Mercurial > hg > orthanc-wsi
annotate Framework/Jpeg2000Reader.cpp @ 318:8ad12abde290
sparse re-encoding with OpenSlide (notably for MIRAX format)
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 11 Sep 2024 16:11:16 +0200 |
| parents | 0683312e21ba |
| children |
| rev | line source |
|---|---|
| 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) 2017-2023 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 | |
|
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24 #include "PrecompiledHeadersWSI.h" |
| 0 | 25 #include "Jpeg2000Reader.h" |
| 26 | |
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27 #include "ImageToolbox.h" |
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28 |
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29 #include <Compatibility.h> // For std::unique_ptr |
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30 #include <Images/ImageProcessing.h> |
| 192 | 31 #include <OrthancException.h> |
| 32 #include <SystemToolbox.h> | |
| 0 | 33 |
| 34 #include <cassert> | |
| 35 #include <string.h> | |
| 36 #include <openjpeg.h> | |
| 37 | |
| 38 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 39 # define OPJ_CLRSPC_GRAY CLRSPC_GRAY | |
| 40 # define OPJ_CLRSPC_SRGB CLRSPC_SRGB | |
| 41 # define OPJ_CODEC_J2K CODEC_J2K | |
| 42 # define OPJ_CODEC_JP2 CODEC_JP2 | |
| 43 typedef opj_dinfo_t opj_codec_t; | |
| 44 typedef opj_cio_t opj_stream_t; | |
| 45 #elif ORTHANC_OPENJPEG_MAJOR_VERSION == 2 | |
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46 // OK, no need for compatibility macros |
| 0 | 47 #else |
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48 # error Unsupported version of OpenJpeg |
| 0 | 49 #endif |
| 50 | |
| 51 | |
| 52 namespace OrthancWSI | |
| 53 { | |
| 54 namespace | |
| 55 { | |
| 56 // Check out opj_dparameters_t::decod_format | |
| 57 enum InputFormat | |
| 58 { | |
| 59 InputFormat_J2K = 0, | |
| 60 InputFormat_JP2 = 1, | |
| 61 InputFormat_JPT = 2 | |
| 62 }; | |
| 63 | |
| 64 enum OutputFormat | |
| 65 { | |
| 66 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 67 OutputFormat_PGX = 1 | |
| 68 #else | |
| 69 OutputFormat_PGX = 11 | |
| 70 #endif | |
| 71 }; | |
| 72 | |
| 73 class OpenJpegDecoder : public boost::noncopyable | |
| 74 { | |
| 75 private: | |
| 76 opj_dparameters_t parameters_; | |
| 77 opj_codec_t* dinfo_; | |
| 78 | |
| 79 void SetupParameters(InputFormat format) | |
| 80 { | |
| 81 opj_set_default_decoder_parameters(¶meters_); | |
| 82 | |
| 83 parameters_.decod_format = format; | |
| 84 parameters_.cod_format = OutputFormat_PGX; | |
| 85 | |
| 86 #if OPENJPEG_MAJOR_VERSION == 1 | |
| 87 parameters_.cp_layer = 0; | |
| 88 parameters_.cp_reduce = 0; | |
| 89 #endif | |
| 90 } | |
| 91 | |
| 92 void Finalize() | |
| 93 { | |
| 94 if (dinfo_ != NULL) | |
| 95 { | |
| 96 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 97 opj_destroy_decompress(dinfo_); | |
| 98 #else | |
| 99 opj_destroy_codec(dinfo_); | |
| 100 #endif | |
| 101 dinfo_ = NULL; | |
| 102 } | |
| 103 } | |
| 104 | |
| 105 public: | |
| 145 | 106 explicit OpenJpegDecoder(Jpeg2000Format format) : |
| 107 dinfo_(NULL) | |
| 0 | 108 { |
| 109 switch (format) | |
| 110 { | |
| 111 case Jpeg2000Format_J2K: | |
| 112 SetupParameters(InputFormat_J2K); | |
| 113 dinfo_ = opj_create_decompress(OPJ_CODEC_J2K); | |
| 114 break; | |
| 115 | |
| 116 case Jpeg2000Format_JP2: | |
| 117 SetupParameters(InputFormat_JP2); | |
| 118 dinfo_ = opj_create_decompress(OPJ_CODEC_JP2); | |
| 119 break; | |
| 120 | |
| 121 default: | |
| 122 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 123 } | |
| 124 | |
| 125 if (!dinfo_) | |
| 126 { | |
| 127 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 128 } | |
| 129 | |
| 130 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 131 opj_setup_decoder(dinfo_, ¶meters_); | |
| 132 #else | |
| 133 if (!opj_setup_decoder(dinfo_, ¶meters_)) | |
| 134 { | |
| 135 Finalize(); | |
| 136 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 137 } | |
