Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 59:7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 25 Nov 2016 16:34:34 +0100 |
parents | 91fc9583b2de |
children | 0cb3ac4f9159 |
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/Outputs/DicomPyramidWriter.h" | |
32 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
33 | |
59
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34 #include "../Resources/Orthanc/Core/HttpClient.h" |
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parents:
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35 #include "../Resources/Orthanc/Core/Logging.h" |
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parents:
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36 #include "../Resources/Orthanc/Core/MultiThreading/BagOfTasksProcessor.h" |
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37 #include "../Resources/Orthanc/Core/SystemToolbox.h" |
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38 #include "../Resources/Orthanc/OrthancServer/FromDcmtkBridge.h" |
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39 |
0 | 40 #include "ApplicationToolbox.h" |
41 | |
42 #include <EmbeddedResources.h> | |
43 | |
44 #include <boost/program_options.hpp> | |
45 | |
46 #include <dcmtk/dcmdata/dcdeftag.h> | |
47 #include <dcmtk/dcmdata/dcuid.h> | |
48 #include <dcmtk/dcmdata/dcvrobow.h> | |
49 #include <dcmtk/dcmdata/dcvrat.h> | |
50 | |
51 | |
52 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, | |
53 OrthancWSI::ITiledPyramid& source, | |
54 const OrthancWSI::DicomizerParameters& parameters) | |
55 { | |
56 Orthanc::BagOfTasks tasks; | |
57 | |
58 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
59 { | |
60 LOG(WARNING) << "Creating level " << i << " of size " | |
61 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
62 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
63 } | |
64 | |
65 LOG(WARNING) << "Transcoding the source pyramid"; | |
66 | |
67 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
68 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
69 } | |
70 | |
71 | |
72 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
73 OrthancWSI::ITiledPyramid& source, | |
74 const OrthancWSI::DicomizerParameters& parameters) | |
75 { | |
76 Orthanc::BagOfTasks tasks; | |
77 | |
78 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
79 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
80 assert(levelsCount >= 1); | |
81 | |
82 for (unsigned int i = 0; i < levelsCount; i++) | |
83 { | |
84 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
85 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
86 | |
87 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
88 target.AddLevel(width, height); | |
89 } | |
90 | |
91 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
92 if (lowerLevelsCount > levelsCount) | |
93 { | |
94 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
95 << ") exceeds the number of levels (" << levelsCount | |
96 << "), cropping it"; | |
97 lowerLevelsCount = levelsCount; | |
98 } | |
99 | |
100 assert(lowerLevelsCount <= levelsCount); | |
101 if (lowerLevelsCount != levelsCount) | |
102 { | |
103 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
104 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount); | |
105 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
106 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
107 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
108 | |
109 assert(tasks.GetSize() == 0); | |
110 | |
111 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
112 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
113 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
114 (tasks, target, truncated.GetUpperLevel(), | |
115 upperLevelsCount, lowerLevelsCount, parameters); | |
116 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
117 } | |
118 else | |
119 { | |
120 LOG(WARNING) << "Constructing the pyramid"; | |
121 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
122 (tasks, target, source, levelsCount, 0, parameters); | |
123 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
124 } | |
125 } | |
126 | |
127 | |
128 static void Recompress(OrthancWSI::IFileTarget& output, | |
129 OrthancWSI::ITiledPyramid& source, | |
130 const DcmDataset& dataset, | |
131 const OrthancWSI::DicomizerParameters& parameters, | |
132 const OrthancWSI::ImagedVolumeParameters& volume) | |
133 { | |
134 OrthancWSI::TiledPyramidStatistics stats(source); | |
135 | |
136 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
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, | |
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341 OrthancWSI::ImageCompression sourceCompression, |
0 | 342 const OrthancWSI::DicomizerParameters& parameters, |
343 const OrthancWSI::ImagedVolumeParameters& volume) | |
344 { | |
345 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
346 | |
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347 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
0 | 348 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
349 { | |
350 // Takes as estimation a 1:10 compression ratio | |
351 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
352 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
353 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
354 } | |
355 else | |
356 { | |
357 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
358 } | |
359 | |
360 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
361 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
362 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
363 | |
364 std::auto_ptr<DcmItem> origin(new DcmItem); | |
365 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
366 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
367 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
368 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
369 | |
370 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
371 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
372 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
373 { | |
