Mercurial > hg > orthanc-wsi
annotate ViewerPlugin/Plugin.cpp @ 217:20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 12 Jan 2021 14:24:18 +0100 |
| parents | 1e864138f0da |
| children | 49f647ed1b4c |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU Affero General Public License | |
| 9 * as published by the Free Software Foundation, either version 3 of | |
| 10 * the License, or (at your option) any later version. | |
| 11 * | |
| 12 * This program is distributed in the hope that it will be useful, but | |
| 13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 15 * Affero General Public License for more details. | |
| 16 * | |
| 17 * You should have received a copy of the GNU Affero General Public License | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
|
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22 #include "../Framework/PrecompiledHeadersWSI.h" |
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23 |
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24 #include "../Framework/ImageToolbox.h" |
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25 #include "../Framework/Jpeg2000Reader.h" |
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26 #include "DicomPyramidCache.h" |
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27 #include "OrthancPluginConnection.h" |
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28 |
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29 #include <Compatibility.h> // For std::unique_ptr |
| 192 | 30 #include <Logging.h> |
| 31 #include <Images/ImageProcessing.h> | |
| 32 #include <Images/PngWriter.h> | |
| 33 #include <MultiThreading/Semaphore.h> | |
| 34 #include <OrthancException.h> | |
| 35 #include <SystemToolbox.h> | |
| 36 | |
| 194 | 37 #include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h" |
| 0 | 38 |
| 39 #include <EmbeddedResources.h> | |
| 40 | |
| 41 #include <cassert> | |
| 42 | |
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43 std::unique_ptr<OrthancWSI::OrthancPluginConnection> orthanc_; |
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44 std::unique_ptr<OrthancWSI::DicomPyramidCache> cache_; |
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45 std::unique_ptr<Orthanc::Semaphore> transcoderSemaphore_; |
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46 |
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47 |
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48 static void AnswerSparseTile(OrthancPluginRestOutput* output, |
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49 unsigned int tileWidth, |
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50 unsigned int tileHeight) |
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51 { |
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52 Orthanc::Image tile(Orthanc::PixelFormat_RGB24, tileWidth, tileHeight, false); |
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53 |
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54 // Black (TODO parameter) |
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55 uint8_t red = 0; |
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56 uint8_t green = 0; |
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57 uint8_t blue = 0; |
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58 Orthanc::ImageProcessing::Set(tile, red, green, blue, 255); |
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59 |
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60 // TODO Cache the tile |
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61 OrthancPluginCompressAndAnswerPngImage(OrthancPlugins::GetGlobalContext(), |
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62 output, OrthancPluginPixelFormat_RGB24, |
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63 tile.GetWidth(), tile.GetHeight(), |
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64 tile.GetPitch(), tile.GetBuffer()); |
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65 } |
| 0 | 66 |
| 67 | |
| 68 static bool DisplayPerformanceWarning() | |
| 69 { | |
| 70 (void) DisplayPerformanceWarning; // Disable warning about unused function | |
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71 OrthancPluginLogWarning(OrthancPlugins::GetGlobalContext(), "Performance warning in whole-slide imaging: " |
| 0 | 72 "Non-release build, runtime debug assertions are turned on"); |
| 73 return true; | |
| 74 } | |
| 75 | |
| 76 | |
| 77 void ServePyramid(OrthancPluginRestOutput* output, | |
| 78 const char* url, | |
| 79 const OrthancPluginHttpRequest* request) | |
| 80 { | |
| 81 std::string seriesId(request->groups[0]); | |
| 82 | |
| 83 char tmp[1024]; | |
| 84 sprintf(tmp, "Accessing whole-slide pyramid of series %s", seriesId.c_str()); | |
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85 OrthancPluginLogInfo(OrthancPlugins::GetGlobalContext(), tmp); |
| 0 | 86 |
| 87 | |
| 88 OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId); | |
| 89 | |
| 90 unsigned int totalWidth = locker.GetPyramid().GetLevelWidth(0); | |
| 91 unsigned int totalHeight = locker.GetPyramid().GetLevelHeight(0); | |
