Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 43:9621fd6f17c9
sync
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 09 Nov 2016 17:34:20 +0100 |
parents | 8e1dfd531335 |
children | 91fc9583b2de |
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 | |
21 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
22 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
23 #include "../Framework/DicomToolbox.h" | |
24 #include "../Framework/DicomizerParameters.h" | |
25 #include "../Framework/ImagedVolumeParameters.h" | |
26 #include "../Framework/Inputs/HierarchicalTiff.h" | |
27 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
28 #include "../Framework/Inputs/TiledJpegImage.h" | |
29 #include "../Framework/Inputs/TiledPngImage.h" | |
30 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
31 #include "../Framework/Orthanc/Core/HttpClient.h" | |
32 #include "../Framework/Orthanc/Core/Logging.h" | |
33 #include "../Framework/Orthanc/Core/MultiThreading/BagOfTasksProcessor.h" | |
43 | 34 #include "../Framework/Orthanc/Core/SystemToolbox.h" |
0 | 35 #include "../Framework/Orthanc/OrthancServer/FromDcmtkBridge.h" |
36 #include "../Framework/Outputs/DicomPyramidWriter.h" | |
37 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
38 | |
39 #include "ApplicationToolbox.h" | |
40 | |
41 #include <EmbeddedResources.h> | |
42 | |
43 #include <boost/program_options.hpp> | |
44 | |
45 #include <dcmtk/dcmdata/dcdeftag.h> | |
46 #include <dcmtk/dcmdata/dcuid.h> | |
47 #include <dcmtk/dcmdata/dcvrobow.h> | |
48 #include <dcmtk/dcmdata/dcvrat.h> | |
49 | |
50 | |
51 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, | |
52 OrthancWSI::ITiledPyramid& source, | |
53 const OrthancWSI::DicomizerParameters& parameters) | |
54 { | |
55 Orthanc::BagOfTasks tasks; | |
56 | |
57 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
58 { | |
59 LOG(WARNING) << "Creating level " << i << " of size " | |
60 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
61 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
62 } | |
63 | |
64 LOG(WARNING) << "Transcoding the source pyramid"; | |
65 | |
66 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
67 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
68 } | |
69 | |
70 | |
71 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
72 OrthancWSI::ITiledPyramid& source, | |
73 const OrthancWSI::DicomizerParameters& parameters) | |
74 { | |
75 Orthanc::BagOfTasks tasks; | |
76 | |
77 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
78 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
79 assert(levelsCount >= 1); | |
80 | |
81 for (unsigned int i = 0; i < levelsCount; i++) | |
82 { | |
83 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
84 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
85 | |
86 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
87 target.AddLevel(width, height); | |
88 } | |
89 | |
90 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
91 if (lowerLevelsCount > levelsCount) | |
92 { | |
93 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
94 << ") exceeds the number of levels (" << levelsCount | |
95 << "), cropping it"; | |
96 lowerLevelsCount = levelsCount; | |
97 } | |
98 | |
99 assert(lowerLevelsCount <= levelsCount); | |
100 if (lowerLevelsCount != levelsCount) | |
101 { | |
102 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
103 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount); | |
104 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
105 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
106 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
107 | |
108 assert(tasks.GetSize() == 0); | |
109 | |
110 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
111 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
112 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
113 (tasks, target, truncated.GetUpperLevel(), | |
114 upperLevelsCount, lowerLevelsCount, parameters); | |
115 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
116 } | |
117 else | |
118 { | |
119 LOG(WARNING) << "Constructing the pyramid"; | |
120 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
121 (tasks, target, source, levelsCount, 0, parameters); | |
122 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
123 } | |
124 } | |
125 | |
126 | |
127 static void Recompress(OrthancWSI::IFileTarget& output, | |
128 OrthancWSI::ITiledPyramid& source, | |
129 const DcmDataset& dataset, | |
130 const OrthancWSI::DicomizerParameters& parameters, | |
131 const OrthancWSI::ImagedVolumeParameters& volume) | |
132 { | |
133 OrthancWSI::TiledPyramidStatistics stats(source); | |
134 | |
135 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
136 LOG(WARNING) << "Source image compression: " << OrthancWSI::EnumerationToString(stats.GetImageCompression()); | |
137 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(stats.GetPixelFormat()); | |
138 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); | |
139 | |
140 if (parameters.IsRepaintBackground()) | |
141 { | |
142 LOG(WARNING) << "Repainting the background with color: (" | |
