Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 26:952b2c6ee0a2
fix msvc
author | jodogne |
---|---|
date | Thu, 27 Oct 2016 12:47:32 +0200 |
parents | 62adabb8c122 |
children | 8ba39f9ce8d4 |
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 | |
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" | |
34 #include "../Framework/Orthanc/Core/Toolbox.h" | |
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); | |
159 | |
160 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
161 | |
162 if (target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) | |
163 { | |
164 LOG(WARNING) << "Target image compression: Jpeg with quality " << static_cast<int>(target.GetJpegQuality()); | |
165 target.SetJpegQuality(target.GetJpegQuality()); | |
166 } | |
167 else | |
168 { | |
169 LOG(WARNING) << "Target image compression: " << OrthancWSI::EnumerationToString(target.GetImageCompression()); | |
170 } | |
171 | |
172 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
173 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
174 { | |
175 LOG(ERROR) << "When resampling the tile size, it must be a integer divisor of the original tile size"; | |
176 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
177 } | |
178 | |
179 if (target.GetTileWidth() <= 16 || | |
180 target.GetTileHeight() <= 16) | |
181 { | |
182 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
183 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
184 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
185 } | |
186 | |
187 if (parameters.IsReconstructPyramid()) | |
188 { | |
189 ReconstructPyramid(target, stats, parameters); | |
190 } | |
191 else | |
192 { | |
193 TranscodePyramid(target, stats, parameters); | |
194 } | |
195 | |
196 target.Flush(); | |
197 } | |
198 | |
199 | |
200 | |
201 static DcmDataset* ParseDataset(const std::string& path) | |
202 { | |
203 Json::Value json; | |
204 | |
205 if (path.empty()) | |
206 { | |
207 json = Json::objectValue; // Empty dataset => TODO EMBED | |
208 } | |
209 else | |
210 { | |
211 std::string content; | |
212 Orthanc::Toolbox::ReadFile(content, path); | |
213 | |
214 Json::Reader reader; | |
215 if (!reader.parse(content, json, false)) | |
216 { | |
217 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
218 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
219 } | |
220 } | |
221 | |
222 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1)); | |
223 if (dataset.get() == NULL) | |
224 { | |
225 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
226 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
227 } | |
228 | |
229 // VL Whole Slide Microscopy Image IOD | |
230 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
231 | |
232 // Slide Microscopy | |
233 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
234 | |
235 // Patient orientation makes no sense in whole-slide images | |
236 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
237 | |
238 // Some basic coordinate information | |
239 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
240 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
241 | |
242 std::string date, time; | |
243 Orthanc::Toolbox::GetNowDicom(date, time); | |
244 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); | |
245 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
246 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
247 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
248 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
249 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
250 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
251 | |
252 return dataset.release(); | |
253 } | |
254 | |
255 | |
256 | |
257 static void SetupDimension(DcmDataset& dataset, | |
258 const std::string& opticalPathId, | |
259 const OrthancWSI::ITiledPyramid& source, | |
260 const OrthancWSI::ImagedVolumeParameters& volume) | |
261 { | |
262 std::string uid; | |
263 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); | |
264 | |
265 if (previous != NULL) | |
266 { | |
267 const char* tmp = NULL; | |
268 if (previous->findAndGetString(DCM_DimensionOrganizationUID, tmp).good() && | |
269 tmp != NULL) | |
270 { | |
271 uid.assign(tmp); | |
272 } | |
273 } | |
274 | |
275 if (uid.empty()) | |
276 { | |
277 // Generate an unique identifier for the Dimension Organization | |
278 uid = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
279 } | |
280 | |
281 dataset.remove(DCM_DimensionIndexSequence); | |
282 | |
283 std::auto_ptr<DcmItem> item(new DcmItem); | |
284 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
285 | |
286 if (!item->putAndInsertString(DCM_DimensionOrganizationUID, uid.c_str()).good() || | |
287 !sequence->insert(item.release(), false, false).good() || | |
288 !dataset.insert(sequence.release(), true, false).good()) | |
289 { | |
290 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
291 } | |
292 | |
293 item.reset(new DcmItem); | |
294 sequence.reset(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); | |
295 | |
296 std::auto_ptr<DcmAttributeTag> a1(new DcmAttributeTag(DCM_FunctionalGroupPointer)); | |
