Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 817:83f0cae7dfcc
little endianness is ok
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 08 May 2014 16:44:39 +0200 |
| parents | 5dcfdd3bfca9 |
| children | a811bdf8b8eb |
| 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 | |
| 75 #ifndef NOMINMAX | |
| 76 #define NOMINMAX | |
| 77 #endif | |
| 78 | |
| 79 #include "ParsedDicomFile.h" | |
| 80 | |
| 81 #include "FromDcmtkBridge.h" | |
| 82 #include "ToDcmtkBridge.h" | |
| 83 #include "../Core/Toolbox.h" | |
| 84 #include "../Core/OrthancException.h" | |
| 799 | 85 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 86 #include "../Core/Uuid.h" |
| 87 #include "../Core/DicomFormat/DicomString.h" | |
| 88 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 89 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
90 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 91 |
| 92 #include <list> | |
| 93 #include <limits> | |
| 94 | |
| 95 #include <boost/lexical_cast.hpp> | |
| 96 | |
| 97 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 98 #include <dcmtk/dcmdata/dcdicent.h> | |
| 99 #include <dcmtk/dcmdata/dcdict.h> | |
| 100 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 101 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 102 #include <dcmtk/dcmdata/dcuid.h> | |
| 103 #include <dcmtk/dcmdata/dcmetinf.h> | |
| 104 | |
| 105 #include <dcmtk/dcmdata/dcvrae.h> | |
| 106 #include <dcmtk/dcmdata/dcvras.h> | |
| 107 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 108 #include <dcmtk/dcmdata/dcvrda.h> | |
| 109 #include <dcmtk/dcmdata/dcvrds.h> | |
| 110 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 111 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 112 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 113 #include <dcmtk/dcmdata/dcvris.h> | |
| 114 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 115 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 116 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 117 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 118 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 119 #include <dcmtk/dcmdata/dcvrss.h> | |
| 120 #include <dcmtk/dcmdata/dcvrst.h> | |
| 121 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 122 #include <dcmtk/dcmdata/dcvrui.h> | |
| 123 #include <dcmtk/dcmdata/dcvrul.h> | |
| 124 #include <dcmtk/dcmdata/dcvrus.h> | |
| 125 #include <dcmtk/dcmdata/dcvrut.h> | |
| 126 #include <dcmtk/dcmdata/dcpixel.h> | |
| 127 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 128 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 129 | |
| 130 | |
| 131 #include <boost/math/special_functions/round.hpp> | |
| 132 #include <glog/logging.h> | |
| 133 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 134 | |
| 135 | |
| 136 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 137 | |
| 138 | |
| 139 | |
| 140 namespace Orthanc | |
| 141 { | |
| 794 | 142 struct ParsedDicomFile::PImpl |
| 143 { | |
| 144 std::auto_ptr<DcmFileFormat> file_; | |
| 145 }; | |
| 146 | |
| 147 | |
| 148 // This method can only be called from the constructors! | |
| 790 | 149 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 150 { | |
| 151 DcmInputBufferStream is; | |
| 152 if (size > 0) | |
| 153 { | |
| 154 is.setBuffer(buffer, size); | |
| 155 } | |
| 156 is.setEos(); | |
| 157 | |
| 794 | 158 pimpl_->file_.reset(new DcmFileFormat); |
| 159 pimpl_->file_->transferInit(); | |
| 160 if (!pimpl_->file_->read(is).good()) | |
| 790 | 161 { |
| 794 | 162 delete pimpl_; // Avoid a memory leak due to exception |
| 163 // throwing, as we are in the constructor | |
| 164 | |
| 790 | 165 throw OrthancException(ErrorCode_BadFileFormat); |
| 166 } | |
| 794 | 167 pimpl_->file_->loadAllDataIntoMemory(); |
| 168 pimpl_->file_->transferEnd(); | |
| 790 | 169 } |
| 170 | |
| 171 | |
| 172 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 173 DcmItem& dicom) | |