143 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
144 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
145 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
146 } | |
147 else | |
148 { | |
149 LOG(WARNING) << "No repainting of the background"; | |
150 } | |
151 | |
152 OrthancWSI::DicomPyramidWriter target(output, dataset, | |
153 source.GetPixelFormat(), | |
154 parameters.GetTargetCompression(), | |
155 parameters.GetTargetTileWidth(source), | |
156 parameters.GetTargetTileHeight(source), | |
157 parameters.GetDicomMaxFileSize(), | |
158 volume); | |
29 | 159 target.SetJpegQuality(parameters.GetJpegQuality()); |
0 | 160 |
161 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
162 | |
163 if (target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) | |
164 { | |
165 LOG(WARNING) << "Target image compression: Jpeg with quality " << static_cast<int>(target.GetJpegQuality()); | |
166 target.SetJpegQuality(target.GetJpegQuality()); | |
167 } | |
168 else | |
169 { | |
170 LOG(WARNING) << "Target image compression: " << OrthancWSI::EnumerationToString(target.GetImageCompression()); | |
171 } | |
172 | |
173 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
174 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
175 { | |
176 LOG(ERROR) << "When resampling the tile size, it must be a integer divisor of the original tile size"; | |
177 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
178 } | |
179 | |
180 if (target.GetTileWidth() <= 16 || | |
181 target.GetTileHeight() <= 16) | |
182 { | |
183 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
184 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
185 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
186 } | |
187 | |
188 if (parameters.IsReconstructPyramid()) | |
189 { | |
190 ReconstructPyramid(target, stats, parameters); | |
191 } | |
192 else | |
193 { | |
194 TranscodePyramid(target, stats, parameters); | |
195 } | |
196 | |
197 target.Flush(); | |
198 } | |
199 | |
200 | |
201 | |
202 static DcmDataset* ParseDataset(const std::string& path) | |
203 { | |
204 Json::Value json; | |
205 | |
206 if (path.empty()) | |
207 { | |
208 json = Json::objectValue; // Empty dataset => TODO EMBED | |
209 } | |
210 else | |
211 { | |
212 std::string content; | |
43 | 213 Orthanc::SystemToolbox::ReadFile(content, path); |
0 | 214 |
215 Json::Reader reader; | |
216 if (!reader.parse(content, json, false)) | |
217 { | |
218 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
219 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
220 } | |
221 } | |
222 | |
223 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1)); | |
224 if (dataset.get() == NULL) | |
225 { | |
226 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
227 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
228 } | |
229 | |
230 // VL Whole Slide Microscopy Image IOD | |
231 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
232 | |
233 // Slide Microscopy | |
234 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
235 | |
236 // Patient orientation makes no sense in whole-slide images | |
237 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
238 | |
239 // Some basic coordinate information | |
240 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
241 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
242 | |
243 std::string date, time; | |
43 | 244 Orthanc::SystemToolbox::GetNowDicom(date, time); |
0 | 245 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
246 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
247 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
248 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
249 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
250 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
251 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
252 | |
253 return dataset.release(); | |
254 } | |
255 | |
256 | |
257 | |
258 static void SetupDimension(DcmDataset& dataset, | |
259 const std::string& opticalPathId, | |
260 const OrthancWSI::ITiledPyramid& source, | |
261 const OrthancWSI::ImagedVolumeParameters& volume) | |
262 { | |
263 std::string uid; | |
264 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); | |
265 | |
266 if (previous != NULL) | |
267 { | |
268 const char* tmp = NULL; | |
269 if (previous->findAndGetString(DCM_DimensionOrganizationUID, tmp).good() && | |
270 tmp != NULL) | |
271 { | |
272 uid.assign(tmp); | |
273 } | |
274 } | |
275 | |
276 if (uid.empty()) | |
277 { | |
278 // Generate an unique identifier for the Dimension Organization | |
279 uid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
280 } | |
281 | |
282 dataset.remove(DCM_DimensionIndexSequence); | |
283 | |
284 std::auto_ptr<DcmItem> item(new DcmItem); | |
285 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
286 | |
287 if (!item->putAndInsertString(DCM_DimensionOrganizationUID, uid.c_str()).good() || | |
288 !sequence->insert(item.release(), false, false).good() || | |
289 !dataset.insert(sequence.release(), true, false).good()) | |
290 { | |
291 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
292 } | |
293 | |
294 item.reset(new DcmItem); | |
