Mercurial > hg > orthanc-wsi
annotate ViewerPlugin/Plugin.cpp @ 57:91fc9583b2de
big refactoring to support sparse tiling
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 24 Nov 2016 17:48:24 +0100 |
| parents | 7a88c614be04 |
| children | 7a3853d51c45 |
| 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 | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU Affero General Public License | |
| 8 * as published by the Free Software Foundation, either version 3 of | |
| 9 * the License, or (at your option) any later version. | |
| 10 * | |
| 11 * This program is distributed in the hope that it will be useful, but | |
| 12 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 14 * Affero General Public License for more details. | |
| 15 * | |
| 16 * You should have received a copy of the GNU Affero General Public License | |
| 17 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 **/ | |
| 19 | |
| 20 | |
|
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21 #include "../Framework/PrecompiledHeadersWSI.h" |
| 0 | 22 #include "../Framework/Inputs/DicomPyramid.h" |
| 23 #include "../Framework/Jpeg2000Reader.h" | |
| 24 #include "../Framework/Messaging/PluginOrthancConnection.h" | |
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25 #include "../Framework/Orthanc/Core/Images/ImageProcessing.h" |
| 0 | 26 #include "../Framework/Orthanc/Core/Images/PngWriter.h" |
| 27 #include "../Framework/Orthanc/Core/MultiThreading/Semaphore.h" | |
| 28 #include "../Framework/Orthanc/Core/OrthancException.h" | |
| 29 #include "../Framework/Orthanc/Plugins/Samples/Common/OrthancPluginCppWrapper.h" | |
| 30 | |
| 31 #include <EmbeddedResources.h> | |
| 32 | |
| 33 #include <cassert> | |
| 34 | |
| 35 | |
| 36 | |
| 37 namespace OrthancWSI | |
| 38 { | |
| 39 // TODO Add LRU recycling policy | |
| 40 class DicomPyramidCache : public boost::noncopyable | |
| 41 { | |
| 42 private: | |
| 43 boost::mutex mutex_; | |
| 44 IOrthancConnection& orthanc_; | |
| 45 std::auto_ptr<DicomPyramid> pyramid_; | |
| 46 | |
| 47 DicomPyramid& GetPyramid(const std::string& seriesId) | |
| 48 { | |
| 49 // Mutex is assumed to be locked | |
| 50 | |
| 51 if (pyramid_.get() == NULL || | |
| 52 pyramid_->GetSeriesId() != seriesId) | |
| 53 { | |
| 54 pyramid_.reset(new DicomPyramid(orthanc_, seriesId)); | |
| 55 } | |
| 56 | |
| 57 if (pyramid_.get() == NULL) | |
| 58 { | |
| 59 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 60 } | |
| 61 | |
| 62 return *pyramid_; | |
| 63 } | |
| 64 | |
| 65 public: | |
| 66 DicomPyramidCache(IOrthancConnection& orthanc) : | |
| 67 orthanc_(orthanc) | |
| 68 { | |
| 69 } | |
| 70 | |
| 71 void Invalidate(const std::string& seriesId) | |
| 72 { | |
| 73 boost::mutex::scoped_lock lock(mutex_); | |
| 74 | |
| 75 if (pyramid_.get() != NULL && | |
| 76 pyramid_->GetSeriesId() == seriesId) | |
| 77 { | |
| 78 pyramid_.reset(NULL); | |
| 79 } | |
| 80 } | |
| 81 | |
| 82 class Locker : public boost::noncopyable | |
| 83 { | |
| 84 private: | |
| 85 boost::mutex::scoped_lock lock_; | |
| 86 DicomPyramid& pyramid_; | |
| 87 | |
| 88 public: | |
| 89 Locker(DicomPyramidCache& cache, | |
| 90 const std::string& seriesId) : | |
| 91 lock_(cache.mutex_), | |
| 92 pyramid_(cache.GetPyramid(seriesId)) | |
| 93 { | |
| 94 } | |
| 95 | |
| 96 DicomPyramid& GetPyramid() const | |
| 97 { | |
| 98 return pyramid_; | |
| 99 } | |
| 100 }; | |
| 101 }; | |
| 102 } | |
| 103 | |
| 104 | |
| 105 OrthancPluginContext* context_ = NULL; | |
| 106 | |
| 107 std::auto_ptr<OrthancWSI::PluginOrthancConnection> orthanc_; | |
| 108 std::auto_ptr<OrthancWSI::DicomPyramidCache> cache_; | |
| 109 std::auto_ptr<Orthanc::Semaphore> transcoderSemaphore_; | |
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110 std::string sparseTile_; |
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111 |
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112 |
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113 static void AnswerSparseTile(OrthancPluginRestOutput* output, |
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114 unsigned int tileWidth, |
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115 unsigned int tileHeight) |
