Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1015:f009f7c75069
fix integration tests
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 10 Jul 2014 11:24:25 +0200 |
| parents | af014624dac1 |
| children | 564e39d6df13 |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, | |
| 4 * Belgium | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 | |
| 34 /*========================================================================= | |
| 35 | |
| 36 This file is based on portions of the following project: | |
| 37 | |
| 38 Program: GDCM (Grassroots DICOM). A DICOM library | |
| 39 Module: http://gdcm.sourceforge.net/Copyright.html | |
| 40 | |
| 41 Copyright (c) 2006-2011 Mathieu Malaterre | |
| 42 Copyright (c) 1993-2005 CREATIS | |
| 43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
| 44 All rights reserved. | |
| 45 | |
| 46 Redistribution and use in source and binary forms, with or without | |
| 47 modification, are permitted provided that the following conditions are met: | |
| 48 | |
| 49 * Redistributions of source code must retain the above copyright notice, | |
| 50 this list of conditions and the following disclaimer. | |
| 51 | |
| 52 * Redistributions in binary form must reproduce the above copyright notice, | |
| 53 this list of conditions and the following disclaimer in the documentation | |
| 54 and/or other materials provided with the distribution. | |
| 55 | |
| 56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
| 57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
| 58 endorse or promote products derived from this software without specific | |
| 59 prior written permission. | |
| 60 | |
| 61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
| 62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| 63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
| 65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
| 66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
| 67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
| 68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
| 69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| 70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 71 | |
| 72 =========================================================================*/ | |
| 73 | |
| 74 | |
|
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75 #include "PrecompiledHeadersServer.h" |
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76 |
| 790 | 77 #ifndef NOMINMAX |
| 78 #define NOMINMAX | |
| 79 #endif | |
| 80 | |
| 81 #include "ParsedDicomFile.h" | |
| 82 | |
| 83 #include "FromDcmtkBridge.h" | |
| 84 #include "ToDcmtkBridge.h" | |
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85 #include "Internals/DicomImageDecoder.h" |
| 790 | 86 #include "../Core/Toolbox.h" |
| 87 #include "../Core/OrthancException.h" | |
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88 #include "../Core/ImageFormats/ImageBuffer.h" |
| 799 | 89 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 90 #include "../Core/Uuid.h" |
| 91 #include "../Core/DicomFormat/DicomString.h" | |
| 92 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 93 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
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94 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 95 |
| 96 #include <list> | |
| 97 #include <limits> | |
| 98 | |
| 99 #include <boost/lexical_cast.hpp> | |
| 100 | |
| 101 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 102 #include <dcmtk/dcmdata/dcdicent.h> | |
| 103 #include <dcmtk/dcmdata/dcdict.h> | |
| 104 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 105 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 106 #include <dcmtk/dcmdata/dcuid.h> | |
| 107 #include <dcmtk/dcmdata/dcmetinf.h> | |
| 108 | |
| 109 #include <dcmtk/dcmdata/dcvrae.h> | |
| 110 #include <dcmtk/dcmdata/dcvras.h> | |
| 111 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 112 #include <dcmtk/dcmdata/dcvrda.h> | |
| 113 #include <dcmtk/dcmdata/dcvrds.h> | |
| 114 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 115 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 116 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 117 #include <dcmtk/dcmdata/dcvris.h> | |
| 118 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 119 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 120 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 121 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 122 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 123 #include <dcmtk/dcmdata/dcvrss.h> | |
| 124 #include <dcmtk/dcmdata/dcvrst.h> | |
| 125 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 126 #include <dcmtk/dcmdata/dcvrui.h> | |
| 127 #include <dcmtk/dcmdata/dcvrul.h> | |
| 128 #include <dcmtk/dcmdata/dcvrus.h> | |
| 129 #include <dcmtk/dcmdata/dcvrut.h> | |
| 130 #include <dcmtk/dcmdata/dcpixel.h> | |
| 131 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 132 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 133 | |
| 134 | |
| 135 #include <boost/math/special_functions/round.hpp> | |
| 136 #include <glog/logging.h> | |
| 137 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 138 | |
| 139 | |
| 140 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 141 | |
| 142 | |
| 143 | |
| 144 namespace Orthanc | |
| 145 { | |
| 794 | 146 struct ParsedDicomFile::PImpl |
| 147 { | |
| 148 std::auto_ptr<DcmFileFormat> file_; | |
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149 Encoding encoding_; |
| 794 | 150 }; |
| 151 | |
| 152 | |
| 153 // This method can only be called from the constructors! | |
| 790 | 154 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 155 { | |
| 156 DcmInputBufferStream is; | |
| 157 if (size > 0) | |
| 158 { | |
| 159 is.setBuffer(buffer, size); | |
| 160 } | |
| 161 is.setEos(); | |
| 162 | |
| 794 | 163 pimpl_->file_.reset(new DcmFileFormat); |
| 164 pimpl_->file_->transferInit(); | |
| 165 if (!pimpl_->file_->read(is).good()) | |
| 790 | 166 { |
| 794 | 167 delete pimpl_; // Avoid a memory leak due to exception |
| 168 // throwing, as we are in the constructor | |