| 174 { | |
| 175 Json::Value v = Json::arrayValue; | |
| 176 | |
| 177 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 178 { | |
| 179 DcmElement* element = dicom.getElement(i); | |
| 180 if (element) | |
| 181 { | |
| 182 char buf[16]; | |
| 183 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 184 v.append(buf); | |
| 185 } | |
| 186 } | |
| 187 | |
| 188 output.AnswerJson(v); | |
| 189 } | |
| 190 | |
| 191 static inline uint16_t GetCharValue(char c) | |
| 192 { | |
| 193 if (c >= '0' && c <= '9') | |
| 194 return c - '0'; | |
| 195 else if (c >= 'a' && c <= 'f') | |
| 196 return c - 'a' + 10; | |
| 197 else if (c >= 'A' && c <= 'F') | |
| 198 return c - 'A' + 10; | |
| 199 else | |
| 200 return 0; | |
| 201 } | |
| 202 | |
| 203 static inline uint16_t GetTagValue(const char* c) | |
| 204 { | |
| 205 return ((GetCharValue(c[0]) << 12) + | |
| 206 (GetCharValue(c[1]) << 8) + | |
| 207 (GetCharValue(c[2]) << 4) + | |
| 208 GetCharValue(c[3])); | |
| 209 } | |
| 210 | |
| 211 static void ParseTagAndGroup(DcmTagKey& key, | |
| 212 const std::string& tag) | |
| 213 { | |
| 214 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 215 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 216 } | |
| 217 | |
| 218 | |
| 219 static void SendSequence(RestApiOutput& output, | |
| 220 DcmSequenceOfItems& sequence) | |
| 221 { | |
| 222 // This element is a sequence | |
| 223 Json::Value v = Json::arrayValue; | |
| 224 | |
| 225 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 226 { | |
| 227 v.append(boost::lexical_cast<std::string>(i)); | |
| 228 } | |
| 229 | |
| 230 output.AnswerJson(v); | |
| 231 } | |
| 232 | |
| 233 | |
| 234 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 235 E_TransferSyntax transferSyntax) | |
| 236 { | |
| 237 DcmPixelSequence* pixelSequence = NULL; | |
| 238 if (pixelData.getEncapsulatedRepresentation | |
| 239 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 240 { | |
| 241 return pixelSequence->card(); | |
| 242 } | |
| 243 else | |
| 244 { | |
| 245 return 1; | |
| 246 } | |
| 247 } | |
| 248 | |
| 249 | |
| 250 static void AnswerDicomField(RestApiOutput& output, | |
| 251 DcmElement& element, | |
| 252 E_TransferSyntax transferSyntax) | |
| 253 { | |
| 254 // This element is nor a sequence, neither a pixel-data | |
| 255 std::string buffer; | |
| 256 buffer.resize(65536); | |
| 257 Uint32 length = element.getLength(transferSyntax); | |
| 258 Uint32 offset = 0; | |
| 259 | |
| 260 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL); | |
| 261 | |
| 262 while (offset < length) | |
| 263 { | |
| 264 Uint32 nbytes; | |
| 265 if (length - offset < buffer.size()) | |
| 266 { | |
| 267 nbytes = length - offset; | |
| 268 } | |
| 269 else | |
| 270 { | |
| 271 nbytes = buffer.size(); | |
| 272 } | |
| 273 | |
| 274 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); | |
| 275 | |
| 276 if (cond.good()) | |
| 277 { | |
| 278 output.GetLowLevelOutput().Send(&buffer[0], nbytes); | |
| 279 offset += nbytes; | |
| 280 } | |
| 281 else | |
| 282 { | |
| 283 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); | |
| 284 return; | |
| 285 } | |
| 286 } | |
| 287 | |
| 288 output.MarkLowLevelOutputDone(); | |
| 289 } | |
| 290 | |
| 291 | |
| 292 static bool AnswerPixelData(RestApiOutput& output, | |
| 293 DcmItem& dicom, | |
| 294 E_TransferSyntax transferSyntax, | |
| 295 const std::string* blockUri) | |
| 296 { | |
| 297 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 298 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 299 | |
| 300 DcmElement *element = NULL; | |
| 301 if (!dicom.findAndGetElement(k, element).good() || | |
| 302 element == NULL) | |
| 303 { | |
| 304 return false; | |
| 305 } | |
| 306 | |
| 307 try | |
| 308 { | |
| 309 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 310 if (blockUri == NULL) | |
| 311 { | |
| 312 // The user asks how many blocks are presents in this pixel data | |
