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annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 334:f011fc199b6a default tip
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 18 Oct 2024 15:44:18 +0200 |
parents | 0683312e21ba |
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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 | |
312
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 8 * |
9 * This program is free software: you can redistribute it and/or | |
10 * modify it under the terms of the GNU Affero General Public License | |
11 * as published by the Free Software Foundation, either version 3 of | |
12 * the License, or (at your option) any later version. | |
13 * | |
14 * This program is distributed in the hope that it will be useful, but | |
15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
17 * Affero General Public License for more details. | |
18 * | |
19 * You should have received a copy of the GNU Affero General Public License | |
20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
21 **/ | |
22 | |
23 | |
16
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24 #include "../PrecompiledHeadersWSI.h" |
0 | 25 #include "HierarchicalTiffWriter.h" |
26 | |
192 | 27 #include <Logging.h> |
28 #include <OrthancException.h> | |
29 #include <TemporaryFile.h> | |
0 | 30 |
31 namespace OrthancWSI | |
32 { | |
33 class HierarchicalTiffWriter::PendingTile | |
34 { | |
35 private: | |
43 | 36 HierarchicalTiffWriter& that_; |
37 unsigned int level_; | |
38 unsigned int tileX_; | |
39 unsigned int tileY_; | |
40 Orthanc::TemporaryFile file_; | |
0 | 41 |
42 public: | |
43 PendingTile(HierarchicalTiffWriter& that, | |
44 unsigned int level, | |
45 unsigned int tileX, | |
46 unsigned int tileY, | |
47 const std::string& tile) : | |
48 that_(that), | |
49 level_(level), | |
50 tileX_(tileX), | |
51 tileY_(tileY) | |
52 { | |
53 file_.Write(tile); | |
54 } | |
55 | |
56 unsigned int GetLevel() const | |
57 { | |
58 return level_; | |
59 } | |
60 | |
61 unsigned int GetTileX() const | |
62 { | |
63 return tileX_; | |
64 } | |
65 | |
66 unsigned int GetTileY() const | |
67 { | |
68 return tileY_; | |
69 } | |
70 | |
71 void Store(TIFF* tiff) | |
72 { | |
73 std::string tile; | |
74 file_.Read(tile); | |
75 that_.StoreTile(tile, tileX_, tileY_); | |
76 } | |
77 }; | |
78 | |
79 | |
80 struct HierarchicalTiffWriter::Comparator | |
81 { | |
82 inline bool operator() (PendingTile* const& a, | |
83 PendingTile* const& b) | |
84 { | |
85 if (a->GetLevel() < b->GetLevel()) | |
86 { | |
87 return true; | |
88 } | |
89 | |
90 if (a->GetLevel() > b->GetLevel()) | |
91 { | |
92 return false; | |
93 } | |
94 | |
95 if (a->GetTileY() < b->GetTileY()) | |
96 { | |
97 return true; | |
98 } | |
99 | |
100 if (a->GetTileY() > b->GetTileY()) | |
101 { | |
102 return false; | |
103 } | |
104 | |
105 return a->GetTileX() < b->GetTileX(); | |
106 } | |
107 }; | |
108 | |
109 | |
110 static uint8_t GetUint8(const std::string& tile, | |
111 size_t index) | |
112 { | |
113 if (index >= tile.size()) | |
114 { | |
115 return 0; | |
116 } | |
117 else | |
118 { | |
119 return static_cast<uint8_t>(tile[index]); | |
120 } | |
121 } | |
122 | |
123 | |
124 #if 0 | |
125 static uint16_t GetUint16(const std::string& tile, | |
126 size_t index) | |
127 { | |
128 if (index + 1 >= tile.size()) | |
129 { | |
130 return 0; | |
131 } | |
132 else | |
133 { | |
134 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
135 } | |
136 } | |
137 #endif | |
138 | |
139 | |
140 static void CheckJpegTile(const std::string& tile, | |
141 Orthanc::PixelFormat pixelFormat) | |
142 { | |
143 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
144 | |
145 if (tile.size() < 3 || | |
146 static_cast<uint8_t>(tile[0]) != 0xff || | |
147 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
148 static_cast<uint8_t>(tile[2]) != 0xff) | |
149 { | |
150 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
151 return; | |
152 } | |
153 | |
154 // Look for the "Start of Frame" header (FF C0) | |
155 for (size_t i = 2; i + 1 < tile.size(); i++) | |
156 { | |
157 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
158 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
159 { | |
160 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
161 | |
162 switch (pixelFormat) | |
163 { | |
164 case Orthanc::PixelFormat_Grayscale8: | |
170
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165 if (numberOfComponents != 1) |
0 | 166 { |
167 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
168 } | |
169 break; | |
170 | |
171 case Orthanc::PixelFormat_RGB24: | |
172 { | |
173 if (numberOfComponents != 3) | |
174 { | |
175 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
176 } | |
177 | |
178 // Read the header corresponding to the first component | |