| 169 | |
| 790 | 170 throw OrthancException(ErrorCode_BadFileFormat); |
| 171 } | |
| 794 | 172 pimpl_->file_->loadAllDataIntoMemory(); |
| 173 pimpl_->file_->transferEnd(); | |
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174 |
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175 pimpl_->encoding_ = FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
| 790 | 176 } |
| 177 | |
| 178 | |
| 179 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 180 DcmItem& dicom) | |
| 181 { | |
| 182 Json::Value v = Json::arrayValue; | |
| 183 | |
| 184 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 185 { | |
| 186 DcmElement* element = dicom.getElement(i); | |
| 187 if (element) | |
| 188 { | |
| 189 char buf[16]; | |
| 190 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 191 v.append(buf); | |
| 192 } | |
| 193 } | |
| 194 | |
| 195 output.AnswerJson(v); | |
| 196 } | |
| 197 | |
| 198 static inline uint16_t GetCharValue(char c) | |
| 199 { | |
| 200 if (c >= '0' && c <= '9') | |
| 201 return c - '0'; | |
| 202 else if (c >= 'a' && c <= 'f') | |
| 203 return c - 'a' + 10; | |
| 204 else if (c >= 'A' && c <= 'F') | |
| 205 return c - 'A' + 10; | |
| 206 else | |
| 207 return 0; | |
| 208 } | |
| 209 | |
| 210 static inline uint16_t GetTagValue(const char* c) | |
| 211 { | |
| 212 return ((GetCharValue(c[0]) << 12) + | |
| 213 (GetCharValue(c[1]) << 8) + | |
| 214 (GetCharValue(c[2]) << 4) + | |
| 215 GetCharValue(c[3])); | |
| 216 } | |
| 217 | |
| 218 static void ParseTagAndGroup(DcmTagKey& key, | |
| 219 const std::string& tag) | |
| 220 { | |
| 221 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 222 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 223 } | |
| 224 | |
| 225 | |
| 226 static void SendSequence(RestApiOutput& output, | |
| 227 DcmSequenceOfItems& sequence) | |
| 228 { | |
| 229 // This element is a sequence | |
| 230 Json::Value v = Json::arrayValue; | |
| 231 | |
| 232 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 233 { | |
| 234 v.append(boost::lexical_cast<std::string>(i)); | |
| 235 } | |
| 236 | |
| 237 output.AnswerJson(v); | |
| 238 } | |
| 239 | |
| 240 | |
| 241 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 242 E_TransferSyntax transferSyntax) | |
| 243 { | |
| 244 DcmPixelSequence* pixelSequence = NULL; | |
| 245 if (pixelData.getEncapsulatedRepresentation | |
| 246 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 247 { | |
| 248 return pixelSequence->card(); | |
| 249 } | |
| 250 else | |
| 251 { | |
| 252 return 1; | |
| 253 } | |
| 254 } | |
| 255 | |
| 256 | |
| 257 static void AnswerDicomField(RestApiOutput& output, | |
| 258 DcmElement& element, | |
| 259 E_TransferSyntax transferSyntax) | |
| 260 { | |
| 261 // This element is nor a sequence, neither a pixel-data | |
| 262 std::string buffer; | |
| 263 buffer.resize(65536); | |
| 264 Uint32 length = element.getLength(transferSyntax); | |
| 265 Uint32 offset = 0; | |
| 266 | |
| 267 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL); | |
| 268 | |
| 269 while (offset < length) | |
| 270 { | |
| 271 Uint32 nbytes; | |
| 272 if (length - offset < buffer.size()) | |
| 273 { | |
| 274 nbytes = length - offset; | |
| 275 } | |
| 276 else | |
| 277 { | |
| 278 nbytes = buffer.size(); | |
| 279 } | |
| 280 | |
| 281 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); | |
| 282 | |
| 283 if (cond.good()) | |
| 284 { | |
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285 output.GetLowLevelOutput().SendBodyData(&buffer[0], nbytes); |
| 790 | 286 offset += nbytes; |
| 287 } | |
| 288 else | |
| 289 { | |
| 290 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); | |
| 291 return; | |
| 292 } | |
| 293 } | |
| 294 | |
| 295 output.MarkLowLevelOutputDone(); | |
| 296 } | |
| 297 | |
| 298 | |
| 299 static bool AnswerPixelData(RestApiOutput& output, | |
| 300 DcmItem& dicom, | |
| 301 E_TransferSyntax transferSyntax, | |
| 302 const std::string* blockUri) | |
| 303 { | |
| 304 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 305 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 306 | |
| 307 DcmElement *element = NULL; | |
| 308 if (!dicom.findAndGetElement(k, element).good() || | |
| 309 element == NULL) | |
| 310 { | |
| 311 return false; | |
| 312 } | |
| 313 | |
| 314 try | |
| 315 { | |
| 316 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 317 if (blockUri == NULL) | |
| 318 { | |
| 319 // The user asks how many blocks are presents in this pixel data | |
| 320 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 321 | |
| 322 Json::Value result(Json::arrayValue); | |
| 323 for (unsigned int i = 0; i < blocks; i++) | |
| 324 { | |
| 325 result.append(boost::lexical_cast<std::string>(i)); | |
| 326 } | |
| 327 | |
| 328 output.AnswerJson(result); | |
| 329 return true; | |
| 330 } | |
| 331 | |
| 332 | |
| 333 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 334 | |
| 335 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 336 { | |
| 337 DcmPixelSequence* pixelSequence = NULL; | |
| 338 if (pixelData.getEncapsulatedRepresentation | |
| 339 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 340 { | |
| 341 // This is the case for JPEG transfer syntaxes | |
| 342 if (block < pixelSequence->card()) | |
| 343 { | |
| 344 DcmPixelItem* pixelItem = NULL; | |
| 345 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 346 { | |
| 347 if (pixelItem->getLength() == 0) | |
| 348 { | |
| 349 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 350 return true; | |
| 351 } | |
| 352 | |
| 353 Uint8* buffer = NULL; | |
| 354 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 355 { | |
| 356 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 357 return true; | |
| 358 } | |
| 359 } | |
| 360 } | |
| 361 } | |
| 362 else | |
| 363 { | |
| 364 // This is the case for raw, uncompressed image buffers | |
| 365 assert(*blockUri == "0"); | |
| 366 AnswerDicomField(output, *element, transferSyntax); | |
| 367 } | |
| 368 } | |
| 369 } | |
| 370 catch (boost::bad_lexical_cast&) | |
| 371 { | |
| 372 // The URI entered by the user is not a number | |