295 sequence.reset(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); | |
296 | |
297 std::auto_ptr<DcmAttributeTag> a1(new DcmAttributeTag(DCM_FunctionalGroupPointer)); | |
298 std::auto_ptr<DcmAttributeTag> a2(new DcmAttributeTag(DCM_DimensionIndexPointer)); | |
299 | |
300 if (!item->putAndInsertString(DCM_DimensionOrganizationUID, uid.c_str()).good() || | |
301 !a1->putTagVal(DCM_FrameContentSequence).good() || | |
302 !a2->putTagVal(DCM_DimensionIndexValues).good() || | |
26 | 303 !item->insert(a1.release()).good() || |
304 !item->insert(a2.release()).good() || | |
0 | 305 !sequence->insert(item.release(), false, false).good() || |
306 !dataset.insert(sequence.release(), true, false).good()) | |
307 { | |
308 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
309 } | |
310 | |
311 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0)); // Remember to switch X/Y! | |
312 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0)); // Remember to switch X/Y! | |
313 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + | |
314 boost::lexical_cast<std::string>(spacingY)); | |
315 | |
316 item.reset(new DcmItem); | |
317 sequence.reset(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); | |
318 std::auto_ptr<DcmItem> item2(new DcmItem); | |
319 std::auto_ptr<DcmItem> item3(new DcmItem); | |
320 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); | |
321 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); | |
322 | |
323 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, boost::lexical_cast<std::string>(volume.GetDepth())); | |
324 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); | |
325 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); | |
326 | |
327 if (!sequence2->insert(item2.release(), false, false).good() || | |
328 !sequence3->insert(item3.release(), false, false).good() || | |
329 !item->insert(sequence2.release(), false, false).good() || | |
330 !item->insert(sequence3.release(), false, false).good() || | |
331 !sequence->insert(item.release(), false, false).good() || | |
332 !dataset.insert(sequence.release(), true, false).good()) | |
333 { | |
334 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
335 } | |
336 } | |
337 | |
338 | |
339 static void EnrichDataset(DcmDataset& dataset, | |
340 const OrthancWSI::ITiledPyramid& source, | |
341 const OrthancWSI::DicomizerParameters& parameters, | |
342 const OrthancWSI::ImagedVolumeParameters& volume) | |
343 { | |
344 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
345 | |
346 if (source.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg || | |
347 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) | |
348 { | |
349 // Takes as estimation a 1:10 compression ratio | |
350 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
351 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
352 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
353 } | |
354 else | |
355 { | |
356 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
357 } | |
358 | |
359 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
360 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
361 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
362 | |
363 std::auto_ptr<DcmItem> origin(new DcmItem); | |
364 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
365 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
366 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
367 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
368 | |
369 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
370 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
371 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
372 { | |
373 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
374 } | |
375 | |
376 | |
377 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
378 { | |
379 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
380 { | |
381 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
382 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
383 } | |
384 | |
385 std::string brightfield; | |
386 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
387 | |
388 Json::Value json; | |
389 Json::Reader reader; | |
390 if (!reader.parse(brightfield, json, false)) | |
391 { | |
392 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
393 } | |
394 | |
395 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
396 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
397 DCM_OpticalPathSequence.getElement()), | |
398 json, false, encoding)); | |
399 if (!dataset.insert(element.release()).good()) | |
400 { | |
401 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
402 } | |
403 } | |
404 | |
405 | |
406 std::string profile; | |
407 if (parameters.GetIccProfilePath().empty()) | |
408 { | |
409 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
410 } | |
411 else | |
412 { | |
43 | 413 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
0 | 414 } |
415 | |
416 | |
417 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
418 if (opticalPath == NULL) | |
419 { | |
420 LOG(ERROR) << "No optical path specified"; | |
421 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