| 138 #endif | |
| 139 } | |
| 140 | |
| 141 ~OpenJpegDecoder() | |
| 142 { | |
| 143 Finalize(); | |
| 144 } | |
| 145 | |
| 146 opj_codec_t* GetObject() | |
| 147 { | |
| 148 return dinfo_; | |
| 149 } | |
| 150 | |
| 151 const opj_dparameters_t& GetParameters() const | |
| 152 { | |
| 153 return parameters_; | |
| 154 } | |
| 155 }; | |
| 156 | |
| 157 | |
| 158 class OpenJpegInput : public boost::noncopyable | |
| 159 { | |
| 160 private: | |
| 161 opj_stream_t* cio_; | |
| 162 | |
| 163 const uint8_t* buffer_; | |
| 164 size_t size_; | |
| 165 size_t position_; | |
| 166 | |
| 167 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 2 | |
| 168 static void Free(void *userData) | |
| 169 { | |
| 170 } | |
| 171 | |
| 172 static OPJ_SIZE_T Read(void *target, | |
| 173 OPJ_SIZE_T size, | |
| 174 void *userData) | |
| 175 { | |
| 176 OpenJpegInput& that = *reinterpret_cast<OpenJpegInput*>(userData); | |
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177 assert(that.position_ <= that.size_); |
| 0 | 178 assert(size >= 0); |
| 179 | |
| 180 if (that.position_ == that.size_) | |
| 181 { | |
| 182 // End of file | |
| 183 return -1; | |
| 184 } | |
| 185 else | |
| 186 { | |
| 187 if (that.position_ + size > that.size_) | |
| 188 { | |
| 189 size = that.size_ - that.position_; | |
| 190 } | |
| 191 | |
| 192 if (size > 0) | |
| 193 { | |
| 194 memcpy(target, that.buffer_ + that.position_, size); | |
| 195 } | |
| 196 | |
| 197 that.position_ += size; | |
| 198 return size; | |
| 199 } | |
| 200 } | |
| 201 | |
| 202 static OPJ_OFF_T Skip(OPJ_OFF_T skip, | |
| 203 void *userData) | |
| 204 { | |
| 205 assert(skip >= 0); | |
| 206 OpenJpegInput& that = *reinterpret_cast<OpenJpegInput*>(userData); | |
| 207 | |
| 208 if (that.position_ == that.size_) | |
| 209 { | |
| 210 // End of file | |
| 211 return -1; | |
| 212 } | |
| 213 else if (that.position_ + skip > that.size_) | |
| 214 { | |
| 215 size_t offset = that.size_ - that.position_; | |
| 216 that.position_ = that.size_; | |
| 217 return offset; | |
| 218 } | |
| 219 else | |
| 220 { | |
| 221 that.position_ += skip; | |
| 222 return skip; | |
| 223 } | |
| 224 } | |
| 225 | |
| 226 static OPJ_BOOL Seek(OPJ_OFF_T position, | |
| 227 void *userData) | |
| 228 { | |
| 229 assert(position >= 0); | |
| 230 OpenJpegInput& that = *reinterpret_cast<OpenJpegInput*>(userData); | |
| 231 | |
| 232 if (static_cast<size_t>(position) > that.size_) | |
| 233 { | |
| 234 that.position_ = that.size_; | |
| 235 return false; | |
| 236 } | |
| 237 else | |
| 238 { | |
| 239 that.position_ = position; | |
| 240 return true; | |
| 241 } | |
| 242 } | |
| 243 #endif | |
| 244 | |
| 245 public: | |
| 246 OpenJpegInput(OpenJpegDecoder& decoder, | |
| 247 const void* buffer, | |
| 248 size_t size) : | |
| 249 buffer_(reinterpret_cast<const uint8_t*>(buffer)), | |
| 250 size_(size), | |
| 251 position_(0) | |
| 252 { | |
| 253 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 254 cio_ = opj_cio_open(reinterpret_cast<opj_common_ptr>(decoder.GetObject()), | |
| 255 reinterpret_cast<unsigned char*>(const_cast<void*>(buffer)), | |
| 256 size); | |
| 257 #else | |
| 258 cio_ = opj_stream_create(size_, 1 /* input stream */); | |
| 259 if (!cio_) | |
| 260 { | |
| 261 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 262 } | |
| 263 | |
| 264 // http://openjpeg.narkive.com/zHqG2fMe/opj-stream-set-user-data-length | |
| 265 // "I'd suggest to precise in the documentation that the skip | |
| 266 // and read callback functions should return -1 on end of | |
| 267 // stream, and the seek callback function should return false | |
| 268 // on end of stream." | |
| 269 | |
| 270 opj_stream_set_user_data(cio_, this, Free); | |
| 271 opj_stream_set_user_data_length(cio_, size); | |
| 272 opj_stream_set_read_function(cio_, Read); | |
| 273 opj_stream_set_skip_function(cio_, Skip); | |
| 274 opj_stream_set_seek_function(cio_, Seek); | |
| 275 #endif | |
| 276 } | |
| 277 | |
| 278 ~OpenJpegInput() | |
| 279 { | |