| 373 } | |
| 374 catch (std::bad_cast&) | |
| 375 { | |
| 376 // This should never happen | |
| 377 } | |
| 378 | |
| 379 return false; | |
| 380 } | |
| 381 | |
| 382 | |
| 383 | |
| 384 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 385 const std::string& tag, | |
| 386 DcmItem& dicom, | |
| 387 E_TransferSyntax transferSyntax) | |
| 388 { | |
| 389 DcmTagKey k; | |
| 390 ParseTagAndGroup(k, tag); | |
| 391 | |
| 392 DcmSequenceOfItems* sequence = NULL; | |
| 393 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 394 sequence != NULL && | |
| 395 sequence->getVR() == EVR_SQ) | |
| 396 { | |
| 397 SendSequence(output, *sequence); | |
| 398 return; | |
| 399 } | |
| 400 | |
| 401 DcmElement* element = NULL; | |
| 402 if (dicom.findAndGetElement(k, element).good() && | |
| 403 element != NULL && | |
| 404 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 405 element->getVR() != EVR_SQ) | |
| 406 { | |
| 407 AnswerDicomField(output, *element, transferSyntax); | |
| 408 } | |
| 409 } | |
| 410 | |
| 411 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 412 const UriComponents& uri) | |
| 413 { | |
| 794 | 414 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 415 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 416 |
| 417 // Special case: Accessing the pixel data | |
| 418 if (uri.size() == 1 || | |
| 419 uri.size() == 2) | |
| 420 { | |
| 421 DcmTagKey tag; | |
| 422 ParseTagAndGroup(tag, uri[0]); | |
| 423 | |
| 424 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 425 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 426 { | |
| 427 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 428 return; | |
| 429 } | |
| 430 } | |
| 431 | |
| 432 // Go down in the tag hierarchy according to the URI | |
| 433 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 434 { | |
| 435 size_t index; | |
| 436 try | |
| 437 { | |
| 438 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 439 } | |
| 440 catch (boost::bad_lexical_cast&) | |
| 441 { | |
| 442 return; | |
| 443 } | |
| 444 | |
| 445 DcmTagKey k; | |
| 446 DcmItem *child = NULL; | |
| 447 ParseTagAndGroup(k, uri[2 * pos]); | |
| 448 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 449 child == NULL) | |
| 450 { | |
| 451 return; | |
| 452 } | |
| 453 | |
| 454 dicom = child; | |
| 455 } | |
| 456 | |
| 457 // We have reached the end of the URI | |
| 458 if (uri.size() % 2 == 0) | |
| 459 { | |
| 460 SendPathValueForDictionary(output, *dicom); | |
| 461 } | |
| 462 else | |
| 463 { | |
| 464 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 465 } | |
| 466 } | |
| 467 | |
| 468 | |
| 469 | |
| 470 | |
| 471 | |
| 472 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 473 { | |
| 474 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 475 | |
| 476 switch (key.getEVR()) | |
| 477 { | |
| 478 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 479 | |
| 480 /** | |
| 481 * TODO. | |
| 482 **/ | |
| 483 | |
| 484 case EVR_OB: // other byte | |
| 485 case EVR_OF: // other float | |
| 486 case EVR_OW: // other word | |
| 487 case EVR_AT: // attribute tag | |
| 488 throw OrthancException(ErrorCode_NotImplemented); | |
| 489 | |
| 490 case EVR_UN: // unknown value representation | |
| 491 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 492 | |
| 493 | |
| 494 /** | |
| 495 * String types. | |
| 496 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 497 **/ | |
| 498 | |
| 499 case EVR_AS: // age string | |
| 500 return new DcmAgeString(key); | |
| 501 | |
| 502 case EVR_AE: // application entity title | |
| 503 return new DcmApplicationEntity(key); | |
| 504 | |
| 505 case EVR_CS: // code string | |
| 506 return new DcmCodeString(key); | |
| 507 | |
| 508 case EVR_DA: // date string | |
| 509 return new DcmDate(key); | |
| 510 | |
| 511 case EVR_DT: // date time string | |
| 512 return new DcmDateTime(key); | |
| 513 | |
| 514 case EVR_DS: // decimal string | |
| 515 return new DcmDecimalString(key); | |
| 516 | |
| 517 case EVR_IS: // integer string | |
| 518 return new DcmIntegerString(key); | |
| 519 | |
| 520 case EVR_TM: // time string | |
| 521 return new DcmTime(key); | |
| 522 | |
| 523 case EVR_UI: // unique identifier | |
| 524 return new DcmUniqueIdentifier(key); | |
| 525 | |
| 526 case EVR_ST: // short text | |
| 527 return new DcmShortText(key); | |
| 528 | |
| 529 case EVR_LO: // long string | |
| 530 return new DcmLongString(key); | |
| 531 | |
| 532 case EVR_LT: // long text | |
| 533 return new DcmLongText(key); | |
| 534 | |
| 535 case EVR_UT: // unlimited text | |
| 536 return new DcmUnlimitedText(key); | |
| 537 | |
| 538 case EVR_SH: // short string | |
| 539 return new DcmShortString(key); | |
| 540 | |
| 541 case EVR_PN: // person name | |
| 542 return new DcmPersonName(key); | |
| 543 | |
| 544 | |
| 545 /** | |
| 546 * Numerical types | |
| 547 **/ | |
| 548 | |
| 549 case EVR_SL: // signed long | |
| 550 return new DcmSignedLong(key); | |
| 551 | |
| 552 case EVR_SS: // signed short | |
| 553 return new DcmSignedShort(key); | |
| 554 | |
| 555 case EVR_UL: // unsigned long | |
| 556 return new DcmUnsignedLong(key); | |
| 557 | |
| 558 case EVR_US: // unsigned short | |
| 559 return new DcmUnsignedShort(key); | |
| 560 | |
| 561 case EVR_FL: // float single-precision | |
| 562 return new DcmFloatingPointSingle(key); | |
| 563 | |
| 564 case EVR_FD: // float double-precision | |
| 565 return new DcmFloatingPointDouble(key); | |
| 566 | |
| 567 | |
| 568 /** | |
| 569 * Sequence types, should never occur at this point. | |
| 570 **/ | |
| 571 | |
| 572 case EVR_SQ: // sequence of items | |
| 573 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 574 | |
| 575 | |
| 576 /** | |
| 577 * Internal to DCMTK. | |
| 578 **/ | |
| 579 | |
| 580 case EVR_ox: // OB or OW depending on context | |
| 581 case EVR_xs: // SS or US depending on context | |
| 582 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 583 case EVR_na: // na="not applicable", for data which has no VR | |
| 584 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 585 case EVR_item: // used internally for items | |