422 } | |
423 | |
424 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
425 { | |
426 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
427 | |
428 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
429 !opticalPath->insert(icc.release()).good()) | |
430 { | |
431 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
432 } | |
433 } | |
434 | |
435 const char* opticalPathId = NULL; | |
436 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
437 opticalPathId == NULL) | |
438 { | |
439 LOG(ERROR) << "No identifier in the optical path"; | |
440 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
441 } | |
442 | |
443 SetupDimension(dataset, opticalPathId, source, volume); | |
444 } | |
445 | |
446 | |
447 static bool ParseParameters(int& exitStatus, | |
448 OrthancWSI::DicomizerParameters& parameters, | |
449 OrthancWSI::ImagedVolumeParameters& volume, | |
450 int argc, | |
451 char* argv[]) | |
452 { | |
453 // Declare the supported parameters | |
454 boost::program_options::options_description generic("Generic options"); | |
455 generic.add_options() | |
456 ("help", "Display this help and exit") | |
8
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
457 ("version", "Output version information and exit") |
0 | 458 ("verbose", "Be verbose in logs") |
459 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), | |
460 "Number of processing threads to be used") | |
461 ("openslide", boost::program_options::value<std::string>(), | |
462 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)") | |
463 ; | |
464 | |
465 boost::program_options::options_description source("Options for the source image"); | |
466 source.add_options() | |
467 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset") | |
468 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit") | |
31 | 469 ("reencode", boost::program_options::value<bool>(), "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
0 | 470 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)") |
471 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")") | |
472 ; | |
473 | |
474 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
475 pyramid.add_options() | |
476 ("pyramid", boost::program_options::value<bool>()->default_value(false), | |
477 "Reconstruct the full pyramid (slow) (Boolean)") | |
478 ("smooth", boost::program_options::value<bool>()->default_value(false), | |
479 "Apply smoothing when reconstructing the pyramid " | |
480 "(slower, but higher quality) (Boolean)") | |
481 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid") | |
482 ; | |
483 | |
484 boost::program_options::options_description target("Options for the target image"); | |
485 target.add_options() | |
486 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image") | |
487 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image") | |
488 ("compression", boost::program_options::value<std::string>(), | |
489 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") | |
490 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") | |
491 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)") | |
492 ("folder", boost::program_options::value<std::string>(), | |
493 "Folder where to store the output DICOM instances") | |
494 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), | |
495 "Pattern for the files in the output folder") | |
496 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
497 "URL to the REST API of the target Orthanc server") | |
498 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
499 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
500 ; | |
501 | |
502 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
503 volumeOptions.add_options() | |
504 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)") | |
505 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)") | |
506 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)") | |
507 ("offset-x", boost::program_options::value<float>()->default_value(20), | |
508 "X offset the specimen, wrt. slide coordinates origin (in mm)") | |
509 ("offset-y", boost::program_options::value<float>()->default_value(40), | |
510 "Y offset the specimen, wrt. slide coordinates origin (in mm)") | |
511 ; | |
512 | |
513 boost::program_options::options_description advancedOptions("Advanced options"); | |
514 advancedOptions.add_options() | |
515 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"), | |
516 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") | |
517 ("icc-profile", boost::program_options::value<std::string>(), | |
518 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") | |
519 ("safety", boost::program_options::value<bool>()->default_value(true), | |
520 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") | |
521 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading " | |
522 "should be applied (only for performance/memory tuning)") | |
523 ; | |
524 | |
525 boost::program_options::options_description hidden; | |
526 hidden.add_options() | |
527 ("input", boost::program_options::value<std::string>(), "Input file"); | |
528 ; | |
529 | |
530 boost::program_options::options_description allWithoutHidden; | |