179 const size_t component = 0; | |
180 const size_t offset = i + 10 + component * 3; | |
181 const uint8_t sampling = GetUint8(tile, offset + 1); | |
182 const int samplingH = sampling / 16; | |
183 const int samplingV = sampling % 16; | |
184 | |
185 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
186 | |
187 if (samplingH != 2 || | |
188 samplingV != 2) | |
189 { | |
190 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
191 << "you should consider using option \"--reencode\""; | |
192 } | |
193 | |
194 break; | |
195 } | |
196 | |
197 default: | |
198 break; | |
199 } | |
200 } | |
201 } | |
202 } | |
203 | |
204 | |
205 | |
206 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
207 unsigned int tileX, | |
208 unsigned int tileY) | |
209 { | |
210 // Get the index of the tile | |
211 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
212 | |
213 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
214 static_cast<tsize_t>(tile.size())) | |
215 { | |
216 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
217 } | |
218 | |
219 if (isFirst_ && | |
220 GetImageCompression() == ImageCompression_Jpeg) | |
221 { | |
222 CheckJpegTile(tile, GetPixelFormat()); | |
223 } | |
224 | |
225 isFirst_ = false; | |
226 } | |
227 | |
228 | |
229 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
230 bool createLevel) | |
231 { | |
232 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
233 { | |
234 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
235 } | |
236 | |
237 if (TIFFFlush(tiff_) != 1) | |
238 { | |
239 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
240 } | |
241 | |
242 currentLevel_ = level.z_; | |
243 nextX_ = 0; | |
244 nextY_ = 0; | |
245 | |
246 switch (GetImageCompression()) | |
247 { | |
248 case ImageCompression_Jpeg: | |
249 { | |
250 uint16_t c = COMPRESSION_JPEG; | |
251 | |
252 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
253 { | |
254 Close(); | |
255 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
256 } | |
257 | |
258 break; | |
259 } | |
260 | |
261 default: | |
262 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
263 } | |
264 | |
265 | |
266 switch (GetPixelFormat()) | |
267 { | |
268 case Orthanc::PixelFormat_RGB24: | |
269 { | |
270 uint16_t samplesPerPixel = 3; | |
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271 uint16_t photometric; |
0 | 272 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB |
273 uint16_t bpp = 8; | |
274 uint16_t subsampleHorizontal = 2; | |
275 uint16_t subsampleVertical = 2; | |
276 | |
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277 switch (photometric_) |
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278 { |
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279 case Orthanc::PhotometricInterpretation_YBRFull422: |
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280 photometric = PHOTOMETRIC_YCBCR; |
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281 break; |
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282 |
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283 case Orthanc::PhotometricInterpretation_RGB: |
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284 photometric = PHOTOMETRIC_RGB; |
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285 break; |
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286 |
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287 default: |
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288 throw Orthanc::OrthancException( |
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289 Orthanc::ErrorCode_ParameterOutOfRange, |
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290 "Unsupported photometric interpreation: " + |
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291 std::string(Orthanc::EnumerationToString(photometric_))); |
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292 } |
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293 |
0 | 294 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
295 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
296 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
297 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
298 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
299 { | |
300 Close(); | |
301 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
302 } | |
303 | |
304 break; | |
305 } | |
306 | |
170
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307 case Orthanc::PixelFormat_Grayscale8: |
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308 { |
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309 uint16_t samplesPerPixel = 1; |
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310 uint16_t bpp = 8; |
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311 uint16_t photometric = PHOTOMETRIC_MINISBLACK; |