297 std::auto_ptr<DcmAttributeTag> a2(new DcmAttributeTag(DCM_DimensionIndexPointer)); | |
298 | |
299 if (!item->putAndInsertString(DCM_DimensionOrganizationUID, uid.c_str()).good() || | |
300 !a1->putTagVal(DCM_FrameContentSequence).good() || | |
301 !a2->putTagVal(DCM_DimensionIndexValues).good() || | |
26 | 302 !item->insert(a1.release()).good() || |
303 !item->insert(a2.release()).good() || | |
0 | 304 !sequence->insert(item.release(), false, false).good() || |
305 !dataset.insert(sequence.release(), true, false).good()) | |
306 { | |
307 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
308 } | |
309 | |
310 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0)); // Remember to switch X/Y! | |
311 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0)); // Remember to switch X/Y! | |
312 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + | |
313 boost::lexical_cast<std::string>(spacingY)); | |
314 | |
315 item.reset(new DcmItem); | |
316 sequence.reset(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); | |
317 std::auto_ptr<DcmItem> item2(new DcmItem); | |
318 std::auto_ptr<DcmItem> item3(new DcmItem); | |
319 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); | |
320 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); | |
321 | |
322 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, boost::lexical_cast<std::string>(volume.GetDepth())); | |
323 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); | |
324 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); | |
325 | |
326 if (!sequence2->insert(item2.release(), false, false).good() || | |
327 !sequence3->insert(item3.release(), false, false).good() || | |
328 !item->insert(sequence2.release(), false, false).good() || | |
329 !item->insert(sequence3.release(), false, false).good() || | |
330 !sequence->insert(item.release(), false, false).good() || | |
331 !dataset.insert(sequence.release(), true, false).good()) | |
332 { | |
333 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
334 } | |
335 } | |
336 | |
337 | |
338 static void EnrichDataset(DcmDataset& dataset, | |
339 const OrthancWSI::ITiledPyramid& source, | |
340 const OrthancWSI::DicomizerParameters& parameters, | |
341 const OrthancWSI::ImagedVolumeParameters& volume) | |
342 { | |
343 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
344 | |
345 if (source.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg || | |
346 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) | |
347 { | |
348 // Takes as estimation a 1:10 compression ratio | |
349 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
350 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
351 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
352 } | |
353 else | |
354 { | |
355 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
356 } | |
357 | |
358 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
359 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
360 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
361 | |
362 std::auto_ptr<DcmItem> origin(new DcmItem); | |
363 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
364 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
365 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
366 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
367 | |
368 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
369 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
370 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
371 { | |
372 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
373 } | |
374 | |
375 | |
376 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
377 { | |
378 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
379 { | |
380 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
381 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
382 } | |
383 | |
384 std::string brightfield; | |
385 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
386 | |
387 Json::Value json; | |
388 Json::Reader reader; | |
389 if (!reader.parse(brightfield, json, false)) | |
390 { | |
391 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
392 } | |
393 | |
394 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
395 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
396 DCM_OpticalPathSequence.getElement()), | |
397 json, false, encoding)); | |
398 if (!dataset.insert(element.release()).good()) | |
399 { | |
400 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
401 } | |
402 } | |
403 | |
404 | |
405 std::string profile; | |
406 if (parameters.GetIccProfilePath().empty()) | |
407 { | |
408 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
409 } | |
410 else | |
411 { | |
412 Orthanc::Toolbox::ReadFile(profile, parameters.GetIccProfilePath()); | |
413 } | |
414 | |
415 | |
416 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
417 if (opticalPath == NULL) | |
418 { | |
419 LOG(ERROR) << "No optical path specified"; | |
420 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
421 } | |
422 | |
423 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
424 { | |