| 313 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 314 | |
| 315 Json::Value result(Json::arrayValue); | |
| 316 for (unsigned int i = 0; i < blocks; i++) | |
| 317 { | |
| 318 result.append(boost::lexical_cast<std::string>(i)); | |
| 319 } | |
| 320 | |
| 321 output.AnswerJson(result); | |
| 322 return true; | |
| 323 } | |
| 324 | |
| 325 | |
| 326 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 327 | |
| 328 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 329 { | |
| 330 DcmPixelSequence* pixelSequence = NULL; | |
| 331 if (pixelData.getEncapsulatedRepresentation | |
| 332 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 333 { | |
| 334 // This is the case for JPEG transfer syntaxes | |
| 335 if (block < pixelSequence->card()) | |
| 336 { | |
| 337 DcmPixelItem* pixelItem = NULL; | |
| 338 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 339 { | |
| 340 if (pixelItem->getLength() == 0) | |
| 341 { | |
| 342 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 343 return true; | |
| 344 } | |
| 345 | |
| 346 Uint8* buffer = NULL; | |
| 347 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 348 { | |
| 349 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 350 return true; | |
| 351 } | |
| 352 } | |
| 353 } | |
| 354 } | |
| 355 else | |
| 356 { | |
| 357 // This is the case for raw, uncompressed image buffers | |
| 358 assert(*blockUri == "0"); | |
| 359 AnswerDicomField(output, *element, transferSyntax); | |
| 360 } | |
| 361 } | |
| 362 } | |
| 363 catch (boost::bad_lexical_cast&) | |
| 364 { | |
| 365 // The URI entered by the user is not a number | |
| 366 } | |
| 367 catch (std::bad_cast&) | |
| 368 { | |
| 369 // This should never happen | |
| 370 } | |
| 371 | |
| 372 return false; | |
| 373 } | |
| 374 | |
| 375 | |
| 376 | |
| 377 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 378 const std::string& tag, | |
| 379 DcmItem& dicom, | |
| 380 E_TransferSyntax transferSyntax) | |
| 381 { | |
| 382 DcmTagKey k; | |
| 383 ParseTagAndGroup(k, tag); | |
| 384 | |
| 385 DcmSequenceOfItems* sequence = NULL; | |
| 386 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 387 sequence != NULL && | |
| 388 sequence->getVR() == EVR_SQ) | |
| 389 { | |
| 390 SendSequence(output, *sequence); | |
| 391 return; | |
| 392 } | |
| 393 | |
| 394 DcmElement* element = NULL; | |
| 395 if (dicom.findAndGetElement(k, element).good() && | |
| 396 element != NULL && | |
| 397 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 398 element->getVR() != EVR_SQ) | |
| 399 { | |
| 400 AnswerDicomField(output, *element, transferSyntax); | |
| 401 } | |
| 402 } | |
| 403 | |
| 404 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 405 const UriComponents& uri) | |
| 406 { | |
| 794 | 407 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 408 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 409 |
| 410 // Special case: Accessing the pixel data | |
| 411 if (uri.size() == 1 || | |
| 412 uri.size() == 2) | |
| 413 { | |
| 414 DcmTagKey tag; | |
| 415 ParseTagAndGroup(tag, uri[0]); | |
| 416 | |
| 417 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 418 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 419 { | |
| 420 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 421 return; | |
| 422 } | |
| 423 } | |
| 424 | |
| 425 // Go down in the tag hierarchy according to the URI | |
| 426 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 427 { | |
| 428 size_t index; | |
| 429 try | |
| 430 { | |
| 431 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 432 } | |
| 433 catch (boost::bad_lexical_cast&) | |
| 434 { | |
| 435 return; | |
| 436 } | |
| 437 | |
| 438 DcmTagKey k; | |
| 439 DcmItem *child = NULL; | |
| 440 ParseTagAndGroup(k, uri[2 * pos]); | |
| 441 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 442 child == NULL) | |
| 443 { | |
| 444 return; | |
| 445 } | |
| 446 | |