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116 { |
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117 Orthanc::Image tile(Orthanc::PixelFormat_RGB24, tileWidth, tileHeight, false); |
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118 |
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119 // Black (TODO parameter) |
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120 uint8_t red = 0; |
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121 uint8_t green = 0; |
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122 uint8_t blue = 0; |
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123 Orthanc::ImageProcessing::Set(tile, red, green, blue, 255); |
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124 |
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125 // TODO Cache the tile |
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126 OrthancPluginCompressAndAnswerPngImage(context_, output, OrthancPluginPixelFormat_RGB24, |
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127 tile.GetWidth(), tile.GetHeight(), |
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128 tile.GetPitch(), tile.GetBuffer()); |
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129 } |
| 0 | 130 |
| 131 | |
| 132 static bool DisplayPerformanceWarning() | |
| 133 { | |
| 134 (void) DisplayPerformanceWarning; // Disable warning about unused function | |
| 135 OrthancPluginLogWarning(context_, "Performance warning in whole-slide imaging: " | |
| 136 "Non-release build, runtime debug assertions are turned on"); | |
| 137 return true; | |
| 138 } | |
| 139 | |
| 140 | |
| 141 void ServePyramid(OrthancPluginRestOutput* output, | |
| 142 const char* url, | |
| 143 const OrthancPluginHttpRequest* request) | |
| 144 { | |
| 145 std::string seriesId(request->groups[0]); | |
| 146 | |
| 147 char tmp[1024]; | |
| 148 sprintf(tmp, "Accessing whole-slide pyramid of series %s", seriesId.c_str()); | |
| 149 OrthancPluginLogInfo(context_, tmp); | |
| 150 | |
| 151 | |
| 152 OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId); | |
| 153 | |
| 154 unsigned int totalWidth = locker.GetPyramid().GetLevelWidth(0); | |
| 155 unsigned int totalHeight = locker.GetPyramid().GetLevelHeight(0); | |
| 156 | |
| 157 Json::Value resolutions = Json::arrayValue; | |
| 158 for (unsigned int i = 0; i < locker.GetPyramid().GetLevelCount(); i++) | |
| 159 { | |
| 160 resolutions.append(static_cast<float>(totalWidth) / | |
| 161 static_cast<float>(locker.GetPyramid().GetLevelWidth(i))); | |
| 162 } | |
| 163 | |
| 164 Json::Value result; | |
| 165 result["ID"] = seriesId; | |
| 166 result["TotalWidth"] = totalWidth; | |
| 167 result["TotalHeight"] = totalHeight; | |
| 168 result["TileWidth"] = locker.GetPyramid().GetTileWidth(); | |
| 169 result["TileHeight"] = locker.GetPyramid().GetTileHeight(); | |
| 170 result["Resolutions"] = resolutions; | |
| 171 | |
| 172 std::string s = result.toStyledString(); | |
| 173 OrthancPluginAnswerBuffer(context_, output, s.c_str(), s.size(), "application/json"); | |
| 174 } | |
| 175 | |
| 176 | |
| 177 void ServeTile(OrthancPluginRestOutput* output, | |
| 178 const char* url, | |
| 179 const OrthancPluginHttpRequest* request) | |
| 180 { | |
| 181 std::string seriesId(request->groups[0]); | |
| 182 int level = boost::lexical_cast<int>(request->groups[1]); | |
| 183 int tileY = boost::lexical_cast<int>(request->groups[3]); | |
| 184 int tileX = boost::lexical_cast<int>(request->groups[2]); | |
| 185 | |
| 186 char tmp[1024]; | |
| 187 sprintf(tmp, "Accessing tile in series %s: (%d,%d) at level %d", seriesId.c_str(), tileX, tileY, level); | |
| 188 OrthancPluginLogInfo(context_, tmp); | |
| 189 | |
| 190 if (level < 0 || | |
| 191 tileX < 0 || | |
| 192 tileY < 0) | |
| 193 { | |
| 194 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 195 } | |
| 196 | |
| 197 // Retrieve the raw tile from the WSI pyramid | |
| 198 OrthancWSI::ImageCompression compression; | |
| 199 Orthanc::PixelFormat format; | |
| 200 std::string tile; | |
| 201 unsigned int tileWidth, tileHeight; | |
| 202 | |
| 203 { | |
| 204 OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId); | |
| 205 | |
| 206 format = locker.GetPyramid().GetPixelFormat(); | |