374 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
375 } | |
376 | |
377 | |
378 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
379 { | |
380 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
381 { | |
382 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
383 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
384 } | |
385 | |
386 std::string brightfield; | |
387 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
388 | |
389 Json::Value json; | |
390 Json::Reader reader; | |
391 if (!reader.parse(brightfield, json, false)) | |
392 { | |
393 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
394 } | |
395 | |
396 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
397 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
398 DCM_OpticalPathSequence.getElement()), | |
399 json, false, encoding)); | |
400 if (!dataset.insert(element.release()).good()) | |
401 { | |
402 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
403 } | |
404 } | |
405 | |
406 | |
407 std::string profile; | |
408 if (parameters.GetIccProfilePath().empty()) | |
409 { | |
410 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
411 } | |
412 else | |
413 { | |
43 | 414 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
0 | 415 } |
416 | |
417 | |
418 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
419 if (opticalPath == NULL) | |
420 { | |
421 LOG(ERROR) << "No optical path specified"; | |
422 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
423 } | |
424 | |
425 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
426 { | |
427 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
428 | |
429 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
430 !opticalPath->insert(icc.release()).good()) | |
431 { | |
432 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
433 } | |
434 } | |
435 | |
436 const char* opticalPathId = NULL; | |
437 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
438 opticalPathId == NULL) | |
439 { | |
440 LOG(ERROR) << "No identifier in the optical path"; | |
441 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
442 } | |
443 | |
444 SetupDimension(dataset, opticalPathId, source, volume); | |
445 } | |
446 | |
447 | |
448 static bool ParseParameters(int& exitStatus, | |
449 OrthancWSI::DicomizerParameters& parameters, | |
450 OrthancWSI::ImagedVolumeParameters& volume, | |
451 int argc, | |
452 char* argv[]) | |
453 { | |
454 // Declare the supported parameters | |
455 boost::program_options::options_description generic("Generic options"); | |
456 generic.add_options() | |
457 ("help", "Display this help and exit") | |
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458 ("version", "Output version information and exit") |
0 | 459 ("verbose", "Be verbose in logs") |
460 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), | |
461 "Number of processing threads to be used") | |
462 ("openslide", boost::program_options::value<std::string>(), | |
463 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)") | |
464 ; | |
465 | |
466 boost::program_options::options_description source("Options for the source image"); | |
467 source.add_options() | |
468 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset") | |
469 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit") | |
31 | 470 ("reencode", boost::program_options::value<bool>(), "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
0 | 471 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)") |
472 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")") | |
473 ; | |
474 | |
475 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
476 pyramid.add_options() | |
477 ("pyramid", boost::program_options::value<bool>()->default_value(false), | |
478 "Reconstruct the full pyramid (slow) (Boolean)") | |
479 ("smooth", boost::program_options::value<bool>()->default_value(false), | |
480 "Apply smoothing when reconstructing the pyramid " | |
481 "(slower, but higher quality) (Boolean)") | |
482 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid") | |
483 ; | |
484 | |
485 boost::program_options::options_description target("Options for the target image"); | |
486 target.add_options() | |
487 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image") | |
488 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image") | |
489 ("compression", boost::program_options::value<std::string>(), | |
490 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") | |
491 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") | |
492 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)") | |
493 ("folder", boost::program_options::value<std::string>(), | |
494 "Folder where to store the output DICOM instances") | |
495 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), | |
496 "Pattern for the files in the output folder") | |
497 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
498 "URL to the REST API of the target Orthanc server") | |
499 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
500 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
501 ; | |
502 | |
503 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
504 volumeOptions.add_options() | |
505 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)") | |
506 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)") | |
507 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)") | |
508 ("offset-x", boost::program_options::value<float>()->default_value(20), | |
509 "X offset the specimen, wrt. slide coordinates origin (in mm)") | |
510 ("offset-y", boost::program_options::value<float>()->default_value(40), | |
511 "Y offset the specimen, wrt. slide coordinates origin (in mm)") | |
512 ; | |
513 | |
514 boost::program_options::options_description advancedOptions("Advanced options"); | |
515 advancedOptions.add_options() | |
516 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"), | |
517 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") | |
518 ("icc-profile", boost::program_options::value<std::string>(), | |
519 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") | |
520 ("safety", boost::program_options::value<bool>()->default_value(true), | |