| 280 if (cio_) | |
| 281 { | |
| 282 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 283 opj_cio_close(cio_); | |
| 284 #else | |
| 285 opj_stream_destroy(cio_); | |
| 286 #endif | |
| 287 cio_ = NULL; | |
| 288 } | |
| 289 } | |
| 290 | |
| 291 opj_stream_t* GetObject() | |
| 292 { | |
| 293 return cio_; | |
| 294 } | |
| 295 }; | |
| 296 | |
| 297 | |
| 298 class OpenJpegImage | |
| 299 { | |
| 300 private: | |
| 301 opj_image_t* image_; | |
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302 |
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303 Orthanc::ImageAccessor* ExtractChannel(unsigned int channel) |
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304 { |
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305 const unsigned int width = image_->comps[channel].w; |
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306 const unsigned int height = image_->comps[channel].h; |
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307 |
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308 std::unique_ptr<Orthanc::ImageAccessor> target( |
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309 new Orthanc::Image(Orthanc::PixelFormat_Grayscale8, width, height, false)); |
| 0 | 310 |
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311 const int32_t* q = image_->comps[channel].data; |
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312 assert(q != NULL); |
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313 |
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314 for (unsigned int y = 0; y < height; y++) |
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315 { |
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316 uint8_t *p = reinterpret_cast<uint8_t*>(target->GetRow(y)); |
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317 |
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318 for (unsigned int x = 0; x < width; x++, p++, q++) |
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319 { |
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320 *p = *q; |
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321 } |
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322 } |
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323 |
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324 return target.release(); |
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325 } |
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326 |
| 0 | 327 void CopyChannel(Orthanc::ImageAccessor& target, |
| 328 unsigned int channel, | |
| 329 unsigned int targetIncrement) | |
| 330 { | |
| 209 | 331 const unsigned int width = target.GetWidth(); |
| 332 const unsigned int height = target.GetHeight(); | |
| 333 | |
| 227 | 334 if (width == static_cast<unsigned int>(image_->comps[channel].w) && |
| 335 height == static_cast<unsigned int>(image_->comps[channel].h)) | |
| 0 | 336 { |
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337 const int32_t* q = image_->comps[channel].data; |
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338 assert(q != NULL); |
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339 |
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340 for (unsigned int y = 0; y < height; y++) |
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341 { |
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342 uint8_t *p = reinterpret_cast<uint8_t*>(target.GetRow(y)) + channel; |
| 0 | 343 |
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344 for (unsigned int x = 0; x < width; x++, p += targetIncrement) |
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345 { |
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346 *p = *q; |
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347 q++; |
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348 } |
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349 } |
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350 } |
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351 else |
