Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 84:727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 15 Dec 2016 12:36:20 +0100 |
parents | 0cb3ac4f9159 |
children | 14146ecd1688 |
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 | |
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34 #include "../Resources/Orthanc/Core/HttpClient.h" |
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35 #include "../Resources/Orthanc/Core/Logging.h" |
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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 { | |
83 | 263 // Extract the identifier of the Dimension Organization, if provided |
264 std::string organization; | |
0 | 265 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
266 | |
83 | 267 if (previous != NULL && |
268 previous->tagExists(DCM_DimensionOrganizationUID)) | |
269 { | |
270 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
271 } | |
272 else | |
0 | 273 { |
83 | 274 // No Dimension Organization provided: Generate an unique identifier |
275 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
276 } | |
277 | |
278 | |
279 { | |
280 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
281 std::auto_ptr<DcmItem> item(new DcmItem); | |
282 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
283 | |
284 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
285 | |
286 if (!sequence->insert(item.release(), false, false).good() || | |
287 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
0 | 288 { |
83 | 289 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
0 | 290 } |
291 } | |
292 | |
83 | 293 |
0 | 294 { |
83 | 295 // Construct tag "Dimension Index Sequence" (0020,9222) |
296 std::auto_ptr<DcmItem> item(new DcmItem); | |
297 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
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298 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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parents:
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299 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix); |
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300 |
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301 std::auto_ptr<DcmItem> item2(new DcmItem); |
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302 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization); |
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parents:
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303 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence); |
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parents:
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304 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
0 | 305 |
83 | 306 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
0 | 307 |
83 | 308 if (!sequence->insert(item.release(), false, false).good() || |
84
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309 !sequence->insert(item2.release(), false, false).good() || |
83 | 310 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
311 { | |
312 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
313 } | |
0 | 314 } |
315 | |
316 | |
83 | 317 { |
318 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
0 | 319 |
83 | 320 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
321 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0)); | |
322 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0)); | |
323 | |
324 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' + | |
325 boost::lexical_cast<std::string>(spacingY)); | |
326 | |
327 std::auto_ptr<DcmItem> item(new DcmItem); | |
0 | 328 |
83 | 329 std::auto_ptr<DcmItem> item2(new DcmItem); |
330 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness, | |
331 boost::lexical_cast<std::string>(volume.GetDepth())); | |
332 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing); | |
0 | 333 |
83 | 334 std::auto_ptr<DcmItem> item3(new DcmItem); |
335 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); | |
0 | 336 |
83 | 337 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
338 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence)); | |
339 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); | |
0 | 340 |
83 | 341 if (!sequence2->insert(item2.release(), false, false).good() || |
342 !sequence3->insert(item3.release(), false, false).good() || | |
343 !item->insert(sequence2.release(), false, false).good() || | |
344 !item->insert(sequence3.release(), false, false).good() || | |
345 !sequence->insert(item.release(), false, false).good() || | |
346 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
347 { | |
348 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
349 } | |
0 | 350 } |
351 } | |
352 | |
353 | |
354 static void EnrichDataset(DcmDataset& dataset, | |
355 const OrthancWSI::ITiledPyramid& source, | |
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356 OrthancWSI::ImageCompression sourceCompression, |
0 | 357 const OrthancWSI::DicomizerParameters& parameters, |
358 const OrthancWSI::ImagedVolumeParameters& volume) | |
359 { | |
360 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
361 | |
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362 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
0 | 363 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
364 { | |
365 // Takes as estimation a 1:10 compression ratio | |
366 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
367 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
368 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
369 } | |
370 else | |
371 { | |
372 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
373 } | |
374 | |
375 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
376 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
377 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
378 | |
379 std::auto_ptr<DcmItem> origin(new DcmItem); | |
380 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
381 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
382 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
383 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
384 | |