| 586 case EVR_metainfo: // used internally for meta info datasets | |
| 587 case EVR_dataset: // used internally for datasets | |
| 588 case EVR_fileFormat: // used internally for DICOM files | |
| 589 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 590 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 591 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 592 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 593 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 594 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 595 case EVR_OverlayData: // used internally for overlay data | |
| 596 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 597 default: | |
| 598 break; | |
| 599 } | |
| 600 | |
| 601 throw OrthancException(ErrorCode_InternalError); | |
| 602 } | |
| 603 | |
| 604 | |
| 605 | |
| 606 static void FillElementWithString(DcmElement& element, | |
| 607 const DicomTag& tag, | |
| 608 const std::string& value) | |
| 609 { | |
| 610 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 611 bool ok = false; | |
| 612 | |
| 613 try | |
| 614 { | |
| 615 switch (key.getEVR()) | |
| 616 { | |
| 617 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 618 | |
| 619 /** | |
| 620 * TODO. | |
| 621 **/ | |
| 622 | |
| 623 case EVR_OB: // other byte | |
| 624 case EVR_OF: // other float | |
| 625 case EVR_OW: // other word | |
| 626 case EVR_AT: // attribute tag | |
| 627 throw OrthancException(ErrorCode_NotImplemented); | |
| 628 | |
| 629 case EVR_UN: // unknown value representation | |
| 630 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 631 | |
| 632 | |
| 633 /** | |
| 634 * String types. | |
| 635 **/ | |
| 636 | |
| 637 case EVR_DS: // decimal string | |
| 638 case EVR_IS: // integer string | |
| 639 case EVR_AS: // age string | |
| 640 case EVR_DA: // date string | |
| 641 case EVR_DT: // date time string | |
| 642 case EVR_TM: // time string | |
| 643 case EVR_AE: // application entity title | |
| 644 case EVR_CS: // code string | |
| 645 case EVR_SH: // short string | |
| 646 case EVR_LO: // long string | |
| 647 case EVR_ST: // short text | |
| 648 case EVR_LT: // long text | |
| 649 case EVR_UT: // unlimited text | |
| 650 case EVR_PN: // person name | |
| 651 case EVR_UI: // unique identifier | |
| 652 { | |
| 653 ok = element.putString(value.c_str()).good(); | |
| 654 break; | |
| 655 } | |
| 656 | |
| 657 | |
| 658 /** | |
| 659 * Numerical types | |
| 660 **/ | |
| 661 | |
| 662 case EVR_SL: // signed long | |
| 663 { | |
| 664 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 665 break; | |
| 666 } | |
| 667 | |
| 668 case EVR_SS: // signed short | |
| 669 { | |
| 670 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 671 break; | |
| 672 } | |
| 673 | |
| 674 case EVR_UL: // unsigned long | |
| 675 { | |
| 676 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 677 break; | |
| 678 } | |
| 679 | |
| 680 case EVR_US: // unsigned short | |
| 681 { | |
| 682 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 683 break; | |
| 684 } | |
| 685 | |
| 686 case EVR_FL: // float single-precision | |
| 687 { | |
| 688 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 689 break; | |
| 690 } | |
| 691 | |
| 692 case EVR_FD: // float double-precision | |
| 693 { | |
| 694 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 695 break; | |
| 696 } | |
| 697 | |
| 698 | |
| 699 /** | |
| 700 * Sequence types, should never occur at this point. | |
| 701 **/ | |
| 702 | |
| 703 case EVR_SQ: // sequence of items | |
| 704 { | |
| 705 ok = false; | |
| 706 break; | |
| 707 } | |
| 708 | |
| 709 | |
| 710 /** | |
| 711 * Internal to DCMTK. | |
| 712 **/ | |
| 713 | |
| 714 case EVR_ox: // OB or OW depending on context | |
| 715 case EVR_xs: // SS or US depending on context | |
| 716 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 717 case EVR_na: // na="not applicable", for data which has no VR | |
| 718 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 719 case EVR_item: // used internally for items | |
| 720 case EVR_metainfo: // used internally for meta info datasets | |
| 721 case EVR_dataset: // used internally for datasets | |
| 722 case EVR_fileFormat: // used internally for DICOM files | |
| 723 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 724 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 725 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 726 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 727 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 728 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 729 case EVR_OverlayData: // used internally for overlay data | |
| 730 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 731 default: | |
| 732 break; | |
| 733 } | |
| 734 } | |
| 735 catch (boost::bad_lexical_cast&) | |
| 736 { | |
| 737 ok = false; | |
| 738 } | |
| 739 | |
| 740 if (!ok) | |
| 741 { | |
| 742 throw OrthancException(ErrorCode_InternalError); | |
| 743 } | |
| 744 } | |
| 745 | |
| 746 | |
| 747 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 748 { | |
| 749 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 750 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 751 if (element != NULL) |
| 752 { | |
| 753 delete element; | |
| 754 } | |
| 755 } | |
| 756 | |
| 757 | |
| 758 | |
|
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759 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 760 { |
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761 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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762 |
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763 // Loop over the dataset to detect its private tags |
| 790 | 764 typedef std::list<DcmElement*> Tags; |
| 765 Tags privateTags; | |
| 766 | |
| 767 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 768 { | |
| 769 DcmElement* element = dataset.getElement(i); | |
| 770 DcmTag tag(element->getTag()); | |
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771 |
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772 // Is this a private tag? |