| 207 tileWidth = locker.GetPyramid().GetTileWidth(); | |
| 208 tileHeight = locker.GetPyramid().GetTileHeight(); | |
| 209 | |
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210 if (!locker.GetPyramid().ReadRawTile(tile, compression, |
| 0 | 211 static_cast<unsigned int>(level), |
| 212 static_cast<unsigned int>(tileX), | |
| 213 static_cast<unsigned int>(tileY))) | |
| 214 { | |
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215 // Handling of missing tile (for sparse tiling): TODO parameter? |
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216 // AnswerSparseTile(output, tileWidth, tileHeight); return; |
| 0 | 217 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
| 218 } | |
| 219 } | |
| 220 | |
| 221 | |
| 222 // Test whether the tile is a JPEG image. In such a case, we can | |
| 223 // serve it as such, because any Web browser can handle JPEG | |
| 224 | |
| 225 if (compression == OrthancWSI::ImageCompression_Jpeg) | |
| 226 { | |
| 227 OrthancPluginAnswerBuffer(context_, output, tile.c_str(), tile.size(), "image/jpeg"); | |
| 228 return; // We're done | |
| 229 } | |
| 230 | |
| 231 | |
| 232 // The tile does not come from a DICOM-JPEG instance, we need to | |
| 233 // decompress the raw tile | |
| 234 std::auto_ptr<Orthanc::ImageAccessor> decoded; | |
| 235 | |
| 236 Orthanc::Semaphore::Locker locker(*transcoderSemaphore_); | |
| 237 | |
| 238 switch (compression) | |
| 239 { | |
| 240 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 241 decoded.reset(new OrthancWSI::Jpeg2000Reader); | |
| 242 dynamic_cast<OrthancWSI::Jpeg2000Reader&>(*decoded).ReadFromMemory(tile); | |
| 243 break; | |
| 244 | |
| 245 case OrthancWSI::ImageCompression_None: | |
| 246 { | |
| 247 unsigned int bpp = Orthanc::GetBytesPerPixel(format); | |
| 248 if (bpp * tileWidth * tileHeight != tile.size()) | |
| 249 { | |
| 250 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 251 } | |
| 252 | |
| 253 decoded.reset(new Orthanc::ImageAccessor); | |
| 254 decoded->AssignReadOnly(format, tileWidth, tileHeight, bpp * tileWidth, tile.c_str()); | |
| 255 break; | |
| 256 } | |
| 257 | |
| 258 default: | |
| 259 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 260 } | |
| 261 | |
| 262 | |
| 263 // This is a lossless frame (coming from a JPEG2000 or uncompressed | |
| 264 // DICOM instance), serve it as a PNG image so as to prevent lossy | |
| 265 // compression | |
| 266 | |
| 267 std::string png; | |
| 268 Orthanc::PngWriter writer; | |
| 269 writer.WriteToMemory(png, *decoded); | |
| 270 | |
| 271 OrthancPluginAnswerBuffer(context_, output, png.c_str(), png.size(), "image/png"); | |
| 272 } | |
| 273 | |
| 274 | |
| 275 OrthancPluginErrorCode OnChangeCallback(OrthancPluginChangeType changeType, | |
| 276 OrthancPluginResourceType resourceType, | |
| 277 const char *resourceId) | |
| 278 { | |
| 279 if (resourceType == OrthancPluginResourceType_Series && | |
| 280 changeType == OrthancPluginChangeType_NewChildInstance) | |
| 281 { | |
| 282 char tmp[1024]; | |
| 283 sprintf(tmp, "New instance has been added to series %s, invalidating it", resourceId); | |
| 284 OrthancPluginLogInfo(context_, tmp); | |
| 285 | |
| 286 cache_->Invalidate(resourceId); | |
| 287 } | |
| 288 | |
| 289 return OrthancPluginErrorCode_Success; | |
| 290 } | |
| 291 | |
| 292 | |
| 293 | |
| 294 void ServeFile(OrthancPluginRestOutput* output, | |
| 295 const char* url, | |
| 296 const OrthancPluginHttpRequest* request) | |
| 297 { | |
| 298 Orthanc::EmbeddedResources::FileResourceId resource; | |
| 299 | |
| 300 std::string f(request->groups[0]); | |
| 301 std::string mime; | |
| 302 | |
| 303 if (f == "viewer.html") | |
| 304 { | |
| 305 resource = Orthanc::EmbeddedResources::VIEWER_HTML; | |
| 306 mime = "text/html"; | |
| 307 } | |
| 308 else if (f == "viewer.js") | |
| 309 { | |
| 310 resource = Orthanc::EmbeddedResources::VIEWER_JS; | |
| 311 mime = "application/javascript"; | |
| 312 } | |
| 313 else if (f == "ol.js") | |
| 314 { | |
| 315 resource = Orthanc::EmbeddedResources::OPENLAYERS_JS; | |
| 316 mime = "application/javascript"; | |
| 317 } | |
| 318 else if (f == "ol.css") | |
| 319 { | |
| 320 resource = Orthanc::EmbeddedResources::OPENLAYERS_CSS; | |