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352 { |
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353 // This component is subsampled |
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354 std::unique_ptr<Orthanc::ImageAccessor> source(ExtractChannel(channel)); |
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355 Orthanc::Image resized(Orthanc::PixelFormat_Grayscale8, width, height, false); |
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356 Orthanc::ImageProcessing::Resize(resized, *source); |
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357 |
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358 assert(resized.GetWidth() == target.GetWidth() && |
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359 resized.GetHeight() == target.GetHeight() && |
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360 resized.GetFormat() == Orthanc::PixelFormat_Grayscale8 && |
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361 source->GetFormat() == Orthanc::PixelFormat_Grayscale8); |
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362 |
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363 for (unsigned int y = 0; y < height; y++) |
| 0 | 364 { |
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365 const uint8_t *q = reinterpret_cast<const uint8_t*>(resized.GetConstRow(y)); |
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366 uint8_t *p = reinterpret_cast<uint8_t*>(target.GetRow(y)) + channel; |
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367 |
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368 for (unsigned int x = 0; x < width; x++, p += targetIncrement) |
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369 { |
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370 *p = *q; |
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371 q++; |
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372 } |
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373 } |
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374 } |
| 0 | 375 } |
| 376 | |
| 377 public: | |
| 378 OpenJpegImage(OpenJpegDecoder& decoder, | |
| 379 OpenJpegInput& input) : | |
| 380 image_(NULL) | |
| 381 { | |
| 382 #if ORTHANC_OPENJPEG_MAJOR_VERSION == 1 | |
| 383 image_ = opj_decode(decoder.GetObject(), input.GetObject()); | |
| 384 if (image_ == NULL) | |
| 385 { | |
| 386 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 387 } | |
| 388 #else | |
| 389 if (!opj_read_header(input.GetObject(), decoder.GetObject(), &image_) || | |
| 390 image_ == NULL) | |
| 391 { | |
| 392 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 393 } | |
| 394 | |
| 395 if (!opj_set_decode_area(decoder.GetObject(), image_, | |
| 396 static_cast<int32_t>(decoder.GetParameters().DA_x0), | |
| 397 static_cast<int32_t>(decoder.GetParameters().DA_y0), | |
| 398 static_cast<int32_t>(decoder.GetParameters().DA_x1), | |
| 399 static_cast<int32_t>(decoder.GetParameters().DA_y1)) || // Decode the whole image | |
| 400 !opj_decode(decoder.GetObject(), input.GetObject(), image_) || | |
| 401 !opj_end_decompress(decoder.GetObject(), input.GetObject())) | |
| 402 { | |
| 403 opj_image_destroy(image_); | |
| 404 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 405 } | |
| 406 #endif | |
| 407 } | |
| 408 | |
| 409 ~OpenJpegImage() | |
| 410 { | |
| 411 if (image_ != NULL) | |
| 412 { | |
| 413 opj_image_destroy(image_); | |
| 414 image_ = NULL; | |
| 415 } | |
| 416 } | |
| 417 | |
| 418 Orthanc::ImageAccessor* ProvideImage() | |
| 419 { | |
| 420 if (image_->x1 < 0 || | |
| 421 image_->y1 < 0) | |
| 422 { | |
| 423 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 424 } | |
| 425 | |
| 426 if (image_->x0 != 0 || | |
| 427 image_->y0 != 0) | |
| 428 { | |
| 429 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 430 } | |
| 431 | |
| 432 for (unsigned int c = 0; c < static_cast<unsigned int>(image_->numcomps); c++) | |
| 433 { | |
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434 if (image_->comps[c].x0 != 0 || |