| 447 dicom = child; | |
| 448 } | |
| 449 | |
| 450 // We have reached the end of the URI | |
| 451 if (uri.size() % 2 == 0) | |
| 452 { | |
| 453 SendPathValueForDictionary(output, *dicom); | |
| 454 } | |
| 455 else | |
| 456 { | |
| 457 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 458 } | |
| 459 } | |
| 460 | |
| 461 | |
| 462 | |
| 463 | |
| 464 | |
| 465 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 466 { | |
| 467 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 468 | |
| 469 switch (key.getEVR()) | |
| 470 { | |
| 471 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 472 | |
| 473 /** | |
| 474 * TODO. | |
| 475 **/ | |
| 476 | |
| 477 case EVR_OB: // other byte | |
| 478 case EVR_OF: // other float | |
| 479 case EVR_OW: // other word | |
| 480 case EVR_AT: // attribute tag | |
| 481 throw OrthancException(ErrorCode_NotImplemented); | |
| 482 | |
| 483 case EVR_UN: // unknown value representation | |
| 484 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 485 | |
| 486 | |
| 487 /** | |
| 488 * String types. | |
| 489 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 490 **/ | |
| 491 | |
| 492 case EVR_AS: // age string | |
| 493 return new DcmAgeString(key); | |
| 494 | |
| 495 case EVR_AE: // application entity title | |
| 496 return new DcmApplicationEntity(key); | |
| 497 | |
| 498 case EVR_CS: // code string | |
| 499 return new DcmCodeString(key); | |
| 500 | |
| 501 case EVR_DA: // date string | |
| 502 return new DcmDate(key); | |
| 503 | |
| 504 case EVR_DT: // date time string | |
| 505 return new DcmDateTime(key); | |
| 506 | |
| 507 case EVR_DS: // decimal string | |
| 508 return new DcmDecimalString(key); | |
| 509 | |
| 510 case EVR_IS: // integer string | |
| 511 return new DcmIntegerString(key); | |
| 512 | |
| 513 case EVR_TM: // time string | |
| 514 return new DcmTime(key); | |
| 515 | |
| 516 case EVR_UI: // unique identifier | |
| 517 return new DcmUniqueIdentifier(key); | |
| 518 | |
| 519 case EVR_ST: // short text | |
| 520 return new DcmShortText(key); | |
| 521 | |
| 522 case EVR_LO: // long string | |
| 523 return new DcmLongString(key); | |
| 524 | |
| 525 case EVR_LT: // long text | |
| 526 return new DcmLongText(key); | |
| 527 | |
| 528 case EVR_UT: // unlimited text | |
| 529 return new DcmUnlimitedText(key); | |
| 530 | |
| 531 case EVR_SH: // short string | |
| 532 return new DcmShortString(key); | |
| 533 | |
| 534 case EVR_PN: // person name | |
| 535 return new DcmPersonName(key); | |
| 536 | |
| 537 | |
| 538 /** | |
| 539 * Numerical types | |
| 540 **/ | |
| 541 | |
| 542 case EVR_SL: // signed long | |
| 543 return new DcmSignedLong(key); | |
| 544 | |
| 545 case EVR_SS: // signed short | |
| 546 return new DcmSignedShort(key); | |
| 547 | |
| 548 case EVR_UL: // unsigned long | |
| 549 return new DcmUnsignedLong(key); | |
| 550 | |
| 551 case EVR_US: // unsigned short | |
| 552 return new DcmUnsignedShort(key); | |
| 553 | |
| 554 case EVR_FL: // float single-precision | |
| 555 return new DcmFloatingPointSingle(key); | |
| 556 | |
| 557 case EVR_FD: // float double-precision | |
| 558 return new DcmFloatingPointDouble(key); | |
| 559 | |
| 560 | |
| 561 /** | |
| 562 * Sequence types, should never occur at this point. | |
| 563 **/ | |
| 564 | |
| 565 case EVR_SQ: // sequence of items | |
| 566 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 567 | |
| 568 | |
| 569 /** | |
| 570 * Internal to DCMTK. | |
| 571 **/ | |
| 572 | |
| 573 case EVR_ox: // OB or OW depending on context | |
| 574 case EVR_xs: // SS or US depending on context | |
| 575 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 576 case EVR_na: // na="not applicable", for data which has no VR | |
| 577 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 578 case EVR_item: // used internally for items | |
| 579 case EVR_metainfo: // used internally for meta info datasets | |
