Mercurial > hg > orthanc-wsi
annotate Framework/Outputs/HierarchicalTiffWriter.cpp @ 214:1e864138f0da
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 06 Jan 2021 18:10:07 +0100 |
parents | f299c191cd76 |
children | 49f647ed1b4c |
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 | |
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
16
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22 #include "../PrecompiledHeadersWSI.h" |
0 | 23 #include "HierarchicalTiffWriter.h" |
24 | |
192 | 25 #include <Logging.h> |
26 #include <OrthancException.h> | |
27 #include <TemporaryFile.h> | |
0 | 28 |
29 namespace OrthancWSI | |
30 { | |
31 class HierarchicalTiffWriter::PendingTile | |
32 { | |
33 private: | |
43 | 34 HierarchicalTiffWriter& that_; |
35 unsigned int level_; | |
36 unsigned int tileX_; | |
37 unsigned int tileY_; | |
38 Orthanc::TemporaryFile file_; | |
0 | 39 |
40 public: | |
41 PendingTile(HierarchicalTiffWriter& that, | |
42 unsigned int level, | |
43 unsigned int tileX, | |
44 unsigned int tileY, | |
45 const std::string& tile) : | |
46 that_(that), | |
47 level_(level), | |
48 tileX_(tileX), | |
49 tileY_(tileY) | |
50 { | |
51 file_.Write(tile); | |
52 } | |
53 | |
54 unsigned int GetLevel() const | |
55 { | |
56 return level_; | |
57 } | |
58 | |
59 unsigned int GetTileX() const | |
60 { | |
61 return tileX_; | |
62 } | |
63 | |
64 unsigned int GetTileY() const | |
65 { | |
66 return tileY_; | |
67 } | |
68 | |
69 void Store(TIFF* tiff) | |
70 { | |
71 std::string tile; | |
72 file_.Read(tile); | |
73 that_.StoreTile(tile, tileX_, tileY_); | |
74 } | |
75 }; | |
76 | |
77 | |
78 struct HierarchicalTiffWriter::Comparator | |
79 { | |
80 inline bool operator() (PendingTile* const& a, | |
81 PendingTile* const& b) | |
82 { | |
83 if (a->GetLevel() < b->GetLevel()) | |
84 { | |
85 return true; | |
86 } | |
87 | |
88 if (a->GetLevel() > b->GetLevel()) | |
89 { | |
90 return false; | |
91 } | |
92 | |
93 if (a->GetTileY() < b->GetTileY()) | |
94 { | |
95 return true; | |
96 } | |
97 | |
98 if (a->GetTileY() > b->GetTileY()) | |
99 { | |
100 return false; | |
101 } | |
102 | |
103 return a->GetTileX() < b->GetTileX(); | |
104 } | |
105 }; | |
106 | |
107 | |
108 static uint8_t GetUint8(const std::string& tile, | |
109 size_t index) | |
110 { | |
111 if (index >= tile.size()) | |
112 { | |
113 return 0; | |
114 } | |
115 else | |
116 { | |
117 return static_cast<uint8_t>(tile[index]); | |
118 } | |
119 } | |
120 | |
121 | |
122 #if 0 | |
123 static uint16_t GetUint16(const std::string& tile, | |
124 size_t index) | |
125 { | |
126 if (index + 1 >= tile.size()) | |
127 { | |
128 return 0; | |
129 } | |
130 else | |
131 { | |
132 return static_cast<uint16_t>(tile[index]) * 256 + static_cast<uint16_t>(tile[index + 1]); | |
133 } | |
134 } | |
135 #endif | |
136 | |
137 | |
138 static void CheckJpegTile(const std::string& tile, | |
139 Orthanc::PixelFormat pixelFormat) | |
140 { | |
141 // Check the sampling by accessing the "Start of Frame" header of JPEG | |
142 | |
143 if (tile.size() < 3 || | |
144 static_cast<uint8_t>(tile[0]) != 0xff || | |
145 static_cast<uint8_t>(tile[1]) != 0xd8 || | |
146 static_cast<uint8_t>(tile[2]) != 0xff) | |
147 { | |
148 LOG(WARNING) << "The source image does not contain JPEG tiles"; | |
149 return; | |
150 } | |
151 | |
152 // Look for the "Start of Frame" header (FF C0) | |
153 for (size_t i = 2; i + 1 < tile.size(); i++) | |
154 { | |
155 if (static_cast<uint8_t>(tile[i]) == 0xff && | |
156 static_cast<uint8_t>(tile[i + 1]) == 0xc0) | |
157 { | |
158 uint8_t numberOfComponents = GetUint8(tile, i + 9); | |
159 | |
160 switch (pixelFormat) | |
161 { | |
162 case Orthanc::PixelFormat_Grayscale8: | |
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163 if (numberOfComponents != 1) |
0 | 164 { |
165 LOG(WARNING) << "The source image does not contain a grayscale image as expected"; | |
166 } | |
167 break; | |
168 | |
169 case Orthanc::PixelFormat_RGB24: | |
170 { | |
171 if (numberOfComponents != 3) | |
172 { | |
173 LOG(WARNING) << "The source image does not contain a RGB24 color image as expected"; | |
174 } | |
175 | |
176 // Read the header corresponding to the first component | |
177 const size_t component = 0; | |
178 const size_t offset = i + 10 + component * 3; | |
179 const uint8_t sampling = GetUint8(tile, offset + 1); | |
180 const int samplingH = sampling / 16; | |
181 const int samplingV = sampling % 16; | |
182 | |
183 LOG(WARNING) << "The source image uses chroma sampling " << samplingH << ":" << samplingV; | |
184 | |
185 if (samplingH != 2 || | |
186 samplingV != 2) | |
187 { | |
188 LOG(WARNING) << "The source image has not a chroma sampling of 2:2, " | |
189 << "you should consider using option \"--reencode\""; | |