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773 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 774 { |
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775 bool remove = true; |
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776 |
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777 // Check whether this private tag is to be kept |
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778 if (toKeep != NULL) |
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779 { |
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780 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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781 if (toKeep->find(tmp) != toKeep->end()) |
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782 { |
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783 remove = false; // Keep it |
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784 } |
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785 } |
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786 |
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787 if (remove) |
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788 { |
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789 privateTags.push_back(element); |
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790 } |
| 790 | 791 } |
| 792 } | |
| 793 | |
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794 // Loop over the detected private tags to remove them |
| 790 | 795 for (Tags::iterator it = privateTags.begin(); |
| 796 it != privateTags.end(); ++it) | |
| 797 { | |
| 798 DcmElement* tmp = dataset.remove(*it); | |
| 799 if (tmp != NULL) | |
| 800 { | |
| 801 delete tmp; | |
| 802 } | |
| 803 } | |
| 804 } | |
| 805 | |
| 806 | |
| 807 | |
| 808 void ParsedDicomFile::Insert(const DicomTag& tag, | |
| 809 const std::string& value) | |
| 810 { | |
| 811 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); | |
| 812 FillElementWithString(*element, tag, value); | |
| 813 | |
| 794 | 814 if (!pimpl_->file_->getDataset()->insert(element.release(), false, false).good()) |
| 790 | 815 { |
| 816 // This field already exists | |
| 817 throw OrthancException(ErrorCode_InternalError); | |
| 818 } | |
| 819 } | |
| 820 | |
| 821 | |
| 822 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 823 const std::string& value, | |
| 824 DicomReplaceMode mode) | |
| 825 { | |
| 826 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 827 DcmElement* element = NULL; | |
| 828 | |
| 794 | 829 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 830 element == NULL) |
| 831 { | |
| 832 // This field does not exist, act wrt. the specified "mode" | |
| 833 switch (mode) | |
| 834 { | |
| 835 case DicomReplaceMode_InsertIfAbsent: | |
| 836 Insert(tag, value); | |
| 837 break; | |
| 838 | |
| 839 case DicomReplaceMode_ThrowIfAbsent: | |
| 840 throw OrthancException(ErrorCode_InexistentItem); | |
| 841 | |
| 842 case DicomReplaceMode_IgnoreIfAbsent: | |
| 843 return; | |
| 844 } | |
| 845 } | |
| 846 else | |
| 847 { | |
| 848 FillElementWithString(*element, tag, value); | |
| 849 } | |
| 850 | |
| 851 | |
| 852 /** | |
| 853 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 854 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 855 * you make changes to the related tags in the dataset ('SOP Class | |
| 856 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 857 * options. You can disable this behaviour by using the -nmu | |
| 858 * option. | |
| 859 **/ | |
| 860 | |
| 861 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 862 { | |
| 863 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 864 } | |
| 865 | |
| 866 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 867 { | |
| 868 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 869 } | |
| 870 } | |
| 871 | |
| 872 | |
| 873 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 874 { | |
| 875 std::string serialized; | |
| 794 | 876 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, pimpl_->file_->getDataset())) |
| 790 | 877 { |
| 878 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 879 } | |
| 880 } | |
| 881 | |
| 882 | |
| 883 | |
| 884 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 885 const DicomTag& tag) | |
| 886 { | |
| 887 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 888 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 889 DcmElement* element = NULL; |
| 890 if (!dataset.findAndGetElement(k, element).good() || | |
| 891 element == NULL) | |
| 892 { | |
| 893 return false; | |
| 894 } | |
| 895 | |
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896 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
| 790 | 897 |
| 898 if (v.get() == NULL) | |
| 899 { | |
| 900 value = ""; | |
| 901 } | |
| 902 else | |
| 903 { | |
| 904 value = v->AsString(); | |
| 905 } | |
| 906 | |
| 907 return true; | |
| 908 } | |
| 909 | |
| 910 | |
| 911 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 912 { | |
| 913 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 914 | |
| 915 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 916 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 917 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 918 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 919 { | |
| 920 throw OrthancException(ErrorCode_BadFileFormat); | |
| 921 } | |
| 922 | |
| 923 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 924 } | |
| 925 | |
| 926 | |
| 927 template <typename T> | |
| 928 static void ExtractPngImageTruncate(std::string& result, | |
| 929 DicomIntegerPixelAccessor& accessor, | |
| 930 PixelFormat format) | |
| 931 { | |
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932 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 933 |
| 934 PngWriter w; | |
| 935 | |
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936 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 937 T* pixel = &image[0]; |
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938 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 939 { |