| 580 case EVR_dataset: // used internally for datasets | |
| 581 case EVR_fileFormat: // used internally for DICOM files | |
| 582 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 583 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 584 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 585 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 586 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 587 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 588 case EVR_OverlayData: // used internally for overlay data | |
| 589 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 590 default: | |
| 591 break; | |
| 592 } | |
| 593 | |
| 594 throw OrthancException(ErrorCode_InternalError); | |
| 595 } | |
| 596 | |
| 597 | |
| 598 | |
| 599 static void FillElementWithString(DcmElement& element, | |
| 600 const DicomTag& tag, | |
| 601 const std::string& value) | |
| 602 { | |
| 603 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 604 bool ok = false; | |
| 605 | |
| 606 try | |
| 607 { | |
| 608 switch (key.getEVR()) | |
| 609 { | |
| 610 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 611 | |
| 612 /** | |
| 613 * TODO. | |
| 614 **/ | |
| 615 | |
| 616 case EVR_OB: // other byte | |
| 617 case EVR_OF: // other float | |
| 618 case EVR_OW: // other word | |
| 619 case EVR_AT: // attribute tag | |
| 620 throw OrthancException(ErrorCode_NotImplemented); | |
| 621 | |
| 622 case EVR_UN: // unknown value representation | |
| 623 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 624 | |
| 625 | |
| 626 /** | |
| 627 * String types. | |
| 628 **/ | |
| 629 | |
| 630 case EVR_DS: // decimal string | |
| 631 case EVR_IS: // integer string | |
| 632 case EVR_AS: // age string | |
| 633 case EVR_DA: // date string | |
| 634 case EVR_DT: // date time string | |
| 635 case EVR_TM: // time string | |
| 636 case EVR_AE: // application entity title | |
| 637 case EVR_CS: // code string | |
| 638 case EVR_SH: // short string | |
| 639 case EVR_LO: // long string | |
| 640 case EVR_ST: // short text | |
| 641 case EVR_LT: // long text | |
| 642 case EVR_UT: // unlimited text | |
| 643 case EVR_PN: // person name | |
| 644 case EVR_UI: // unique identifier | |
| 645 { | |
| 646 ok = element.putString(value.c_str()).good(); | |
| 647 break; | |
| 648 } | |
| 649 | |
| 650 | |
| 651 /** | |
| 652 * Numerical types | |
| 653 **/ | |
| 654 | |
| 655 case EVR_SL: // signed long | |
| 656 { | |
| 657 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 658 break; | |
| 659 } | |
| 660 | |
| 661 case EVR_SS: // signed short | |
| 662 { | |
| 663 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 664 break; | |
| 665 } | |
| 666 | |
| 667 case EVR_UL: // unsigned long | |
| 668 { | |
| 669 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 670 break; | |
| 671 } | |
| 672 | |
| 673 case EVR_US: // unsigned short | |
| 674 { | |
| 675 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 676 break; | |
| 677 } | |
| 678 | |
| 679 case EVR_FL: // float single-precision | |
| 680 { | |
| 681 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 682 break; | |
| 683 } | |
| 684 | |
| 685 case EVR_FD: // float double-precision | |
| 686 { | |
| 687 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 688 break; | |
| 689 } | |
| 690 | |
| 691 | |
| 692 /** | |
| 693 * Sequence types, should never occur at this point. | |
| 694 **/ | |
| 695 | |
| 696 case EVR_SQ: // sequence of items | |
| 697 { | |
| 698 ok = false; | |
| 699 break; | |
| 700 } | |
| 701 | |
| 702 | |
| 703 /** | |
| 704 * Internal to DCMTK. | |
| 705 **/ | |
| 706 | |
| 707 case EVR_ox: // OB or OW depending on context | |
| 708 case EVR_xs: // SS or US depending on context | |
| 709 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 710 case EVR_na: // na="not applicable", for data which has no VR | |
| 711 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 712 case EVR_item: // used internally for items | |