| 321 mime = "text/css"; | |
| 322 } | |
| 323 else | |
| 324 { | |
| 325 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); | |
| 326 } | |
| 327 | |
| 328 std::string content; | |
| 329 Orthanc::EmbeddedResources::GetFileResource(content, resource); | |
| 330 | |
| 331 OrthancPluginAnswerBuffer(context_, output, content.c_str(), content.size(), mime.c_str()); | |
| 332 } | |
| 333 | |
| 334 | |
| 335 | |
| 336 extern "C" | |
| 337 { | |
| 338 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context) | |
| 339 { | |
| 340 context_ = context; | |
| 341 assert(DisplayPerformanceWarning()); | |
| 342 | |
| 343 /* Check the version of the Orthanc core */ | |
| 344 if (OrthancPluginCheckVersion(context_) == 0) | |
| 345 { | |
| 346 char info[1024]; | |
| 347 sprintf(info, "Your version of Orthanc (%s) must be above %d.%d.%d to run this plugin", | |
| 348 context_->orthancVersion, | |
| 349 ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER, | |
| 350 ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER, | |
| 351 ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER); | |
| 352 OrthancPluginLogError(context_, info); | |
| 353 return -1; | |
| 354 } | |
| 355 | |
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356 if (!OrthancPlugins::CheckMinimalOrthancVersion(context_, 1, 1, 0)) |
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357 { |
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358 // We need the "/instances/.../frames/.../raw" URI that was introduced in Orthanc 1.1.0 |
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359 return -1; |
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360 } |
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361 |
| 0 | 362 // Limit the number of PNG transcoders to the number of available |
| 363 // hardware threads (e.g. number of CPUs or cores or | |
| 364 // hyperthreading units) | |
| 365 unsigned int threads = boost::thread::hardware_concurrency(); | |
| 366 | |
| 367 if (threads <= 0) | |
| 368 { | |
| 369 threads = 1; | |
| 370 } | |
| 371 | |
| 372 transcoderSemaphore_.reset(new Orthanc::Semaphore(threads)); | |
| 373 | |
| 374 char info[1024]; | |
| 375 sprintf(info, "The whole-slide imaging plugin will use at most %d threads to transcode the tiles", threads); | |
| 376 OrthancPluginLogWarning(context_, info); | |
| 377 | |
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378 OrthancPluginSetDescription(context, "Provides a Web viewer of whole-slide microscopic images within Orthanc."); |
| 0 | 379 |
| 380 orthanc_.reset(new OrthancWSI::PluginOrthancConnection(context)); | |
| 381 cache_.reset(new OrthancWSI::DicomPyramidCache(*orthanc_)); | |
| 382 | |
| 383 OrthancPluginRegisterOnChangeCallback(context_, OnChangeCallback); | |
| 384 | |
| 385 OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(ol.css)", true); | |
| 386 OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(ol.js)", true); | |
| 387 OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(viewer.html)", true); | |
| 388 OrthancPlugins::RegisterRestCallback<ServeFile>(context, "/wsi/app/(viewer.js)", true); | |
| 389 OrthancPlugins::RegisterRestCallback<ServePyramid>(context, "/wsi/pyramids/([0-9a-f-]+)", true); | |
| 390 OrthancPlugins::RegisterRestCallback<ServeTile>(context, "/wsi/tiles/([0-9a-f-]+)/([0-9-]+)/([0-9-]+)/([0-9-]+)", true); | |
| 391 | |
| 392 // Extend the default Orthanc Explorer with custom JavaScript for WSI | |
| 393 std::string explorer; | |
| 394 Orthanc::EmbeddedResources::GetFileResource(explorer, Orthanc::EmbeddedResources::ORTHANC_EXPLORER); | |
| 395 OrthancPluginExtendOrthancExplorer(context_, explorer.c_str()); | |
| 396 | |
| 397 return 0; | |
| 398 } | |
| 399 | |
| 400 | |
| 401 ORTHANC_PLUGINS_API void OrthancPluginFinalize() | |
| 402 { | |
| 403 cache_.reset(NULL); | |
| 404 orthanc_.reset(NULL); | |
| 405 transcoderSemaphore_.reset(NULL); | |
| 406 } | |
| 407 | |
| 408 | |
| 409 ORTHANC_PLUGINS_API const char* OrthancPluginGetName() | |
| 410 { | |
| 411 return "wsi"; | |
| 412 } | |
| 413 | |
| 414 | |
| 415 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion() | |
| 416 { | |
| 417 return ORTHANC_WSI_VERSION; | |
| 418 } | |
| 419 } |