521 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") | |
522 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading " | |
523 "should be applied (only for performance/memory tuning)") | |
524 ; | |
525 | |
526 boost::program_options::options_description hidden; | |
527 hidden.add_options() | |
528 ("input", boost::program_options::value<std::string>(), "Input file"); | |
529 ; | |
530 | |
531 boost::program_options::options_description allWithoutHidden; | |
532 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions); | |
533 | |
534 boost::program_options::options_description all = allWithoutHidden; | |
535 all.add(hidden); | |
536 | |
537 boost::program_options::positional_options_description positional; | |
538 positional.add("input", 1); | |
539 | |
540 boost::program_options::variables_map options; | |
541 bool error = false; | |
542 | |
543 try | |
544 { | |
545 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
546 options(all).positional(positional).run(), options); | |
547 boost::program_options::notify(options); | |
548 } | |
549 catch (boost::program_options::error& e) | |
550 { | |
551 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
552 error = true; | |
553 } | |
554 | |
555 if (!error && | |
556 options.count("sample-dataset")) | |
557 { | |
558 std::string sample; | |
559 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
560 | |
561 std::cout << std::endl << sample << std::endl; | |
562 | |
563 return false; | |
564 } | |
565 | |
566 if (!error && | |
567 options.count("help") == 0 && | |
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568 options.count("version") == 0 && |
0 | 569 options.count("input") != 1) |
570 { | |
571 LOG(ERROR) << "No input file was specified"; | |
572 error = true; | |
573 } | |
574 | |
575 if (error || options.count("help")) | |
576 { | |
577 std::cout << std::endl | |
578 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
579 << std::endl | |
580 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
581 << std::endl << std::endl | |
582 << "Create a DICOM file from a digital pathology image." | |
583 << std::endl; | |
584 | |
585 std::cout << allWithoutHidden << "\n"; | |
586 | |
587 if (error) | |
588 { | |
589 exitStatus = -1; | |
590 } | |
591 | |
592 return false; | |
593 } | |
594 | |
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595 if (options.count("version")) |
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596 { |
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597 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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598 return false; |
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599 } |
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600 |
0 | 601 if (options.count("verbose")) |
602 { | |
603 Orthanc::Logging::EnableInfoLevel(true); | |
604 } | |
605 | |
606 if (options.count("openslide")) | |
607 { | |
608 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>()); | |
609 } | |
610 | |
611 if (options.count("pyramid") && | |
612 options["pyramid"].as<bool>()) | |
613 { | |
614 parameters.SetReconstructPyramid(true); | |
615 } | |
616 | |
617 if (options.count("smooth") && | |
618 options["smooth"].as<bool>()) | |
619 { | |
620 parameters.SetSmoothEnabled(true); | |
621 } | |
622 | |
623 if (options.count("safety") && | |
624 options["safety"].as<bool>()) | |
625 { | |
626 parameters.SetSafetyCheck(true); | |
627 } | |
628 | |
629 if (options.count("reencode") && | |
630 options["reencode"].as<bool>()) | |
631 { | |
632 parameters.SetForceReencode(true); | |
633 } | |
634 | |
635 if (options.count("repaint") && | |
636 options["repaint"].as<bool>()) | |
637 { | |
638 parameters.SetRepaintBackground(true); | |
639 } | |
640 | |
641 if (options.count("tile-width") || | |
642 options.count("tile-height")) | |
643 { | |
644 int w = 0; | |
645 if (options.count("tile-width")) | |
646 { | |
647 w = options["tile-width"].as<int>(); | |
648 } | |
649 | |
650 unsigned int h = 0; | |
651 if (options.count("tile-height")) | |
652 { | |
653 h = options["tile-height"].as<int>(); | |
654 } | |
655 | |
656 if (w < 0 || h < 0) | |
657 { | |
658 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
659 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
660 } | |
661 | |
662 parameters.SetTargetTileSize(w, h); | |
663 } | |
664 | |
665 parameters.SetInputFile(options["input"].as<std::string>()); | |
666 | |
667 if (options.count("color")) | |
668 { | |
669 uint8_t r, g, b; | |
670 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>()); | |
671 parameters.SetBackgroundColor(r, g, b); | |
672 } | |
673 | |
674 if (options.count("compression")) | |
675 { | |
676 std::string s = options["compression"].as<std::string>(); | |
677 if (s == "none") | |
678 { | |
679 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
680 } | |
681 else if (s == "jpeg") | |
682 { | |
683 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
684 } | |
685 else if (s == "jpeg2000") | |
686 { | |
687 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
688 } | |
689 else | |
690 { | |
691 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
692 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
693 } | |
694 } | |
695 | |
696 if (options.count("jpeg-quality")) | |
697 { | |
698 parameters.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
699 } | |
700 | |
701 if (options.count("levels")) | |
702 { | |
703 parameters.SetPyramidLevelsCount(options["levels"].as<int>()); | |
704 } | |
705 | |
706 if (options.count("lower-levels")) | |
707 { | |
708 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>()); | |
709 } | |
710 | |
711 if (options.count("threads")) | |
712 { | |
713 parameters.SetThreadsCount(options["threads"].as<int>()); | |
714 } | |
715 | |
716 if (options.count("max-size")) | |
717 { | |
718 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024); | |
719 } | |
720 | |
721 if (options.count("folder")) | |
722 { | |
723 parameters.SetTargetFolder(options["folder"].as<std::string>()); | |
724 } | |