385 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
386 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
387 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
388 { | |
389 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
390 } | |
391 | |
392 | |
393 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
394 { | |
395 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
396 { | |
397 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
398 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
399 } | |
400 | |
401 std::string brightfield; | |
402 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
403 | |
404 Json::Value json; | |
405 Json::Reader reader; | |
406 if (!reader.parse(brightfield, json, false)) | |
407 { | |
408 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
409 } | |
410 | |
411 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
412 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
413 DCM_OpticalPathSequence.getElement()), | |
414 json, false, encoding)); | |
415 if (!dataset.insert(element.release()).good()) | |
416 { | |
417 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
418 } | |
419 } | |
420 | |
421 | |
422 std::string profile; | |
423 if (parameters.GetIccProfilePath().empty()) | |
424 { | |
425 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
426 } | |
427 else | |
428 { | |
43 | 429 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
0 | 430 } |
431 | |
432 | |
433 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
434 if (opticalPath == NULL) | |
435 { | |
436 LOG(ERROR) << "No optical path specified"; | |
437 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
438 } | |
439 | |
440 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
441 { | |
442 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
443 | |
444 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
445 !opticalPath->insert(icc.release()).good()) | |
446 { | |
447 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
448 } | |
449 } | |
450 | |
451 const char* opticalPathId = NULL; | |
452 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
453 opticalPathId == NULL) | |
454 { | |
455 LOG(ERROR) << "No identifier in the optical path"; | |
456 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
457 } | |
458 | |
459 SetupDimension(dataset, opticalPathId, source, volume); | |
460 } | |
461 | |
462 | |
463 static bool ParseParameters(int& exitStatus, | |
464 OrthancWSI::DicomizerParameters& parameters, | |
465 OrthancWSI::ImagedVolumeParameters& volume, | |
466 int argc, | |
467 char* argv[]) | |
468 { | |
469 // Declare the supported parameters | |
470 boost::program_options::options_description generic("Generic options"); | |
471 generic.add_options() | |
472 ("help", "Display this help and exit") | |
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473 ("version", "Output version information and exit") |
0 | 474 ("verbose", "Be verbose in logs") |
475 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), | |
476 "Number of processing threads to be used") | |
477 ("openslide", boost::program_options::value<std::string>(), | |
478 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)") | |
479 ; | |
480 | |
481 boost::program_options::options_description source("Options for the source image"); | |
482 source.add_options() | |
483 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset") | |
484 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit") | |
31 | 485 ("reencode", boost::program_options::value<bool>(), "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
0 | 486 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)") |
487 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")") | |
488 ; | |
489 | |
490 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
491 pyramid.add_options() | |
492 ("pyramid", boost::program_options::value<bool>()->default_value(false), | |
493 "Reconstruct the full pyramid (slow) (Boolean)") | |
494 ("smooth", boost::program_options::value<bool>()->default_value(false), | |
495 "Apply smoothing when reconstructing the pyramid " | |
496 "(slower, but higher quality) (Boolean)") | |
497 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid") | |
498 ; | |
499 | |
500 boost::program_options::options_description target("Options for the target image"); | |
501 target.add_options() | |
502 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image") | |
503 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image") | |
504 ("compression", boost::program_options::value<std::string>(), | |
505 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") | |
506 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)") | |
507 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)") | |
508 ("folder", boost::program_options::value<std::string>(), | |
509 "Folder where to store the output DICOM instances") | |
510 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), | |
511 "Pattern for the files in the output folder") | |
512 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
513 "URL to the REST API of the target Orthanc server") | |
514 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server") | |
515 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server") | |
516 ; | |
517 | |
518 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
519 volumeOptions.add_options() | |
520 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)") | |
521 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)") | |
522 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)") | |
523 ("offset-x", boost::program_options::value<float>()->default_value(20), | |
524 "X offset the specimen, wrt. slide coordinates origin (in mm)") | |
525 ("offset-y", boost::program_options::value<float>()->default_value(40), | |
526 "Y offset the specimen, wrt. slide coordinates origin (in mm)") | |
527 ; | |
528 | |
529 boost::program_options::options_description advancedOptions("Advanced options"); | |
530 advancedOptions.add_options() | |
531 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"), | |
532 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") | |
533 ("icc-profile", boost::program_options::value<std::string>(), | |