425 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
426 | |
427 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
428 !opticalPath->insert(icc.release()).good()) | |
429 { | |
430 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
431 } | |
432 } | |
433 | |
434 const char* opticalPathId = NULL; | |
435 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
436 opticalPathId == NULL) | |
437 { | |
438 LOG(ERROR) << "No identifier in the optical path"; | |
439 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
440 } | |
441 | |
442 SetupDimension(dataset, opticalPathId, source, volume); | |
443 } | |
444 | |
445 | |
446 static bool ParseParameters(int& exitStatus, | |
447 OrthancWSI::DicomizerParameters& parameters, | |
448 OrthancWSI::ImagedVolumeParameters& volume, | |
449 int argc, | |
450 char* argv[]) | |
451 { | |
452 // Declare the supported parameters | |
453 boost::program_options::options_description generic("Generic options"); | |
454 generic.add_options() | |
455 ("help", "Display this help and exit") | |
8
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
456 ("version", "Output version information and exit") |
0 | 457 ("verbose", "Be verbose in logs") |
458 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), | |
459 "Number of processing threads to be used") | |
460 ("openslide", boost::program_options::value<std::string>(), | |
461 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)") | |
462 ; | |
463 | |
464 boost::program_options::options_description source("Options for the source image"); | |
465 source.add_options() | |
466 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset") | |
467 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit") | |
468 ("reencode", boost::program_options::value<bool>(), "Whether to reencode each tile (no transcoding, much slower) (Boolean)") | |
469 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)") | |
470 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")") | |
471 ; | |
472 | |
473 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
474 pyramid.add_options() | |
475 ("pyramid", boost::program_options::value<bool>()->default_value(false), | |
476 "Reconstruct the full pyramid (slow) (Boolean)") | |
477 ("smooth", boost::program_options::value<bool>()->default_value(false), | |
478 "Apply smoothing when reconstructing the pyramid " | |
479 "(slower, but higher quality) (Boolean)") | |
480 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid") | |
481 ; | |
482 | |
483 boost::program_options::options_description target("Options for the target image"); | |
484 target.add_options() | |
485 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image") | |
486 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image") | |
487 ("compression", boost::program_options::value<std::string>(), | |
488 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") | |
489 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") | |
490 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)") | |
491 ("folder", boost::program_options::value<std::string>(), | |
492 "Folder where to store the output DICOM instances") | |
493 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), | |
494 "Pattern for the files in the output folder") | |
495 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
496 "URL to the REST API of the target Orthanc server") | |
497 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
498 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
499 ; | |
500 | |
501 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
502 volumeOptions.add_options() | |
503 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)") | |
504 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)") | |
505 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)") | |
506 ("offset-x", boost::program_options::value<float>()->default_value(20), | |
507 "X offset the specimen, wrt. slide coordinates origin (in mm)") | |
508 ("offset-y", boost::program_options::value<float>()->default_value(40), | |
509 "Y offset the specimen, wrt. slide coordinates origin (in mm)") | |
510 ; | |
511 | |
512 boost::program_options::options_description advancedOptions("Advanced options"); | |
513 advancedOptions.add_options() | |
514 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"), | |
515 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") | |
516 ("icc-profile", boost::program_options::value<std::string>(), | |
517 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") | |
518 ("safety", boost::program_options::value<bool>()->default_value(true), | |
519 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") | |
520 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading " | |
521 "should be applied (only for performance/memory tuning)") | |
522 ; | |
523 | |
524 boost::program_options::options_description hidden; | |
525 hidden.add_options() | |
526 ("input", boost::program_options::value<std::string>(), "Input file"); | |
527 ; | |
528 | |
529 boost::program_options::options_description allWithoutHidden; | |
530 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions); | |