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940 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 941 { |
| 942 int32_t v = accessor.GetValue(x, y); | |
| 943 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 944 *pixel = std::numeric_limits<T>::min(); | |
| 945 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 946 *pixel = std::numeric_limits<T>::max(); | |
| 947 else | |
| 948 *pixel = static_cast<T>(v); | |
| 949 } | |
| 950 } | |
| 951 | |
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952 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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953 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 954 } |
| 955 | |
| 956 | |
| 957 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 958 { | |
| 794 | 959 FromDcmtkBridge::SaveToMemoryBuffer(buffer, pimpl_->file_->getDataset()); |
| 790 | 960 } |
| 961 | |
| 962 | |
| 963 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 964 { | |
| 965 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 966 std::string content; | |
| 967 SaveToMemoryBuffer(content); | |
| 968 Toolbox::WriteFile(content, path); | |
| 969 } | |
| 970 | |
| 971 | |
| 794 | 972 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 973 { |
| 794 | 974 pimpl_->file_.reset(new DcmFileFormat); |
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975 pimpl_->encoding_ = Encoding_Ascii; |
| 790 | 976 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 977 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 978 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 979 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 980 } | |
| 981 | |
| 791 | 982 |
| 794 | 983 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 984 { |
| 985 Setup(content, size); | |
| 986 } | |
| 987 | |
| 794 | 988 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 989 { |
| 990 if (content.size() == 0) | |
| 991 { | |
| 992 Setup(NULL, 0); | |
| 993 } | |
| 994 else | |
| 995 { | |
| 996 Setup(&content[0], content.size()); | |
| 997 } | |
| 998 } | |
| 792 | 999 |
| 1000 | |
| 794 | 1001 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1002 pimpl_(new PImpl) | |
| 792 | 1003 { |
| 794 | 1004 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
956
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|
1005 |
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1006 pimpl_->encoding_ = other.pimpl_->encoding_; |
| 792 | 1007 } |
| 1008 | |
| 1009 | |
| 1010 ParsedDicomFile::~ParsedDicomFile() | |
| 1011 { | |
| 794 | 1012 delete pimpl_; |
| 792 | 1013 } |
| 1014 | |
| 793 | 1015 |
| 1016 void* ParsedDicomFile::GetDcmtkObject() | |
| 1017 { | |
| 794 | 1018 return pimpl_->file_.get(); |
| 793 | 1019 } |
| 1020 | |
| 1021 | |
| 1022 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1023 { | |
| 794 | 1024 return new ParsedDicomFile(*this); |
| 793 | 1025 } |
|
800
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|
1026 |
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1027 |
|
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1028 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
|
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1029 { |
|
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1030 std::string mime, content; |
|
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1031 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
|
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1032 |
|
809
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1033 std::string decoded; |
|
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1034 Toolbox::DecodeBase64(decoded, content); |
|
800
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1035 |
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1036 if (mime == "image/png") |
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1037 { |
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1038 PngReader reader; |
|
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1039 reader.ReadFromMemory(decoded); |
|
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1040 EmbedImage(reader); |
|
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1041 } |
|
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1042 else |
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1043 { |
|
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1044 throw OrthancException(ErrorCode_NotImplemented); |
|
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1045 } |
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1046 } |
|
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1047 |
|
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1048 |
|
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1049 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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1050 { |
|
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1051 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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1052 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
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1053 accessor.GetFormat() != PixelFormat_RGB24 && |
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1054 accessor.GetFormat() != PixelFormat_RGBA32) |
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1055 { |
|
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1056 throw OrthancException(ErrorCode_NotImplemented); |
|
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1057 } |
|
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1058 |
|
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1059 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1060 { |
|
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1061 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1062 } |
|
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1063 |
|
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1064 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
|
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1065 |
|
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1066 Remove(DICOM_TAG_PIXEL_DATA); |
|