725 | |
726 if (options.count("folder-pattern")) | |
727 { | |
728 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>()); | |
729 } | |
730 | |
731 if (options.count("orthanc")) | |
732 { | |
733 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>()); | |
734 | |
735 if (options.count("username") && | |
736 options.count("password")) | |
737 { | |
738 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>()); | |
739 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>()); | |
740 } | |
741 } | |
742 | |
743 if (options.count("dataset")) | |
744 { | |
745 parameters.SetDatasetPath(options["dataset"].as<std::string>()); | |
746 } | |
747 | |
748 if (options.count("imaged-width")) | |
749 { | |
750 volume.SetWidth(options["imaged-width"].as<float>()); | |
751 } | |
752 | |
753 if (options.count("imaged-height")) | |
754 { | |
755 volume.SetHeight(options["imaged-height"].as<float>()); | |
756 } | |
757 | |
758 if (options.count("imaged-depth")) | |
759 { | |
760 volume.SetDepth(options["imaged-depth"].as<float>()); | |
761 } | |
762 | |
763 if (options.count("offset-x")) | |
764 { | |
765 volume.SetOffsetX(options["offset-x"].as<float>()); | |
766 } | |
767 | |
768 if (options.count("offset-y")) | |
769 { | |
770 volume.SetOffsetY(options["offset-y"].as<float>()); | |
771 } | |
772 | |
773 if (options.count("optical-path")) | |
774 { | |
775 std::string s = options["optical-path"].as<std::string>(); | |
776 if (s == "none") | |
777 { | |
778 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
779 } | |
780 else if (s == "brightfield") | |
781 { | |
782 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
783 } | |
784 else | |
785 { | |
786 LOG(ERROR) << "Unknown optical path definition: " << s; | |
787 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
788 } | |
789 } | |
790 | |
791 if (options.count("icc-profile")) | |
792 { | |
793 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>()); | |
794 } | |
795 | |
796 return true; | |
797 } | |
798 | |
799 | |
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800 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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801 const std::string& path, |
0 | 802 const OrthancWSI::DicomizerParameters& parameters) |
803 { | |
804 LOG(WARNING) << "The input image is: " << path; | |
805 | |
806 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
807 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
808 | |
809 switch (format) | |
810 { | |
811 case OrthancWSI::ImageCompression_Png: | |
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812 { |
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813 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 814 return new OrthancWSI::TiledPngImage(path, |
815 parameters.GetTargetTileWidth(512), | |
816 parameters.GetTargetTileHeight(512)); | |
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817 } |
0 | 818 |
819 case OrthancWSI::ImageCompression_Jpeg: | |
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820 { |
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821 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 822 return new OrthancWSI::TiledJpegImage(path, |
823 parameters.GetTargetTileWidth(512), | |
824 parameters.GetTargetTileHeight(512)); | |
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825 } |
0 | 826 |
827 case OrthancWSI::ImageCompression_Tiff: | |
828 { | |
829 try | |
830 { | |
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831 std::auto_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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832 sourceCompression = tiff->GetImageCompression(); |
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833 return tiff.release(); |
0 | 834 } |
835 catch (Orthanc::OrthancException&) | |
836 { | |
837 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
838 } | |
839 } | |
840 | |
841 default: | |
842 break; | |
843 } | |
844 | |
845 try | |
846 { | |
847 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
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848 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 849 return new OrthancWSI::OpenSlidePyramid(path, |
850 parameters.GetTargetTileWidth(512), | |
851 parameters.GetTargetTileHeight(512)); | |
852 } | |
853 catch (Orthanc::OrthancException&) | |
854 { | |
855 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
856 return NULL; | |
857 } | |
858 } | |
859 | |
860 | |
861 int main(int argc, char* argv[]) | |
862 { | |
863 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
864 | |
865 int exitStatus = 0; | |
866 | |
867 try | |
868 { | |
869 OrthancWSI::DicomizerParameters parameters; | |
870 OrthancWSI::ImagedVolumeParameters volume; | |
871 | |
872 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
873 { | |
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874 OrthancWSI::ImageCompression sourceCompression; |
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875 std::auto_ptr<OrthancWSI::ITiledPyramid> source; |
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876 |
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877 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
0 | 878 if (source.get() == NULL) |
879 { | |
880 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
881 } | |
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882 |
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883 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
0 | 884 |
885 // Create the shared DICOM tags | |
886 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
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887 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
0 | 888 |
889 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
890 Recompress(*output, *source, *dataset, parameters, volume); | |
891 } | |
892 } | |
893 catch (Orthanc::OrthancException& e) | |
894 { | |
895 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
896 exitStatus = -1; | |
897 } | |
898 | |
899 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
900 | |
901 return exitStatus; | |
902 } |