190 } | |
191 | |
192 break; | |
193 } | |
194 | |
195 default: | |
196 break; | |
197 } | |
198 } | |
199 } | |
200 } | |
201 | |
202 | |
203 | |
204 void HierarchicalTiffWriter::StoreTile(const std::string& tile, | |
205 unsigned int tileX, | |
206 unsigned int tileY) | |
207 { | |
208 // Get the index of the tile | |
209 ttile_t index = TIFFComputeTile(tiff_, tileX * GetTileWidth(), tileY * GetTileHeight(), 0 /*z*/, 0 /*sample*/); | |
210 | |
211 if (TIFFWriteRawTile(tiff_, index, tile.size() ? const_cast<char*>(&tile[0]) : NULL, tile.size()) != | |
212 static_cast<tsize_t>(tile.size())) | |
213 { | |
214 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
215 } | |
216 | |
217 if (isFirst_ && | |
218 GetImageCompression() == ImageCompression_Jpeg) | |
219 { | |
220 CheckJpegTile(tile, GetPixelFormat()); | |
221 } | |
222 | |
223 isFirst_ = false; | |
224 } | |
225 | |
226 | |
227 void HierarchicalTiffWriter::ConfigureLevel(const Level& level, | |
228 bool createLevel) | |
229 { | |
230 if (createLevel && TIFFWriteDirectory(tiff_) != 1) | |
231 { | |
232 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
233 } | |
234 | |
235 if (TIFFFlush(tiff_) != 1) | |
236 { | |
237 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
238 } | |
239 | |
240 currentLevel_ = level.z_; | |
241 nextX_ = 0; | |
242 nextY_ = 0; | |
243 | |
244 switch (GetImageCompression()) | |
245 { | |
246 case ImageCompression_Jpeg: | |
247 { | |
248 uint16_t c = COMPRESSION_JPEG; | |
249 | |
250 if (TIFFSetField(tiff_, TIFFTAG_COMPRESSION, c) != 1) | |
251 { | |
252 Close(); | |
253 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
254 } | |
255 | |
256 break; | |
257 } | |
258 | |
259 default: | |
260 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
261 } | |
262 | |
263 | |
264 switch (GetPixelFormat()) | |
265 { | |
266 case Orthanc::PixelFormat_RGB24: | |
267 { | |
268 uint16_t samplesPerPixel = 3; | |
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269 uint16_t photometric; |
0 | 270 uint16_t planar = PLANARCONFIG_CONTIG; // Interleaved RGB |
271 uint16_t bpp = 8; | |
272 uint16_t subsampleHorizontal = 2; | |
273 uint16_t subsampleVertical = 2; | |
274 | |
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275 switch (photometric_) |
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276 { |
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277 case Orthanc::PhotometricInterpretation_YBRFull422: |
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278 photometric = PHOTOMETRIC_YCBCR; |
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279 break; |
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280 |
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281 case Orthanc::PhotometricInterpretation_RGB: |
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282 photometric = PHOTOMETRIC_RGB; |
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283 break; |
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284 |
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285 default: |
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286 throw Orthanc::OrthancException( |
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287 Orthanc::ErrorCode_ParameterOutOfRange, |
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288 "Unsupported photometric interpreation: " + |
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289 std::string(Orthanc::EnumerationToString(photometric_))); |
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290 } |
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291 |
0 | 292 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
293 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || | |
294 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1 || | |
295 TIFFSetField(tiff_, TIFFTAG_PLANARCONFIG, planar) != 1 || | |
296 TIFFSetField(tiff_, TIFFTAG_YCBCRSUBSAMPLING, subsampleHorizontal, subsampleVertical) != 1) | |
297 { | |
298 Close(); | |
299 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
300 } | |
301 | |
302 break; | |
303 } | |
304 | |
170
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305 case Orthanc::PixelFormat_Grayscale8: |
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306 { |
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307 uint16_t samplesPerPixel = 1; |
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308 uint16_t bpp = 8; |
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309 uint16_t photometric = PHOTOMETRIC_MINISBLACK; |
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310 |
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311 if (TIFFSetField(tiff_, TIFFTAG_SAMPLESPERPIXEL, samplesPerPixel) != 1 || |