531 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions); | |
532 | |
533 boost::program_options::options_description all = allWithoutHidden; | |
534 all.add(hidden); | |
535 | |
536 boost::program_options::positional_options_description positional; | |
537 positional.add("input", 1); | |
538 | |
539 boost::program_options::variables_map options; | |
540 bool error = false; | |
541 | |
542 try | |
543 { | |
544 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
545 options(all).positional(positional).run(), options); | |
546 boost::program_options::notify(options); | |
547 } | |
548 catch (boost::program_options::error& e) | |
549 { | |
550 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
551 error = true; | |
552 } | |
553 | |
554 if (!error && | |
555 options.count("sample-dataset")) | |
556 { | |
557 std::string sample; | |
558 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
559 | |
560 std::cout << std::endl << sample << std::endl; | |
561 | |
562 return false; | |
563 } | |
564 | |
565 if (!error && | |
566 options.count("help") == 0 && | |
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567 options.count("version") == 0 && |
0 | 568 options.count("input") != 1) |
569 { | |
570 LOG(ERROR) << "No input file was specified"; | |
571 error = true; | |
572 } | |
573 | |
574 if (error || options.count("help")) | |
575 { | |
576 std::cout << std::endl | |
577 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
578 << std::endl | |
579 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
580 << std::endl << std::endl | |
581 << "Create a DICOM file from a digital pathology image." | |
582 << std::endl; | |
583 | |
584 std::cout << allWithoutHidden << "\n"; | |
585 | |
586 if (error) | |
587 { | |
588 exitStatus = -1; | |
589 } | |
590 | |
591 return false; | |
592 } | |
593 | |
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594 if (options.count("version")) |
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595 { |
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596 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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597 return false; |
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598 } |
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599 |
0 | 600 if (options.count("verbose")) |
601 { | |
602 Orthanc::Logging::EnableInfoLevel(true); | |
603 } | |
604 | |
605 if (options.count("openslide")) | |
606 { | |
607 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>()); | |
608 } | |
609 | |
610 if (options.count("pyramid") && | |
611 options["pyramid"].as<bool>()) | |
612 { | |
613 parameters.SetReconstructPyramid(true); | |
614 } | |
615 | |
616 if (options.count("smooth") && | |
617 options["smooth"].as<bool>()) | |
618 { | |
619 parameters.SetSmoothEnabled(true); | |
620 } | |
621 | |
622 if (options.count("safety") && | |
623 options["safety"].as<bool>()) | |
624 { | |
625 parameters.SetSafetyCheck(true); | |
626 } | |
627 | |
628 if (options.count("reencode") && | |
629 options["reencode"].as<bool>()) | |
630 { | |
631 parameters.SetForceReencode(true); | |
632 } | |
633 | |
634 if (options.count("repaint") && | |
635 options["repaint"].as<bool>()) | |
636 { | |
637 parameters.SetRepaintBackground(true); | |
638 } | |
639 | |
640 if (options.count("tile-width") || | |
641 options.count("tile-height")) | |
642 { | |
643 int w = 0; | |
644 if (options.count("tile-width")) | |
645 { | |
646 w = options["tile-width"].as<int>(); | |
647 } | |
648 | |
649 unsigned int h = 0; | |
650 if (options.count("tile-height")) | |
651 { | |
652 h = options["tile-height"].as<int>(); | |
653 } | |
654 | |
655 if (w < 0 || h < 0) | |
656 { | |
657 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
658 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
659 } | |
660 | |
661 parameters.SetTargetTileSize(w, h); | |
662 } | |
663 | |
664 parameters.SetInputFile(options["input"].as<std::string>()); | |
665 | |
666 if (options.count("color")) | |
667 { | |
668 uint8_t r, g, b; | |
669 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>()); | |
670 parameters.SetBackgroundColor(r, g, b); | |
671 } | |
672 | |
673 if (options.count("compression")) | |
674 { | |
675 std::string s = options["compression"].as<std::string>(); | |
676 if (s == "none") | |
677 { | |
678 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
679 } | |
680 else if (s == "jpeg") | |
681 { | |
682 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
683 } | |
684 else if (s == "jpeg2000") | |
685 { | |
686 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
687 } | |
688 else | |
689 { | |
690 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
691 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
692 } | |
693 } | |
694 | |
695 if (options.count("jpeg-quality")) | |
696 { | |
697 parameters.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
698 } | |
699 | |
700 if (options.count("levels")) | |
701 { | |
702 parameters.SetPyramidLevelsCount(options["levels"].as<int>()); | |
703 } | |
704 | |
705 if (options.count("lower-levels")) | |
706 { | |