| 92 | |
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93 Json::Value sizes = Json::arrayValue; |
| 0 | 94 Json::Value resolutions = Json::arrayValue; |
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95 Json::Value tilesCount = Json::arrayValue; |
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96 Json::Value tilesSizes = Json::arrayValue; |
| 0 | 97 for (unsigned int i = 0; i < locker.GetPyramid().GetLevelCount(); i++) |
| 98 { | |
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99 const unsigned int levelWidth = locker.GetPyramid().GetLevelWidth(i); |
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100 const unsigned int levelHeight = locker.GetPyramid().GetLevelHeight(i); |
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101 const unsigned int tileWidth = locker.GetPyramid().GetTileWidth(i); |
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102 const unsigned int tileHeight = locker.GetPyramid().GetTileHeight(i); |
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103 |
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104 resolutions.append(static_cast<float>(totalWidth) / static_cast<float>(levelWidth)); |
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105 |
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106 Json::Value s = Json::arrayValue; |
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107 s.append(levelWidth); |
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108 s.append(levelHeight); |
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109 sizes.append(s); |
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110 |
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111 s = Json::arrayValue; |
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112 s.append(OrthancWSI::CeilingDivision(levelWidth, tileWidth)); |
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113 s.append(OrthancWSI::CeilingDivision(levelHeight, tileHeight)); |
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114 tilesCount.append(s); |
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115 |
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116 s = Json::arrayValue; |
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117 s.append(tileWidth); |
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118 s.append(tileHeight); |
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119 tilesSizes.append(s); |
| 0 | 120 } |
| 121 | |
| 122 Json::Value result; | |
| 123 result["ID"] = seriesId; | |
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124 result["Resolutions"] = resolutions; |
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125 result["Sizes"] = sizes; |
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126 result["TilesCount"] = tilesCount; |
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127 result["TilesSizes"] = tilesSizes; |
| 0 | 128 result["TotalHeight"] = totalHeight; |
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129 result["TotalWidth"] = totalWidth; |
| 0 | 130 |
| 131 std::string s = result.toStyledString(); | |
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132 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json"); |
| 0 | 133 } |
| 134 | |
| 135 | |
| 136 void ServeTile(OrthancPluginRestOutput* output, | |
| 137 const char* url, | |
| 138 const OrthancPluginHttpRequest* request) | |
| 139 { | |
| 140 std::string seriesId(request->groups[0]); | |
| 141 int level = boost::lexical_cast<int>(request->groups[1]); | |
| 142 int tileY = boost::lexical_cast<int>(request->groups[3]); | |
| 143 int tileX = boost::lexical_cast<int>(request->groups[2]); | |
| 144 | |
| 145 char tmp[1024]; | |
| 146 sprintf(tmp, "Accessing tile in series %s: (%d,%d) at level %d", seriesId.c_str(), tileX, tileY, level); | |
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147 OrthancPluginLogInfo(OrthancPlugins::GetGlobalContext(), tmp); |
| 0 | 148 |
| 149 if (level < 0 || | |
| 150 tileX < 0 || | |
| 151 tileY < 0) | |
| 152 { | |
| 153 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 154 } | |
| 155 | |
| 156 // Retrieve the raw tile from the WSI pyramid | |
| 157 OrthancWSI::ImageCompression compression; | |
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158 Orthanc::PhotometricInterpretation photometric; |
| 0 | 159 Orthanc::PixelFormat format; |
| 160 std::string tile; | |
| 161 unsigned int tileWidth, tileHeight; | |
| 162 | |
| 163 { | |
| 164 OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId); | |
| 165 | |
| 166 format = locker.GetPyramid().GetPixelFormat(); | |
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167 tileWidth = locker.GetPyramid().GetTileWidth(level); |
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168 tileHeight = locker.GetPyramid().GetTileHeight(level); |
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169 photometric = locker.GetPyramid().GetPhotometricInterpretation(); |
| 0 | 170 |
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171 if (!locker.GetPyramid().ReadRawTile(tile, compression, |
