
598 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
599 |
7 | 600 std::string frameOfReferenceUid; |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
601 if (structureSet.HasFrameOfReferenceUid()) |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
602 { |
7 | 603 frameOfReferenceUid = structureSet.GetFrameOfReferenceUid(); |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
604 } |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
605 else |
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
606 { |
7 | 607 frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
608 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
609 |
7 | 610 Json::Value answer; |
611 CallCreateDicom(answer, stl, body, structureSet.HashStudy(), seriesDescription, | |
612 frameOfReferenceUid, "STL model generated from DICOM RT-STRUCT"); | |
4
5ee4448a8ff8
generated STL pass dciodvfy
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3
diff
changeset
|
613 |
7 | 614 std::string s = answer.toStyledString(); |
615 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
|
616 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
617 } |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
618 |
0f03a8a0bd6f
encoding of RT-STRUCT as STL
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
619 |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
620 void ExtractStl(OrthancPluginRestOutput* output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
621 const char* url, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
622 const OrthancPluginHttpRequest* request) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
623 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
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diff
changeset
|
624 if (request->method != OrthancPluginHttpMethod_Get) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
625 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
626 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "GET"); |
0fb06c6a6c87
added route "/instances/{id}/stl"
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diff
changeset
|
627 return; |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
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diff
changeset
|
628 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
629 |
0fb06c6a6c87
added route "/instances/{id}/stl"
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diff
changeset
|
630 const std::string instanceId(request->groups[0]); |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
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diff
changeset
|
631 |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
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diff
changeset
|
632 std::unique_ptr<Orthanc::ParsedDicomFile> dicom(LoadInstance(instanceId)); |
0fb06c6a6c87
added route "/instances/{id}/stl"
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parents:
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diff
changeset
|
633 DcmDataset& dataset = *dicom->GetDcmtkObject().getDataset(); |
0fb06c6a6c87
added route "/instances/{id}/stl"
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diff
changeset
|
634 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
635 std::string stl; |
33 | 636 if (STLToolbox::GetStringValue(dataset, DCM_MIMETypeOfEncapsulatedDocument) != Orthanc::MIME_STL || |
637 STLToolbox::GetStringValue(dataset, DCM_SOPClassUID) != UID_EncapsulatedSTLStorage || | |
3
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
638 !dicom->GetTagValue(stl, Orthanc::DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
639 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
640 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "DICOM instance not encapsulating a STL model: " + instanceId); |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
641 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
642 else |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
643 { |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
644 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
645 stl.empty() ? NULL : stl.c_str(), stl.size(), Orthanc::MIME_STL); |
0fb06c6a6c87
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
646 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
647 } |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
648 |
0fb06c6a6c87
added route "/instances/{id}/stl"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2
diff
changeset
|
649 |
6 | 650 |
8
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
651 void EncodeNifti(OrthancPluginRestOutput* output, |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
652 const char* url, |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
653 const OrthancPluginHttpRequest* request) |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
654 { |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
655 static const char* const KEY_NIFTI = "Nifti"; |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
656 static const char* const KEY_RESOLUTION = "Resolution"; |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
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diff
changeset
|
657 static const char* const KEY_PARENT_STUDY = "ParentStudy"; |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
658 static const char* const KEY_SMOOTH = "Smooth"; |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
659 |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
660 if (request->method != OrthancPluginHttpMethod_Post) |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
661 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
662 OrthancPluginSendMethodNotAllowed(OrthancPlugins::GetGlobalContext(), output, "POST"); |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
663 return; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
664 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
665 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
666 Json::Value body; |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
667 if (!Orthanc::Toolbox::ReadJson(body, request->body, request->bodySize)) |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
668 { |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
669 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
670 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
671 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
672 std::string mime, nifti; |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
673 if (!Orthanc::Toolbox::DecodeDataUriScheme(mime, nifti, Orthanc::SerializationToolbox::ReadString(body, KEY_NIFTI))) |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
674 { |
d1267c6c33e1
added route /stl/encode-nifti
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parents:
7
diff
changeset
|
675 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Missing the \"Nifti\" argument containing the NIfTI file"); |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
676 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
677 |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
678 const std::string parentStudy = Orthanc::SerializationToolbox::ReadString(body, KEY_PARENT_STUDY); |
d1267c6c33e1
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diff
changeset
|
679 const bool smooth = (body.isMember(KEY_SMOOTH) ? |
d1267c6c33e1
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diff
changeset
|
680 Orthanc::SerializationToolbox::ReadBoolean(body, KEY_SMOOTH) : |
d1267c6c33e1
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diff
changeset
|
681 true /* smooth by default */); |
d1267c6c33e1
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diff
changeset
|
682 const unsigned int resolution = (body.isMember(KEY_RESOLUTION) ? |
d1267c6c33e1
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7
diff
changeset
|
683 Orthanc::SerializationToolbox::ReadUnsignedInteger(body, KEY_RESOLUTION) : |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
684 256 /* default value */); |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
685 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
686 vtkNew<vtkImageData> volume; |
32 | 687 VTKToolbox::LoadNifti(volume.Get(), nifti); |
8
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
688 |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
689 std::string stl; |
32 | 690 if (!VTKToolbox::EncodeVolume(stl, volume.Get(), resolution, smooth)) |
8
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
691 { |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
692 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Cannot encode STL from NIfTI"); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
693 } |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
694 else |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
695 { |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
696 const std::string title = "STL model generated from NIfTI"; |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