531 | |
532 boost::program_options::options_description all = allWithoutHidden; | |
533 all.add(hidden); | |
534 | |
535 boost::program_options::positional_options_description positional; | |
536 positional.add("input", 1); | |
537 | |
538 boost::program_options::variables_map options; | |
539 bool error = false; | |
540 | |
541 try | |
542 { | |
543 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
544 options(all).positional(positional).run(), options); | |
545 boost::program_options::notify(options); | |
546 } | |
547 catch (boost::program_options::error& e) | |
548 { | |
549 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
550 error = true; | |
551 } | |
552 | |
553 if (!error && | |
554 options.count("sample-dataset")) | |
555 { | |
556 std::string sample; | |
557 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
558 | |
559 std::cout << std::endl << sample << std::endl; | |
560 | |
561 return false; | |
562 } | |
563 | |
564 if (!error && | |
565 options.count("help") == 0 && | |
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566 options.count("version") == 0 && |
0 | 567 options.count("input") != 1) |
568 { | |
569 LOG(ERROR) << "No input file was specified"; | |
570 error = true; | |
571 } | |
572 | |
573 if (error || options.count("help")) | |
574 { | |
575 std::cout << std::endl | |
576 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
577 << std::endl | |
578 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
579 << std::endl << std::endl | |
580 << "Create a DICOM file from a digital pathology image." | |
581 << std::endl; | |
582 | |
583 std::cout << allWithoutHidden << "\n"; | |
584 | |
585 if (error) | |
586 { | |
587 exitStatus = -1; | |
588 } | |
589 | |
590 return false; | |
591 } | |
592 | |
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593 if (options.count("version")) |
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594 { |
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595 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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596 return false; |
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597 } |
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598 |
0 | 599 if (options.count("verbose")) |
600 { | |
601 Orthanc::Logging::EnableInfoLevel(true); | |
602 } | |
603 | |
604 if (options.count("openslide")) | |
605 { | |
606 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>()); | |
607 } | |
608 | |
609 if (options.count("pyramid") && | |
610 options["pyramid"].as<bool>()) | |
611 { | |
612 parameters.SetReconstructPyramid(true); | |
613 } | |
614 | |
615 if (options.count("smooth") && | |
616 options["smooth"].as<bool>()) | |
617 { | |
618 parameters.SetSmoothEnabled(true); | |
619 } | |
620 | |
621 if (options.count("safety") && | |
622 options["safety"].as<bool>()) | |
623 { | |
624 parameters.SetSafetyCheck(true); | |
625 } | |
626 | |
627 if (options.count("reencode") && | |
628 options["reencode"].as<bool>()) | |
629 { | |
630 parameters.SetForceReencode(true); | |
631 } | |
632 | |
633 if (options.count("repaint") && | |
634 options["repaint"].as<bool>()) | |
635 { | |
636 parameters.SetRepaintBackground(true); | |
637 } | |
638 | |
639 if (options.count("tile-width") || | |
640 options.count("tile-height")) | |
641 { | |
642 int w = 0; | |
643 if (options.count("tile-width")) | |
644 { | |
645 w = options["tile-width"].as<int>(); | |
646 } | |
647 | |
648 unsigned int h = 0; | |
649 if (options.count("tile-height")) | |
650 { | |
651 h = options["tile-height"].as<int>(); | |
652 } | |
653 | |
654 if (w < 0 || h < 0) | |
655 { | |
656 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
657 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
658 } | |
659 | |
660 parameters.SetTargetTileSize(w, h); | |
661 } | |
662 | |
663 parameters.SetInputFile(options["input"].as<std::string>()); | |
664 | |
665 if (options.count("color")) | |
666 { | |
667 uint8_t r, g, b; | |
668 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>()); | |
669 parameters.SetBackgroundColor(r, g, b); | |
670 } | |
671 | |
672 if (options.count("compression")) | |
673 { | |
674 std::string s = options["compression"].as<std::string>(); | |
675 if (s == "none") | |
676 { | |
677 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
678 } | |
679 else if (s == "jpeg") | |
680 { | |
681 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
682 } | |
683 else if (s == "jpeg2000") | |
684 { | |
685 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
686 } | |
687 else | |
688 { | |
689 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
690 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
691 } | |
692 } | |
693 | |
694 if (options.count("jpeg-quality")) | |
695 { | |
696 parameters.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
697 } | |
698 | |
699 if (options.count("levels")) | |
700 { | |
701 parameters.SetPyramidLevelsCount(options["levels"].as<int>()); | |
702 } | |
703 | |
704 if (options.count("lower-levels")) | |
705 { | |
706 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>()); | |