| 0 | 172 static_cast<unsigned int>(level), |
| 173 static_cast<unsigned int>(tileX), | |
| 174 static_cast<unsigned int>(tileY))) | |
| 175 { | |
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176 // Handling of missing tile (for sparse tiling): TODO parameter? |
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177 // AnswerSparseTile(output, tileWidth, tileHeight); return; |
| 0 | 178 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
| 179 } | |
| 180 } | |
| 181 | |
| 182 | |
| 183 // Test whether the tile is a JPEG image. In such a case, we can | |
| 184 // serve it as such, because any Web browser can handle JPEG | |
| 185 | |
| 186 if (compression == OrthancWSI::ImageCompression_Jpeg) | |
| 187 { | |
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188 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, tile.c_str(), tile.size(), "image/jpeg"); |
| 0 | 189 return; // We're done |
| 190 } | |
| 191 | |
| 192 | |
| 193 // The tile does not come from a DICOM-JPEG instance, we need to | |
| 194 // decompress the raw tile | |
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195 std::unique_ptr<Orthanc::ImageAccessor> decoded; |
| 0 | 196 |
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197 Orthanc::Semaphore::Locker locker(*transcoderSemaphore_); |
| 0 | 198 |
| 199 switch (compression) | |
| 200 { | |
| 201 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 202 decoded.reset(new OrthancWSI::Jpeg2000Reader); | |
| 203 dynamic_cast<OrthancWSI::Jpeg2000Reader&>(*decoded).ReadFromMemory(tile); | |
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204 |
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205 if (photometric == Orthanc::PhotometricInterpretation_YBR_ICT) |
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206 { |
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207 OrthancWSI::ImageToolbox::ConvertJpegYCbCrToRgb(*decoded); |
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208 } |
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209 |
| 0 | 210 break; |
| 211 | |
| 212 case OrthancWSI::ImageCompression_None: | |
| 213 { | |
| 214 unsigned int bpp = Orthanc::GetBytesPerPixel(format); | |
| 215 if (bpp * tileWidth * tileHeight != tile.size()) | |
| 216 { | |
| 217 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 218 } | |
| 219 | |
| 220 decoded.reset(new Orthanc::ImageAccessor); | |
| 221 decoded->AssignReadOnly(format, tileWidth, tileHeight, bpp * tileWidth, tile.c_str()); | |
| 222 break; | |
| 223 } | |
| 224 | |
| 225 default: | |
| 226 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 227 } | |
| 228 | |
| 229 | |
| 230 // This is a lossless frame (coming from a JPEG2000 or uncompressed | |
| 231 // DICOM instance), serve it as a PNG image so as to prevent lossy | |
| 232 // compression | |
| 233 | |
| 234 std::string png; | |
| 235 Orthanc::PngWriter writer; | |
| 211 | 236 Orthanc::IImageWriter::WriteToMemory(writer, png, *decoded); |
| 0 | 237 |
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238 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, png.c_str(), png.size(), "image/png"); |
| 0 | 239 } |
| 240 | |
| 241 | |
| 242 OrthancPluginErrorCode OnChangeCallback(OrthancPluginChangeType changeType, | |
| 243 OrthancPluginResourceType resourceType, | |
| 244 const char *resourceId) | |
| 245 { | |
| 246 if (resourceType == OrthancPluginResourceType_Series && | |
| 247 changeType == OrthancPluginChangeType_NewChildInstance) | |
| 248 { | |
| 249 char tmp[1024]; | |
| 250 sprintf(tmp, "New instance has been added to series %s, invalidating it", resourceId); | |
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251 OrthancPluginLogInfo(OrthancPlugins::GetGlobalContext(), tmp); |
| 0 | 252 |
| 253 cache_->Invalidate(resourceId); | |
| 254 } | |
| 255 | |
| 256 return OrthancPluginErrorCode_Success; | |
| 257 } | |
| 258 | |
| 259 | |
| 260 | |
| 261 void ServeFile(OrthancPluginRestOutput* output, | |
| 262 const char* url, | |
| 263 const OrthancPluginHttpRequest* request) | |
| 264 { | |
| 265 Orthanc::EmbeddedResources::FileResourceId resource; | |
| 266 | |
| 267 std::string f(request->groups[0]); | |
| 268 std::string mime; | |
| 269 | |
| 270 if (f == "viewer.html") | |
| 271 { | |
| 272 resource = Orthanc::EmbeddedResources::VIEWER_HTML; | |
| 273 mime = "text/html"; | |
| 274 } | |
| 275 else if (f == "viewer.js") | |
| 276 { | |
| 277 resource = Orthanc::EmbeddedResources::VIEWER_JS; | |
| 278 mime = "application/javascript"; | |
| 279 } | |
| 280 else if (f == "ol.js") | |
| 281 { | |
| 282 resource = Orthanc::EmbeddedResources::OPENLAYERS_JS; | |
| 283 mime = "application/javascript"; | |
| 284 } | |
| 285 else if (f == "ol.css") | |
| 286 { | |
| 287 resource = Orthanc::EmbeddedResources::OPENLAYERS_CSS; | |
| 288 mime = "text/css"; | |
| 289 } | |
| 290 else | |
| 291 { | |
| 292 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 293 } | |
| 294 | |
| 295 std::string content; | |
| 296 Orthanc::EmbeddedResources::GetFileResource(content, resource); | |
| 297 | |