534 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") | |
535 ("safety", boost::program_options::value<bool>()->default_value(true), | |
536 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") | |
537 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading " | |
538 "should be applied (only for performance/memory tuning)") | |
539 ; | |
540 | |
541 boost::program_options::options_description hidden; | |
542 hidden.add_options() | |
543 ("input", boost::program_options::value<std::string>(), "Input file"); | |
544 ; | |
545 | |
546 boost::program_options::options_description allWithoutHidden; | |
547 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions); | |
548 | |
549 boost::program_options::options_description all = allWithoutHidden; | |
550 all.add(hidden); | |
551 | |
552 boost::program_options::positional_options_description positional; | |
553 positional.add("input", 1); | |
554 | |
555 boost::program_options::variables_map options; | |
556 bool error = false; | |
557 | |
558 try | |
559 { | |
560 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
561 options(all).positional(positional).run(), options); | |
562 boost::program_options::notify(options); | |
563 } | |
564 catch (boost::program_options::error& e) | |
565 { | |
566 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
567 error = true; | |
568 } | |
569 | |
570 if (!error && | |
571 options.count("sample-dataset")) | |
572 { | |
573 std::string sample; | |
574 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
575 | |
576 std::cout << std::endl << sample << std::endl; | |
577 | |
578 return false; | |
579 } | |
580 | |
581 if (!error && | |
582 options.count("help") == 0 && | |
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583 options.count("version") == 0 && |
0 | 584 options.count("input") != 1) |
585 { | |
586 LOG(ERROR) << "No input file was specified"; | |
587 error = true; | |
588 } | |
589 | |
590 if (error || options.count("help")) | |
591 { | |
592 std::cout << std::endl | |
593 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
594 << std::endl | |
595 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
596 << std::endl << std::endl | |
597 << "Create a DICOM file from a digital pathology image." | |
598 << std::endl; | |
599 | |
600 std::cout << allWithoutHidden << "\n"; | |
601 | |
602 if (error) | |
603 { | |
604 exitStatus = -1; | |
605 } | |
606 | |
607 return false; | |
608 } | |
609 | |
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610 if (options.count("version")) |
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611 { |
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612 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
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613 return false; |
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614 } |
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615 |
0 | 616 if (options.count("verbose")) |
617 { | |
618 Orthanc::Logging::EnableInfoLevel(true); | |
619 } | |
620 | |
621 if (options.count("openslide")) | |
622 { | |
623 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>()); | |
624 } | |
625 | |
626 if (options.count("pyramid") && | |
627 options["pyramid"].as<bool>()) | |
628 { | |
629 parameters.SetReconstructPyramid(true); | |
630 } | |
631 | |
632 if (options.count("smooth") && | |
633 options["smooth"].as<bool>()) | |
634 { | |
635 parameters.SetSmoothEnabled(true); | |
636 } | |
637 | |
638 if (options.count("safety") && | |
639 options["safety"].as<bool>()) | |
640 { | |
641 parameters.SetSafetyCheck(true); | |
642 } | |
643 | |
644 if (options.count("reencode") && | |
645 options["reencode"].as<bool>()) | |
646 { | |
647 parameters.SetForceReencode(true); | |
648 } | |
649 | |
650 if (options.count("repaint") && | |
651 options["repaint"].as<bool>()) | |
652 { | |
653 parameters.SetRepaintBackground(true); | |
654 } | |
655 | |
656 if (options.count("tile-width") || | |
657 options.count("tile-height")) | |
658 { | |
659 int w = 0; | |
660 if (options.count("tile-width")) | |
661 { | |
662 w = options["tile-width"].as<int>(); | |
663 } | |
664 | |
665 unsigned int h = 0; | |
666 if (options.count("tile-height")) | |
667 { | |
668 h = options["tile-height"].as<int>(); | |
669 } | |
670 | |
671 if (w < 0 || h < 0) | |
672 { | |
673 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
674 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
675 } | |
676 | |
677 parameters.SetTargetTileSize(w, h); | |
678 } | |
679 | |
680 parameters.SetInputFile(options["input"].as<std::string>()); | |
681 | |
682 if (options.count("color")) | |
683 { | |
684 uint8_t r, g, b; | |
685 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>()); | |
686 parameters.SetBackgroundColor(r, g, b); | |
687 } | |
688 | |
689 if (options.count("compression")) | |
690 { | |
691 std::string s = options["compression"].as<std::string>(); | |
692 if (s == "none") | |
693 { | |
694 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
695 } | |
696 else if (s == "jpeg") | |
697 { | |
698 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
699 } | |
700 else if (s == "jpeg2000") | |
701 { | |
702 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
703 } | |
704 else | |
705 { | |
706 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
707 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
708 } | |
709 } | |
710 | |
711 if (options.count("jpeg-quality")) | |
712 { | |
713 parameters.SetJpegQuality(options["jpeg-quality"].as<int>()); | |
714 } | |
715 | |
716 if (options.count("levels")) | |
717 { | |
718 parameters.SetPyramidLevelsCount(options["levels"].as<int>()); | |
719 } | |
720 | |
721 if (options.count("lower-levels")) | |
722 { | |
723 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>()); | |
724 } | |
725 | |
726 if (options.count("threads")) | |
727 { | |
728 parameters.SetThreadsCount(options["threads"].as<int>()); | |
729 } | |
730 | |
731 if (options.count("max-size")) | |
732 { | |
733 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024); | |
734 } | |
735 | |
736 if (options.count("folder")) | |
737 { | |