707 } | |
708 | |
709 if (options.count("threads")) | |
710 { | |
711 parameters.SetThreadsCount(options["threads"].as<int>()); | |
712 } | |
713 | |
714 if (options.count("max-size")) | |
715 { | |
716 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024); | |
717 } | |
718 | |
719 if (options.count("folder")) | |
720 { | |
721 parameters.SetTargetFolder(options["folder"].as<std::string>()); | |
722 } | |
723 | |
724 if (options.count("folder-pattern")) | |
725 { | |
726 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>()); | |
727 } | |
728 | |
729 if (options.count("orthanc")) | |
730 { | |
731 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>()); | |
732 | |
733 if (options.count("username") && | |
734 options.count("password")) | |
735 { | |
736 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>()); | |
737 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>()); | |
738 } | |
739 } | |
740 | |
741 if (options.count("dataset")) | |
742 { | |
743 parameters.SetDatasetPath(options["dataset"].as<std::string>()); | |
744 } | |
745 | |
746 if (options.count("imaged-width")) | |
747 { | |
748 volume.SetWidth(options["imaged-width"].as<float>()); | |
749 } | |
750 | |
751 if (options.count("imaged-height")) | |
752 { | |
753 volume.SetHeight(options["imaged-height"].as<float>()); | |
754 } | |
755 | |
756 if (options.count("imaged-depth")) | |
757 { | |
758 volume.SetDepth(options["imaged-depth"].as<float>()); | |
759 } | |
760 | |
761 if (options.count("offset-x")) | |
762 { | |
763 volume.SetOffsetX(options["offset-x"].as<float>()); | |
764 } | |
765 | |
766 if (options.count("offset-y")) | |
767 { | |
768 volume.SetOffsetY(options["offset-y"].as<float>()); | |
769 } | |
770 | |
771 if (options.count("optical-path")) | |
772 { | |
773 std::string s = options["optical-path"].as<std::string>(); | |
774 if (s == "none") | |
775 { | |
776 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
777 } | |
778 else if (s == "brightfield") | |
779 { | |
780 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
781 } | |
782 else | |
783 { | |
784 LOG(ERROR) << "Unknown optical path definition: " << s; | |
785 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
786 } | |
787 } | |
788 | |
789 if (options.count("icc-profile")) | |
790 { | |
791 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>()); | |
792 } | |
793 | |
794 return true; | |
795 } | |
796 | |
797 | |
798 OrthancWSI::ITiledPyramid* OpenInputPyramid(const std::string& path, | |
799 const OrthancWSI::DicomizerParameters& parameters) | |
800 { | |
801 LOG(WARNING) << "The input image is: " << path; | |
802 | |
803 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
804 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
805 | |
806 switch (format) | |
807 { | |
808 case OrthancWSI::ImageCompression_Png: | |
809 return new OrthancWSI::TiledPngImage(path, | |
810 parameters.GetTargetTileWidth(512), | |
811 parameters.GetTargetTileHeight(512)); | |
812 | |
813 case OrthancWSI::ImageCompression_Jpeg: | |
814 return new OrthancWSI::TiledJpegImage(path, | |
815 parameters.GetTargetTileWidth(512), | |
816 parameters.GetTargetTileHeight(512)); | |
817 | |
818 case OrthancWSI::ImageCompression_Tiff: | |
819 { | |
820 try | |
821 { | |
822 return new OrthancWSI::HierarchicalTiff(path); | |
823 } | |
824 catch (Orthanc::OrthancException&) | |
825 { | |
826 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
827 } | |
828 } | |
829 | |
830 default: | |
831 break; | |
832 } | |
833 | |
834 try | |
835 { | |
836 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
837 return new OrthancWSI::OpenSlidePyramid(path, | |
838 parameters.GetTargetTileWidth(512), | |
839 parameters.GetTargetTileHeight(512)); | |
840 } | |
841 catch (Orthanc::OrthancException&) | |
842 { | |
843 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
844 return NULL; | |
845 } | |
846 } | |
847 | |
848 | |
849 int main(int argc, char* argv[]) | |
850 { | |
851 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
852 | |
853 int exitStatus = 0; | |
854 | |
855 try | |
856 { | |
857 OrthancWSI::DicomizerParameters parameters; | |
858 OrthancWSI::ImagedVolumeParameters volume; | |
859 | |
860 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
861 { | |
862 std::auto_ptr<OrthancWSI::ITiledPyramid> source(OpenInputPyramid(parameters.GetInputFile(), parameters)); | |
863 if (source.get() == NULL) | |
864 { | |
865 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
866 } | |
867 | |
868 // Create the shared DICOM tags | |
869 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
870 EnrichDataset(*dataset, *source, parameters, volume); | |
871 | |
872 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
873 Recompress(*output, *source, *dataset, parameters, volume); | |
874 } | |
875 } | |
876 catch (Orthanc::OrthancException& e) | |
877 { | |
878 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
879 exitStatus = -1; | |
880 } | |
881 | |
882 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
883 | |
884 return exitStatus; | |
885 } |