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298 OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, content.c_str(), content.size(), mime.c_str()); |
| 0 | 299 } |
| 300 | |
| 301 | |
| 302 | |
| 303 extern "C" | |
| 304 { | |
| 305 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) | |
| 306 { | |
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307 OrthancPlugins::SetGlobalContext(context); |
| 0 | 308 assert(DisplayPerformanceWarning()); |
| 309 | |
| 310 /* Check the version of the Orthanc core */ | |
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311 if (OrthancPluginCheckVersion(OrthancPlugins::GetGlobalContext()) == 0) |
| 0 | 312 { |
| 313 char info[1024]; | |
| 314 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", | |
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315 OrthancPlugins::GetGlobalContext()->orthancVersion, |
| 0 | 316 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, |
| 317 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, | |
| 318 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); | |
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319 OrthancPluginLogError(OrthancPlugins::GetGlobalContext(), info); |
| 0 | 320 return -1; |
| 321 } | |
| 322 | |
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323 if (!OrthancPlugins::CheckMinimalOrthancVersion(1, 1, 0)) |
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324 { |
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325 // We need the "/instances/.../frames/.../raw" URI that was introduced in Orthanc 1.1.0 |
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326 return -1; |
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327 } |
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328 |
| 206 | 329 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 7, 2) |
| 191 | 330 Orthanc::Logging::InitializePluginContext(context); |
| 193 | 331 #else |
| 332 Orthanc::Logging::Initialize(context); | |
| 333 #endif | |
| 151 | 334 |
| 0 | 335 // Limit the number of PNG transcoders to the number of available |
| 336 // hardware threads (e.g. number of CPUs or cores or | |
| 337 // hyperthreading units) | |
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338 unsigned int threads = Orthanc::SystemToolbox::GetHardwareConcurrency(); |
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339 transcoderSemaphore_.reset(new Orthanc::Semaphore(threads)); |
| 0 | 340 |
| 341 char info[1024]; | |
| 145 | 342 sprintf(info, "The whole-slide imaging plugin will use at most %u threads to transcode the tiles", threads); |
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343 OrthancPluginLogWarning(OrthancPlugins::GetGlobalContext(), info); |
| 0 | 344 |
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345 OrthancPluginSetDescription(context, "Provides a Web viewer of whole-slide microscopic images within Orthanc."); |
| 0 | 346 |
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347 orthanc_.reset(new OrthancWSI::OrthancPluginConnection); |
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348 cache_.reset(new OrthancWSI::DicomPyramidCache(*orthanc_, 10 /* Number of pyramids to be cached - TODO parameter */)); |
| 0 | 349 |
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350 OrthancPluginRegisterOnChangeCallback(OrthancPlugins::GetGlobalContext(), OnChangeCallback); |
| 0 | 351 |
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352 OrthancPlugins::RegisterRestCallback<ServeFile>("/wsi/app/(ol.css)", true); |
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353 OrthancPlugins::RegisterRestCallback<ServeFile>("/wsi/app/(ol.js)", true); |
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354 OrthancPlugins::RegisterRestCallback<ServeFile>("/wsi/app/(viewer.html)", true); |
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355 OrthancPlugins::RegisterRestCallback<ServeFile>("/wsi/app/(viewer.js)", true); |
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356 OrthancPlugins::RegisterRestCallback<ServePyramid>("/wsi/pyramids/([0-9a-f-]+)", true); |
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357 OrthancPlugins::RegisterRestCallback<ServeTile>("/wsi/tiles/([0-9a-f-]+)/([0-9-]+)/([0-9-]+)/([0-9-]+)", true); |
| 0 | 358 |
| 359 // Extend the default Orthanc Explorer with custom JavaScript for WSI | |
| 360 std::string explorer; | |
| 361 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); | |
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362 OrthancPluginExtendOrthancExplorer(OrthancPlugins::GetGlobalContext(), explorer.c_str()); |
| 0 | 363 |
| 364 return 0; | |
| 365 } | |
| 366 | |
| 367 | |
| 368 ORTHANC_PLUGINS_API void OrthancPluginFinalize() | |
| 369 { | |
| 370 cache_.reset(NULL); | |
| 371 orthanc_.reset(NULL); | |
| 372 transcoderSemaphore_.reset(NULL); | |
| 373 } | |
| 374 | |
| 375 | |
| 376 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() | |
| 377 { | |
| 378 return "wsi"; | |
| 379 } | |
| 380 | |
| 381 | |
| 382 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() | |
| 383 { | |
| 384 return ORTHANC_WSI_VERSION; | |
| 385 } | |
| 386 } |