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312 |
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313 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
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314 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || |
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315 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1) |
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316 { |
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317 Close(); |
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318 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); |
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319 } |
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320 |
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321 break; |
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322 } |
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323 |
0 | 324 default: |
325 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
326 } | |
327 | |
328 uint32_t w = level.width_; | |
329 uint32_t h = level.height_; | |
330 uint32_t tw = GetTileWidth(); | |
331 uint32_t th = GetTileHeight(); | |
332 | |
333 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
334 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
335 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
336 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
337 { | |
338 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
339 } | |
340 } | |
341 | |
342 | |
343 void HierarchicalTiffWriter::AdvanceToNextTile() | |
344 { | |
345 assert(currentLevel_ < levels_.size()); | |
346 | |
347 nextX_ += 1; | |
348 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
349 { | |
350 nextX_ = 0; | |
351 nextY_ += 1; | |
352 | |
353 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
354 { | |
355 currentLevel_ += 1; | |
356 | |
357 if (currentLevel_ < levels_.size()) | |
358 { | |
359 ConfigureLevel(levels_[currentLevel_], true); | |
360 } | |
361 } | |
362 } | |
363 } | |
364 | |
365 | |
366 void HierarchicalTiffWriter::ScanPending() | |
367 { | |
368 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
369 | |
370 while (currentLevel_ < levels_.size() && | |
371 !pending_.empty() && | |
372 pending_.front()->GetLevel() == currentLevel_ && | |
373 pending_.front()->GetTileX() == nextX_ && | |
374 pending_.front()->GetTileY() == nextY_) | |
375 { | |
376 pending_.front()->Store(tiff_); | |
377 delete pending_.front(); | |
378 pending_.pop_front(); | |
379 AdvanceToNextTile(); | |
380 } | |
381 } | |
382 | |
383 | |
384 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
385 const Level& level, | |
386 unsigned int tileX, | |
387 unsigned int tileY) | |
388 { | |
389 boost::mutex::scoped_lock lock(mutex_); | |
390 | |
391 if (level.z_ == currentLevel_ && | |
392 tileX == nextX_ && | |
393 tileY == nextY_) | |
394 { | |
395 StoreTile(tile, tileX, tileY); | |
396 AdvanceToNextTile(); | |
397 ScanPending(); | |
398 } | |
399 else | |
400 { | |
401 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
402 } | |
403 } | |
404 | |
405 | |
406 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
407 { | |
408 if (level.z_ == 0) | |
409 { | |
410 // Configure the finest level on initialization | |
411 ConfigureLevel(level, false); | |
412 } | |
413 | |
414 levels_.push_back(level); | |
415 } | |
416 | |
417 | |
418 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
419 Orthanc::PixelFormat pixelFormat, | |
420 ImageCompression compression, | |
421 unsigned int tileWidth, | |
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422 unsigned int tileHeight, |
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423 Orthanc::PhotometricInterpretation photometric) : |
0 | 424 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
425 currentLevel_(0), | |
145 | 426 nextX_(0), |
427 nextY_(0), | |
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428 isFirst_(true), |
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429 photometric_(photometric) |
0 | 430 { |
431 tiff_ = TIFFOpen(path.c_str(), "w"); | |
432 if (tiff_ == NULL) | |
433 { | |
434 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
435 } | |
436 } | |
437 | |
438 | |
439 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
440 { | |
441 if (pending_.size()) | |
442 { | |
443 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
444 } | |
445 | |
446 for (size_t i = 0; i < pending_.size(); i++) | |
447 { | |
448 if (pending_[i]) | |
449 { | |
450 delete pending_[i]; | |
451 } | |
452 } | |
453 | |
454 Close(); | |
455 } | |
456 | |
457 | |
458 void HierarchicalTiffWriter::Flush() | |
459 { | |
460 boost::mutex::scoped_lock lock(mutex_); | |
461 ScanPending(); | |
462 } | |
463 } |