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comparison Applications/Dicomizer.cpp @ 0:4a7a53257c7d

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initial commit
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 22 Oct 2016 21:48:33 +0200
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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() ||
302 !item->insert(a1.release(), uid.c_str()).good() ||
303 !item->insert(a2.release(), uid.c_str()).good() ||
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")
456 ("verbose", "Be verbose in logs")
457 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()),
458 "Number of processing threads to be used")
459 ("openslide", boost::program_options::value<std::string>(),
460 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)")
461 ;
462
463 boost::program_options::options_description source("Options for the source image");
464 source.add_options()
465 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset")
466 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit")
467 ("reencode", boost::program_options::value<bool>(), "Whether to reencode each tile (no transcoding, much slower) (Boolean)")
468 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)")
469 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")")
470 ;
471
472 boost::program_options::options_description pyramid("Options to construct the pyramid");
473 pyramid.add_options()
474 ("pyramid", boost::program_options::value<bool>()->default_value(false),
475 "Reconstruct the full pyramid (slow) (Boolean)")
476 ("smooth", boost::program_options::value<bool>()->default_value(false),
477 "Apply smoothing when reconstructing the pyramid "
478 "(slower, but higher quality) (Boolean)")
479 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid")
480 ;
481
482 boost::program_options::options_description target("Options for the target image");
483 target.add_options()
484 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image")
485 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image")
486 ("compression", boost::program_options::value<std::string>(),
487 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")")
488 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)")
489 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB)")
490 ("folder", boost::program_options::value<std::string>(),
491 "Folder where to store the output DICOM instances")
492 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"),
493 "Pattern for the files in the output folder")
494 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
495 "URL to the REST API of the target Orthanc server")
496 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server")
497 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server")
498 ;
499
500 boost::program_options::options_description volumeOptions("Description of the imaged volume");
501 volumeOptions.add_options()
502 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)")
503 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)")
504 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)")
505 ("offset-x", boost::program_options::value<float>()->default_value(20),
506 "X offset the specimen, wrt. slide coordinates origin (in mm)")
507 ("offset-y", boost::program_options::value<float>()->default_value(40),
508 "Y offset the specimen, wrt. slide coordinates origin (in mm)")
509 ;
510
511 boost::program_options::options_description advancedOptions("Advanced options");
512 advancedOptions.add_options()
513 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"),
514 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")")
515 ("icc-profile", boost::program_options::value<std::string>(),
516 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.")
517 ("safety", boost::program_options::value<bool>()->default_value(true),
518 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)")
519 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading "
520 "should be applied (only for performance/memory tuning)")
521 ;
522
523 boost::program_options::options_description hidden;
524 hidden.add_options()
525 ("input", boost::program_options::value<std::string>(), "Input file");
526 ;
527
528 boost::program_options::options_description allWithoutHidden;
529 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions);
530
531 boost::program_options::options_description all = allWithoutHidden;
532 all.add(hidden);
533
534 boost::program_options::positional_options_description positional;
535 positional.add("input", 1);
536
537 boost::program_options::variables_map options;
538 bool error = false;
539
540 try
541 {
542 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
543 options(all).positional(positional).run(), options);
544 boost::program_options::notify(options);
545 }
546 catch (boost::program_options::error& e)
547 {
548 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
549 error = true;
550 }
551
552 if (!error &&
553 options.count("sample-dataset"))
554 {
555 std::string sample;
556 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET);
557
558 std::cout << std::endl << sample << std::endl;
559
560 return false;
561 }
562
563 if (!error &&
564 options.count("help") == 0 &&
565 options.count("input") != 1)
566 {
567 LOG(ERROR) << "No input file was specified";
568 error = true;
569 }
570
571 if (error || options.count("help"))
572 {
573 std::cout << std::endl
574 << "Usage: " << argv[0] << " [OPTION]... [INPUT]"
575 << std::endl
576 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
577 << std::endl << std::endl
578 << "Create a DICOM file from a digital pathology image."