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312 TIFFSetField(tiff_, TIFFTAG_PHOTOMETRIC, photometric) != 1 || |
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313 TIFFSetField(tiff_, TIFFTAG_BITSPERSAMPLE, bpp) != 1) |
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314 { |
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315 Close(); |
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316 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); |
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317 } |
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318 |
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319 break; |
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320 } |
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321 |
0 | 322 default: |
323 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
324 } | |
325 | |
326 uint32_t w = level.width_; | |
327 uint32_t h = level.height_; | |
328 uint32_t tw = GetTileWidth(); | |
329 uint32_t th = GetTileHeight(); | |
330 | |
331 if (TIFFSetField(tiff_, TIFFTAG_IMAGEWIDTH, w) != 1 || | |
332 TIFFSetField(tiff_, TIFFTAG_IMAGELENGTH, h) != 1 || | |
333 TIFFSetField(tiff_, TIFFTAG_TILEWIDTH, tw) != 1 || | |
334 TIFFSetField(tiff_, TIFFTAG_TILELENGTH, th) != 1) | |
335 { | |
336 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
337 } | |
338 } | |
339 | |
340 | |
341 void HierarchicalTiffWriter::AdvanceToNextTile() | |
342 { | |
343 assert(currentLevel_ < levels_.size()); | |
344 | |
345 nextX_ += 1; | |
346 if (nextX_ >= levels_[currentLevel_].countTilesX_) | |
347 { | |
348 nextX_ = 0; | |
349 nextY_ += 1; | |
350 | |
351 if (nextY_ >= levels_[currentLevel_].countTilesY_) | |
352 { | |
353 currentLevel_ += 1; | |
354 | |
355 if (currentLevel_ < levels_.size()) | |
356 { | |
357 ConfigureLevel(levels_[currentLevel_], true); | |
358 } | |
359 } | |
360 } | |
361 } | |
362 | |
363 | |
364 void HierarchicalTiffWriter::ScanPending() | |
365 { | |
366 std::sort(pending_.begin(), pending_.end(), Comparator()); | |
367 | |
368 while (currentLevel_ < levels_.size() && | |
369 !pending_.empty() && | |
370 pending_.front()->GetLevel() == currentLevel_ && | |
371 pending_.front()->GetTileX() == nextX_ && | |
372 pending_.front()->GetTileY() == nextY_) | |
373 { | |
374 pending_.front()->Store(tiff_); | |
375 delete pending_.front(); | |
376 pending_.pop_front(); | |
377 AdvanceToNextTile(); | |
378 } | |
379 } | |
380 | |
381 | |
382 void HierarchicalTiffWriter::WriteRawTileInternal(const std::string& tile, | |
383 const Level& level, | |
384 unsigned int tileX, | |
385 unsigned int tileY) | |
386 { | |
387 boost::mutex::scoped_lock lock(mutex_); | |
388 | |
389 if (level.z_ == currentLevel_ && | |
390 tileX == nextX_ && | |
391 tileY == nextY_) | |
392 { | |
393 StoreTile(tile, tileX, tileY); | |
394 AdvanceToNextTile(); | |
395 ScanPending(); | |
396 } | |
397 else | |
398 { | |
399 pending_.push_back(new PendingTile(*this, level.z_, tileX, tileY, tile)); | |
400 } | |
401 } | |
402 | |
403 | |
404 void HierarchicalTiffWriter::AddLevelInternal(const Level& level) | |
405 { | |
406 if (level.z_ == 0) | |
407 { | |
408 // Configure the finest level on initialization | |
409 ConfigureLevel(level, false); | |
410 } | |
411 | |
412 levels_.push_back(level); | |
413 } | |
414 | |
415 | |
416 HierarchicalTiffWriter::HierarchicalTiffWriter(const std::string& path, | |
417 Orthanc::PixelFormat pixelFormat, | |
418 ImageCompression compression, | |
419 unsigned int tileWidth, | |
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420 unsigned int tileHeight, |
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421 Orthanc::PhotometricInterpretation photometric) : |
0 | 422 PyramidWriterBase(pixelFormat, compression, tileWidth, tileHeight), |
423 currentLevel_(0), | |
145 | 424 nextX_(0), |
425 nextY_(0), | |
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426 isFirst_(true), |
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427 photometric_(photometric) |
0 | 428 { |
429 tiff_ = TIFFOpen(path.c_str(), "w"); | |
430 if (tiff_ == NULL) | |
431 { | |
432 throw Orthanc::OrthancException(Orthanc::ErrorCode_CannotWriteFile); | |
433 } | |
434 } | |
435 | |
436 | |
437 HierarchicalTiffWriter::~HierarchicalTiffWriter() | |
438 { | |
439 if (pending_.size()) | |
440 { | |
441 LOG(ERROR) << "Some tiles (" << pending_.size() << ") were not written to the TIFF file"; | |
442 } | |
443 | |
444 for (size_t i = 0; i < pending_.size(); i++) | |
445 { | |
446 if (pending_[i]) | |
447 { | |
448 delete pending_[i]; | |
449 } | |
450 } | |
451 | |
452 Close(); | |
453 } | |
454 | |
455 | |
456 void HierarchicalTiffWriter::Flush() | |
457 { | |
458 boost::mutex::scoped_lock lock(mutex_); | |
459 ScanPending(); | |
460 } | |
461 } |