Mercurial > hg > orthanc-wsi
annotate ViewerPlugin/Plugin.cpp @ 57:91fc9583b2de
big refactoring to support sparse tiling
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 24 Nov 2016 17:48:24 +0100 |
parents | 7a88c614be04 |
children | 7a3853d51c45 |
rev | line source |
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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 } |