579 << std::endl;
580
581 std::cout << allWithoutHidden << "\n";
582
583 if (error)
584 {
585 exitStatus = -1;
586 }
587
588 return false;
589 }
590
591 if (options.count("verbose"))
592 {
593 Orthanc::Logging::EnableInfoLevel(true);
594 }
595
596 if (options.count("openslide"))
597 {
598 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>());
599 }
600
601 if (options.count("pyramid") &&
602 options["pyramid"].as<bool>())
603 {
604 parameters.SetReconstructPyramid(true);
605 }
606
607 if (options.count("smooth") &&
608 options["smooth"].as<bool>())
609 {
610 parameters.SetSmoothEnabled(true);
611 }
612
613 if (options.count("safety") &&
614 options["safety"].as<bool>())
615 {
616 parameters.SetSafetyCheck(true);
617 }
618
619 if (options.count("reencode") &&
620 options["reencode"].as<bool>())
621 {
622 parameters.SetForceReencode(true);
623 }
624
625 if (options.count("repaint") &&
626 options["repaint"].as<bool>())
627 {
628 parameters.SetRepaintBackground(true);
629 }
630
631 if (options.count("tile-width") ||
632 options.count("tile-height"))
633 {
634 int w = 0;
635 if (options.count("tile-width"))
636 {
637 w = options["tile-width"].as<int>();
638 }
639
640 unsigned int h = 0;
641 if (options.count("tile-height"))
642 {
643 h = options["tile-height"].as<int>();
644 }
645
646 if (w < 0 || h < 0)
647 {
648 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h;
649 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
650 }
651
652 parameters.SetTargetTileSize(w, h);
653 }
654
655 parameters.SetInputFile(options["input"].as<std::string>());
656
657 if (options.count("color"))
658 {
659 uint8_t r, g, b;
660 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>());
661 parameters.SetBackgroundColor(r, g, b);
662 }
663
664 if (options.count("compression"))
665 {
666 std::string s = options["compression"].as<std::string>();
667 if (s == "none")
668 {
669 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None);
670 }
671 else if (s == "jpeg")
672 {
673 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg);
674 }
675 else if (s == "jpeg2000")
676 {
677 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000);
678 }
679 else
680 {
681 LOG(ERROR) << "Unknown image compression for the target image: " << s;
682 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
683 }
684 }
685
686 if (options.count("jpeg-quality"))
687 {
688 parameters.SetJpegQuality(options["jpeg-quality"].as<int>());
689 }
690
691 if (options.count("levels"))
692 {
693 parameters.SetPyramidLevelsCount(options["levels"].as<int>());
694 }
695
696 if (options.count("lower-levels"))
697 {
698 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>());
699 }
700
701 if (options.count("threads"))
702 {
703 parameters.SetThreadsCount(options["threads"].as<int>());
704 }
705
706 if (options.count("max-size"))
707 {
708 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024);
709 }
710
711 if (options.count("folder"))
712 {
713 parameters.SetTargetFolder(options["folder"].as<std::string>());
714 }
715
716 if (options.count("folder-pattern"))
717 {
718 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>());
719 }
720
721 if (options.count("orthanc"))
722 {
723 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>());
724
725 if (options.count("username") &&
726 options.count("password"))
727 {
728 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>());
729 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>());
730 }
731 }
732
733 if (options.count("dataset"))
734 {
735 parameters.SetDatasetPath(options["dataset"].as<std::string>());
736 }
737
738 if (options.count("imaged-width"))
739 {
740 volume.SetWidth(options["imaged-width"].as<float>());
741 }
742
743 if (options.count("imaged-height"))
744 {
745 volume.SetHeight(options["imaged-height"].as<float>());
746 }
747
748 if (options.count("imaged-depth"))
749 {
750 volume.SetDepth(options["imaged-depth"].as<float>());
751 }
752
753 if (options.count("offset-x"))
754 {
755 volume.SetOffsetX(options["offset-x"].as<float>());
756 }
757
758 if (options.count("offset-y"))
759 {
760 volume.SetOffsetY(options["offset-y"].as<float>());
761 }
762
763 if (options.count("optical-path"))
764 {
765 std::string s = options["optical-path"].as<std::string>();
766 if (s == "none")
767 {
768 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None);
769 }
770 else if (s == "brightfield")
771 {
772 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield);
773 }
774 else
775 {
776 LOG(ERROR) << "Unknown optical path definition: " << s;
777 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
778 }
779 }
780
781 if (options.count("icc-profile"))
782 {
783 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>());
784 }
785
786 return true;
787 }
788
789
790 OrthancWSI::ITiledPyramid* OpenInputPyramid(const std::string& path,
791 const OrthancWSI::DicomizerParameters& parameters)
792 {
793 LOG(WARNING) << "The input image is: " << path;
794
795 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path);
796 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format);
797
798 switch (format)
799 {
800 case OrthancWSI::ImageCompression_Png:
801 return new OrthancWSI::TiledPngImage(path,
802 parameters.GetTargetTileWidth(512),
803 parameters.GetTargetTileHeight(512));
804
805 case OrthancWSI::ImageCompression_Jpeg:
806 return new OrthancWSI::TiledJpegImage(path,
807 parameters.GetTargetTileWidth(512),
808 parameters.GetTargetTileHeight(512));
809
810 case OrthancWSI::ImageCompression_Tiff:
811 {
812 try
813 {
814 return new OrthancWSI::HierarchicalTiff(path);
815 }
816 catch (Orthanc::OrthancException&)
817 {
818 LOG(WARNING) << "This is not a standard hierarchical TIFF file";
819 }
820 }
821
822 default:
823 break;
824 }
825
826 try
827 {
828 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide";
829 return new OrthancWSI::OpenSlidePyramid(path,
830 parameters.GetTargetTileWidth(512),
831 parameters.GetTargetTileHeight(512));
832 }
833 catch (Orthanc::OrthancException&)
834 {
835 LOG(ERROR) << "This file is not supported by OpenSlide";
836 return NULL;
837 }
838 }
839
840
841 int main(int argc, char* argv[])
842 {
843 OrthancWSI::ApplicationToolbox::GlobalInitialize();
844
845 int exitStatus = 0;
846
847 try
848 {
849 OrthancWSI::DicomizerParameters parameters;
850 OrthancWSI::ImagedVolumeParameters volume;
851
852 if (ParseParameters(exitStatus, parameters, volume, argc, argv))
853 {
854 std::auto_ptr<OrthancWSI::ITiledPyramid> source(OpenInputPyramid(parameters.GetInputFile(), parameters));
855 if (source.get() == NULL)
856 {
857 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
858 }
859
860 // Create the shared DICOM tags
861 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath()));
862 EnrichDataset(*dataset, *source, parameters, volume);
863
864 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget());
865 Recompress(*output, *source, *dataset, parameters, volume);
866 }
867 }
868 catch (Orthanc::OrthancException& e)
869 {
870 LOG(ERROR) << "Terminating on exception: " << e.What();
871 exitStatus = -1;
872 }
873
874 OrthancWSI::ApplicationToolbox::GlobalFinalize();
875
876 return exitStatus;
877 }