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1067 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
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1068 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
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1069 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
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1070 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
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1071 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
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1072 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
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1073 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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1074 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
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1075 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1076 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
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1077 |
|
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1078 unsigned int bytesPerPixel = 1; |
|
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1079 |
|
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1080 switch (accessor.GetFormat()) |
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1081 { |
|
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1082 case PixelFormat_RGB24: |
|
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1083 case PixelFormat_RGBA32: |
|
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1084 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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1085 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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1086 bytesPerPixel = 3; |
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1087 break; |
|
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1088 |
|
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1089 case PixelFormat_Grayscale8: |
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1090 break; |
|
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1091 |
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1092 case PixelFormat_Grayscale16: |
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1093 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
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1094 Replace(DICOM_TAG_BITS_STORED, "16"); |
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1095 Replace(DICOM_TAG_HIGH_BIT, "15"); |
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1096 bytesPerPixel = 2; |
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1097 break; |
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1098 |
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1099 default: |
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1100 throw OrthancException(ErrorCode_NotImplemented); |
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1101 } |
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1102 |
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1103 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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1104 DICOM_TAG_PIXEL_DATA.GetElement()); |
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1105 |
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1106 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
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1107 |
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1108 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
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1109 Uint8* target = NULL; |
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1110 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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1111 |
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1112 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1113 { |
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1114 switch (accessor.GetFormat()) |
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1115 { |
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1116 case PixelFormat_RGB24: |
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1117 case PixelFormat_Grayscale8: |
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1118 case PixelFormat_Grayscale16: |
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1119 case PixelFormat_SignedGrayscale16: |
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1120 { |
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1121 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
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1122 target += pitch; |
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1123 break; |
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1124 } |
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1125 |
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1126 case PixelFormat_RGBA32: |
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1127 { |
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1128 // The alpha channel is not supported by the DICOM standard |
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1129 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
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1130 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
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1131 { |
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1132 target[0] = source[0]; |
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1133 target[1] = source[1]; |
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1134 target[2] = source[2]; |
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1135 } |
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1136 |
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1137 break; |
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1138 } |