| 0 | 435 image_->comps[c].y0 != 0 || |
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436 image_->comps[c].dx * image_->comps[c].w != image_->x1 || |
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437 image_->comps[c].dy * image_->comps[c].h != image_->y1 || |
| 0 | 438 image_->comps[c].prec != 8 || |
| 439 image_->comps[c].sgnd != 0) | |
| 440 { | |
| 441 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 442 } | |
| 443 } | |
| 444 | |
| 445 unsigned int width = static_cast<unsigned int>(image_->x1); | |
| 446 unsigned int height = static_cast<unsigned int>(image_->y1); | |
| 447 | |
| 448 Orthanc::PixelFormat format; | |
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449 if (image_->numcomps == 1 /*&& image_->color_space != OPJ_CLRSPC_GRAY*/) |
| 0 | 450 { |
| 451 format = Orthanc::PixelFormat_Grayscale8; | |
| 452 } | |
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453 else if (image_->numcomps == 3 /*&& image_->color_space == OPJ_CLRSPC_SRGB*/) |
| 0 | 454 { |
| 455 format = Orthanc::PixelFormat_RGB24; | |
| 456 } | |
| 457 else | |
| 458 { | |
| 459 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
| 460 } | |
| 461 | |
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462 std::unique_ptr<Orthanc::ImageAccessor> image(ImageToolbox::Allocate(format, width, height)); |
| 0 | 463 |
| 464 switch (format) | |
| 465 { | |
| 466 case Orthanc::PixelFormat_Grayscale8: | |
| 467 { | |
| 468 CopyChannel(*image, 0, 1); | |
| 469 break; | |
| 470 } | |
| 471 | |
| 472 case Orthanc::PixelFormat_RGB24: | |
| 473 { | |
| 474 CopyChannel(*image, 0, 3); | |
| 475 CopyChannel(*image, 1, 3); | |
| 476 CopyChannel(*image, 2, 3); | |
| 477 break; | |
| 478 } | |
| 479 | |
| 480 default: | |
| 481 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 482 } | |
| 483 | |
| 484 return image.release(); | |
| 485 } | |
| 486 }; | |
| 487 } | |
| 488 | |
| 489 | |
| 490 void Jpeg2000Reader::ReadFromMemory(const void* buffer, | |
| 491 size_t size) | |
| 492 { | |
| 493 OpenJpegDecoder decoder(DetectFormatFromMemory(buffer, size)); | |
| 494 OpenJpegInput input(decoder, buffer, size); | |
| 495 OpenJpegImage image(decoder, input); | |
| 496 | |
| 497 image_.reset(image.ProvideImage()); | |
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498 AssignWritable(image_->GetFormat(), |
| 0 | 499 image_->GetWidth(), |
| 500 image_->GetHeight(), | |
| 501 image_->GetPitch(), | |
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502 image_->GetBuffer()); |
| 0 | 503 } |
| 504 | |
| 505 | |
| 506 void Jpeg2000Reader::ReadFromMemory(const std::string& buffer) | |
| 507 { | |
| 508 if (buffer.empty()) | |
| 509 { | |
| 510 ReadFromMemory(NULL, 0); | |
| 511 } | |
| 512 else | |
| 513 { | |
| 514 ReadFromMemory(buffer.c_str(), buffer.size()); | |
| 515 } | |
| 516 } | |
| 517 | |
| 518 void Jpeg2000Reader::ReadFromFile(const std::string& filename) | |
| 519 { | |
| 520 // TODO Use opj_stream_create_file_stream() ? | |
| 521 | |
| 522 std::string content; | |
| 43 | 523 Orthanc::SystemToolbox::ReadFile(content, filename); |
| 0 | 524 } |
| 525 | |
| 526 | |
| 527 Jpeg2000Format Jpeg2000Reader::DetectFormatFromMemory(const void* buffer, | |
| 528 size_t size) | |
| 529 { | |
| 530 static const char JP2_RFC3745_HEADER[] = "\x00\x00\x00\x0c\x6a\x50\x20\x20\x0d\x0a\x87\x0a"; | |
| 531 static const char JP2_HEADER[] = "\x0d\x0a\x87\x0a"; | |
| 532 static const char J2K_HEADER[] = "\xff\x4f\xff\x51"; | |
| 533 | |
| 534 if (size < sizeof(JP2_RFC3745_HEADER) - 1) | |
| 535 { | |
| 536 return Jpeg2000Format_Unknown; | |
| 537 } | |
| 538 | |
| 539 if (memcmp(buffer, JP2_RFC3745_HEADER, sizeof(JP2_RFC3745_HEADER) - 1) == 0 || | |
| 540 memcmp(buffer, JP2_HEADER, sizeof(JP2_HEADER) - 1) == 0) | |
| 541 { | |
| 542 return Jpeg2000Format_JP2; | |
| 543 } | |
| 544 else if (memcmp(buffer, J2K_HEADER, sizeof(J2K_HEADER) - 1) == 0) | |
| 545 { | |
| 546 return Jpeg2000Format_J2K; | |
| 547 } | |
| 548 | |
| 549 return Jpeg2000Format_Unknown; | |
| 550 } | |
| 551 } |