738 parameters.SetTargetFolder(options["folder"].as<std::string>()); | |
739 } | |
740 | |
741 if (options.count("folder-pattern")) | |
742 { | |
743 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>()); | |
744 } | |
745 | |
746 if (options.count("orthanc")) | |
747 { | |
748 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>()); | |
749 | |
750 if (options.count("username") && | |
751 options.count("password")) | |
752 { | |
753 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>()); | |
754 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>()); | |
755 } | |
756 } | |
757 | |
758 if (options.count("dataset")) | |
759 { | |
760 parameters.SetDatasetPath(options["dataset"].as<std::string>()); | |
761 } | |
762 | |
763 if (options.count("imaged-width")) | |
764 { | |
765 volume.SetWidth(options["imaged-width"].as<float>()); | |
766 } | |
767 | |
768 if (options.count("imaged-height")) | |
769 { | |
770 volume.SetHeight(options["imaged-height"].as<float>()); | |
771 } | |
772 | |
773 if (options.count("imaged-depth")) | |
774 { | |
775 volume.SetDepth(options["imaged-depth"].as<float>()); | |
776 } | |
777 | |
778 if (options.count("offset-x")) | |
779 { | |
780 volume.SetOffsetX(options["offset-x"].as<float>()); | |
781 } | |
782 | |
783 if (options.count("offset-y")) | |
784 { | |
785 volume.SetOffsetY(options["offset-y"].as<float>()); | |
786 } | |
787 | |
788 if (options.count("optical-path")) | |
789 { | |
790 std::string s = options["optical-path"].as<std::string>(); | |
791 if (s == "none") | |
792 { | |
793 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
794 } | |
795 else if (s == "brightfield") | |
796 { | |
797 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
798 } | |
799 else | |
800 { | |
801 LOG(ERROR) << "Unknown optical path definition: " << s; | |
802 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
803 } | |
804 } | |
805 | |
806 if (options.count("icc-profile")) | |
807 { | |
808 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>()); | |
809 } | |
810 | |
811 return true; | |
812 } | |
813 | |
814 | |
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815 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
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816 const std::string& path, |
0 | 817 const OrthancWSI::DicomizerParameters& parameters) |
818 { | |
819 LOG(WARNING) << "The input image is: " << path; | |
820 | |
821 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
822 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
823 | |
824 switch (format) | |
825 { | |
826 case OrthancWSI::ImageCompression_Png: | |
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827 { |
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828 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 829 return new OrthancWSI::TiledPngImage(path, |
830 parameters.GetTargetTileWidth(512), | |
831 parameters.GetTargetTileHeight(512)); | |
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832 } |
0 | 833 |
834 case OrthancWSI::ImageCompression_Jpeg: | |
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835 { |
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836 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 837 return new OrthancWSI::TiledJpegImage(path, |
838 parameters.GetTargetTileWidth(512), | |
839 parameters.GetTargetTileHeight(512)); | |
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840 } |
0 | 841 |
842 case OrthancWSI::ImageCompression_Tiff: | |
843 { | |
844 try | |
845 { | |
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846 std::auto_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
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847 sourceCompression = tiff->GetImageCompression(); |
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848 return tiff.release(); |
0 | 849 } |
850 catch (Orthanc::OrthancException&) | |
851 { | |
852 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
853 } | |
854 } | |
855 | |
856 default: | |
857 break; | |
858 } | |
859 | |
860 try | |
861 { | |
862 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide"; | |
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863 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 864 return new OrthancWSI::OpenSlidePyramid(path, |
865 parameters.GetTargetTileWidth(512), | |
866 parameters.GetTargetTileHeight(512)); | |
867 } | |
868 catch (Orthanc::OrthancException&) | |
869 { | |
870 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
871 return NULL; | |
872 } | |
873 } | |
874 | |
875 | |
876 int main(int argc, char* argv[]) | |
877 { | |
878 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
879 | |
880 int exitStatus = 0; | |
881 | |
882 try | |
883 { | |
884 OrthancWSI::DicomizerParameters parameters; | |
885 OrthancWSI::ImagedVolumeParameters volume; | |
886 | |
887 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
888 { | |
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889 OrthancWSI::ImageCompression sourceCompression; |
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890 std::auto_ptr<OrthancWSI::ITiledPyramid> source; |
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891 |
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892 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
0 | 893 if (source.get() == NULL) |
894 { | |
895 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
896 } | |
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897 |
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898 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
0 | 899 |
900 // Create the shared DICOM tags | |
901 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); | |
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902 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
0 | 903 |
904 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
905 Recompress(*output, *source, *dataset, parameters, volume); | |
906 } | |
907 } | |
908 catch (Orthanc::OrthancException& e) | |
909 { | |
910 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
911 exitStatus = -1; | |
912 } | |
913 | |
914 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
915 | |
916 return exitStatus; | |
917 } |