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1139 |
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1140 default: |
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1141 throw OrthancException(ErrorCode_NotImplemented); |
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1142 } |
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1143 } |
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1144 |
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1145 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
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1146 { |
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1147 throw OrthancException(ErrorCode_InternalError); |
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1148 } |
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1149 } |
|
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1150 |
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1151 |
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1152 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
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1153 unsigned int frame) |
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1154 { |
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1155 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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1156 |
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1157 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
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1158 { |
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1159 throw OrthancException(ErrorCode_BadFileFormat); |
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1160 } |
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1161 } |
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1162 |
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1163 |
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1164 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
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1165 unsigned int frame, |
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1166 ImageExtractionMode mode) |
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1167 { |
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1168 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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1169 |
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1170 bool ok = false; |
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1171 |
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1172 switch (mode) |
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1173 { |
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1174 case ImageExtractionMode_UInt8: |
|
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1175 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
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1176 break; |
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1177 |
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1178 case ImageExtractionMode_UInt16: |
|
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1179 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
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1180 break; |
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1181 |
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1182 case ImageExtractionMode_Int16: |
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1183 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
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1184 break; |
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1185 |
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1186 case ImageExtractionMode_Preview: |
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1187 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
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|
1188 break; |
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1189 |
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|
1190 default: |
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1191 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1192 } |
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1193 |
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1194 if (!ok) |
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1195 { |
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1196 throw OrthancException(ErrorCode_BadFileFormat); |
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1197 } |
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1198 } |
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1199 |
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1200 |
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1201 void ParsedDicomFile::ExtractPngImage(std::string& result, |
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1202 unsigned int frame, |
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1203 ImageExtractionMode mode) |
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1204 { |
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1205 ImageBuffer buffer; |
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1206 ExtractImage(buffer, frame, mode); |
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1207 |
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1208 ImageAccessor accessor(buffer.GetConstAccessor()); |
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1209 PngWriter writer; |
|
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1210 writer.WriteToMemory(result, accessor); |
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1211 } |
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1212 |
|
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1213 |
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1214 Encoding ParsedDicomFile::GetEncoding() const |
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1215 { |
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1216 return pimpl_->encoding_; |
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1217 } |
| 790 | 1218 } |