697 |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
698 const std::string frameOfReferenceUid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
699 |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
700 Json::Value answer; |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
701 CallCreateDicom(answer, stl, body, parentStudy, title, frameOfReferenceUid, title); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
702 |
d1267c6c33e1
added route /stl/encode-nifti
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7
diff
changeset
|
703 std::string s = answer.toStyledString(); |
d1267c6c33e1
added route /stl/encode-nifti
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diff
changeset
|
704 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), Orthanc::MIME_JSON); |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
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7
diff
changeset
|
705 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
706 } |
d1267c6c33e1
added route /stl/encode-nifti
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
7
diff
changeset
|
707 |
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added route /stl/encode-nifti
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708 |
0
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709 extern "C" |
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710 { |
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711 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) |
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712 { |
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713 OrthancPlugins::SetGlobalContext(context); |
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714 |
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715 /* Check the version of the Orthanc core */ |
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716 if (OrthancPluginCheckVersion(OrthancPlugins::GetGlobalContext()) == 0) |
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717 { |
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718 char info[1024]; |
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719 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", |
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720 OrthancPlugins::GetGlobalContext()->orthancVersion, |
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721 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
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722 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, |
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723 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); |
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724 OrthancPluginLogError(OrthancPlugins::GetGlobalContext(), info); |
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725 return -1; |
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726 } |
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727 |
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728 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
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729 Orthanc::Logging::InitializePluginContext(context); |
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730 #else |
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731 Orthanc::Logging::Initialize(context); |
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732 #endif |
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733 |
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734 Orthanc::InitializeFramework("", false); |
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735 |
0
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736 hasCreateDicomStl_ = OrthancPlugins::CheckMinimalOrthancVersion(1, 12, 1); |
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737 |
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738 if (!hasCreateDicomStl_) |
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739 { |
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740 LOG(WARNING) << "Your version of Orthanc (" << std::string(context->orthancVersion) |
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741 << ") is insufficient to create DICOM STL, it should be above 1.12.1"; |
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742 } |
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743 |
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744 OrthancPlugins::SetDescription(ORTHANC_PLUGIN_NAME, "STL plugin for Orthanc."); |
0
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745 |
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746 OrthancPlugins::RegisterRestCallback<ServeFile>("/stl/app/(.*)", true); |
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747 OrthancPlugins::RegisterRestCallback<ExtractStl>("/instances/([0-9a-f-]+)/stl", true); |
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748 OrthancPlugins::RegisterRestCallback<ListStructures>("/stl/rt-struct/([0-9a-f-]+)", true); |
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749 |
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750 if (hasCreateDicomStl_) |
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751 { |
8
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752 OrthancPlugins::RegisterRestCallback<EncodeStructureSet>("/stl/encode-rtstruct", true); |
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753 OrthancPlugins::RegisterRestCallback<EncodeNifti>("/stl/encode-nifti", true); |
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754 } |
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755 |
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756 OrthancPlugins::OrthancConfiguration globalConfiguration; |
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757 OrthancPlugins::OrthancConfiguration configuration; |
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758 globalConfiguration.GetSection(configuration, "STL"); |
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759 |
2
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760 // Extend the default Orthanc Explorer with custom JavaScript for STL |
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761 std::string explorer; |
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762 |
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763 { |
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764 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); |
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765 |
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766 std::map<std::string, std::string> dictionary; |
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767 dictionary["HAS_CREATE_DICOM_STL"] = (hasCreateDicomStl_ ? "true" : "false"); |
31
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768 dictionary["SHOW_NIFTI_BUTTON"] = (configuration.GetBooleanValue("NIfTI", false) ? "true" : "false"); |
2
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769 explorer = Orthanc::Toolbox::SubstituteVariables(explorer, dictionary); |
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|
770 |
25
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771 OrthancPlugins::ExtendOrthancExplorer(ORTHANC_PLUGIN_NAME, explorer); |
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|
772 } |
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|
773 |
0
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774 return 0; |
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|
775 } |
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|
776 |
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|
777 |
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|
778 ORTHANC_PLUGINS_API void OrthancPluginFinalize() |
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779 { |
1
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780 Orthanc::FinalizeFramework(); |
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781 } |
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|
782 |
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|
783 |
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784 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() |
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785 { |
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diff
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|
786 return ORTHANC_PLUGIN_NAME; |
0
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787 } |
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|
788 |
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|
789 |
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|
790 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() |
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791 { |
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|
792 return ORTHANC_STL_VERSION; |
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793 } |
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794 } |