707 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>()); | |
708 } | |
709 | |
710 if (options.count("threads")) | |
711 { | |
712 parameters.SetThreadsCount(options["threads"].as<int>()); | |
713 } | |
714 | |
715 if (options.count("max-size")) | |
716 { | |
717 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024); | |
718 } | |
719 | |
720 if (options.count("folder")) | |
721 { | |
722 parameters.SetTargetFolder(options["folder"].as<std::string>()); | |
723 } | |
724 | |
725 if (options.count("folder-pattern")) | |
726 { | |
727 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>()); | |
728 } | |
729 | |
730 if (options.count("orthanc")) | |
731 { | |
732 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>()); | |
733 | |
734 if (options.count("username") && | |
735 options.count("password")) | |
736 { | |
737 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>()); | |
738 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>()); | |
739 } | |
740 } | |
741 | |
742 if (options.count("dataset")) | |
743 { | |
744 parameters.SetDatasetPath(options["dataset"].as<std::string>()); | |
745 } | |
746 | |
747 if (options.count("imaged-width")) | |
748 { | |
749 volume.SetWidth(options["imaged-width"].as<float>()); | |
750 } | |
751 | |
752 if (options.count("imaged-height")) | |
753 { | |
754 volume.SetHeight(options["imaged-height"].as<float>()); | |
755 } | |
756 | |
757 if (options.count("imaged-depth")) | |
758 { | |
759 volume.SetDepth(options["imaged-depth"].as<float>()); | |
760 } | |
761 | |
762 if (options.count("offset-x")) | |
763 { | |
764 volume.SetOffsetX(options["offset-x"].as<float>()); | |
765 } | |
766 | |
767 if (options.count("offset-y")) | |
768 { | |
769 volume.SetOffsetY(options["offset-y"].as<float>()); | |
770 } | |
771 | |
772 if (options.count("optical-path")) | |
773 { | |
774 std::string s = options["optical-path"].as<std::string>(); | |
775 if (s == "none") | |
776 { | |
777 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
778 } | |
779 else if (s == "brightfield") | |
780 { | |
781 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
782 } | |
783 else | |
784 { | |
785 LOG(ERROR) << "Unknown optical path definition: " << s; | |
786 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
787 } | |
788 } | |
789 | |
790 if (options.count("icc-profile")) | |
791 { | |
792 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>()); | |
793 } | |
794 | |
795 return true; | |
796 } | |
797 | |
798 | |
799 OrthancWSI::ITiledPyramid* OpenInputPyramid(const std::string& path, | |
800 const OrthancWSI::DicomizerParameters& parameters) | |
801 { | |
802 LOG(WARNING) << "The input image is: " << path; | |
803 | |
804 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
805 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
806 | |
807 switch (format) | |
808 { | |
809 case OrthancWSI::ImageCompression_Png: | |
810 return new OrthancWSI::TiledPngImage(path, | |
811 parameters.GetTargetTileWidth(512), | |
812 parameters.GetTargetTileHeight(512)); | |
813 | |
814 case OrthancWSI::ImageCompression_Jpeg: | |
815 return new OrthancWSI::TiledJpegImage(path, | |
816 parameters.GetTargetTileWidth(512), | |
817 parameters.GetTargetTileHeight(512)); | |
818 | |
819 case OrthancWSI::ImageCompression_Tiff: | |
820 { | |
821 try | |
822 { | |
823 return new OrthancWSI::HierarchicalTiff(path); | |
824 } | |
825 catch (Orthanc::OrthancException&) | |
826 { | |
827 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
828 } | |
829 } | |
830 | |
831 default: | |
832 break; | |
833 } | |
834 | |
835 try | |
836 { | |
837 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
838 return new OrthancWSI::OpenSlidePyramid(path, | |
839 parameters.GetTargetTileWidth(512), | |
840 parameters.GetTargetTileHeight(512)); | |
841 } | |
842 catch (Orthanc::OrthancException&) | |
843 { | |
844 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
845 return NULL; | |
846 } | |
847 } | |
848 | |
849 | |
850 int main(int argc, char* argv[]) | |
851 { | |
852 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
853 | |
854 int exitStatus = 0; | |
855 | |
856 try | |
857 { | |
858 OrthancWSI::DicomizerParameters parameters; | |
859 OrthancWSI::ImagedVolumeParameters volume; | |
860 | |
861 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
862 { | |
863 std::auto_ptr<OrthancWSI::ITiledPyramid> source(OpenInputPyramid(parameters.GetInputFile(), parameters)); | |
864 if (source.get() == NULL) | |
865 { | |
866 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
867 } | |
868 | |
869 // Create the shared DICOM tags | |
870 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
871 EnrichDataset(*dataset, *source, parameters, volume); | |
872 | |
873 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
874 Recompress(*output, *source, *dataset, parameters, volume); | |
875 } | |
876 } | |
877 catch (Orthanc::OrthancException& e) | |
878 { | |
879 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
880 exitStatus = -1; | |
881 } | |
882 | |
883 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
884 | |
885 return exitStatus; | |
886 } |