| 713 case EVR_metainfo: // used internally for meta info datasets | |
| 714 case EVR_dataset: // used internally for datasets | |
| 715 case EVR_fileFormat: // used internally for DICOM files | |
| 716 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 717 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 718 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 719 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 720 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 721 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 722 case EVR_OverlayData: // used internally for overlay data | |
| 723 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 724 default: | |
| 725 break; | |
| 726 } | |
| 727 } | |
| 728 catch (boost::bad_lexical_cast&) | |
| 729 { | |
| 730 ok = false; | |
| 731 } | |
| 732 | |
| 733 if (!ok) | |
| 734 { | |
| 735 throw OrthancException(ErrorCode_InternalError); | |
| 736 } | |
| 737 } | |
| 738 | |
| 739 | |
| 740 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 741 { | |
| 742 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 743 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 744 if (element != NULL) |
| 745 { | |
| 746 delete element; | |
| 747 } | |
| 748 } | |
| 749 | |
| 750 | |
| 751 | |
| 752 void ParsedDicomFile::RemovePrivateTags() | |
| 753 { | |
| 754 typedef std::list<DcmElement*> Tags; | |
| 755 | |
| 756 Tags privateTags; | |
| 757 | |
| 794 | 758 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 759 for (unsigned long i = 0; i < dataset.card(); i++) |
| 760 { | |
| 761 DcmElement* element = dataset.getElement(i); | |
| 762 DcmTag tag(element->getTag()); | |
| 763 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK | |
| 764 tag.getPrivateCreator() != NULL) | |
| 765 { | |
| 766 privateTags.push_back(element); | |
| 767 } | |
| 768 } | |
| 769 | |
| 770 for (Tags::iterator it = privateTags.begin(); | |
| 771 it != privateTags.end(); ++it) | |
| 772 { | |
| 773 DcmElement* tmp = dataset.remove(*it); | |
| 774 if (tmp != NULL) | |
| 775 { | |
| 776 delete tmp; | |
| 777 } | |
| 778 } | |
| 779 } | |
| 780 | |
| 781 | |
| 782 | |
| 783 void ParsedDicomFile::Insert(const DicomTag& tag, | |
| 784 const std::string& value) | |
| 785 { | |
| 786 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); | |
| 787 FillElementWithString(*element, tag, value); | |
| 788 | |
| 794 | 789 if (!pimpl_->file_->getDataset()->insert(element.release(), false, false).good()) |
| 790 | 790 { |
| 791 // This field already exists | |
| 792 throw OrthancException(ErrorCode_InternalError); | |
| 793 } | |
| 794 } | |
| 795 | |
| 796 | |
| 797 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 798 const std::string& value, | |
| 799 DicomReplaceMode mode) | |
| 800 { | |
| 801 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 802 DcmElement* element = NULL; | |
| 803 | |
| 794 | 804 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 805 element == NULL) |
| 806 { | |
| 807 // This field does not exist, act wrt. the specified "mode" | |
| 808 switch (mode) | |
| 809 { | |
| 810 case DicomReplaceMode_InsertIfAbsent: | |
| 811 Insert(tag, value); | |
| 812 break; | |
| 813 | |
| 814 case DicomReplaceMode_ThrowIfAbsent: | |
| 815 throw OrthancException(ErrorCode_InexistentItem); | |
| 816 | |
| 817 case DicomReplaceMode_IgnoreIfAbsent: | |
| 818 return; | |
| 819 } | |
| 820 } | |
| 821 else | |
| 822 { | |
| 823 FillElementWithString(*element, tag, value); | |
| 824 } | |
| 825 | |
| 826 | |
| 827 /** | |
| 828 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 829 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 830 * you make changes to the related tags in the dataset ('SOP Class | |
| 831 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 832 * options. You can disable this behaviour by using the -nmu | |
| 833 * option. | |
| 834 **/ | |
| 835 | |
| 836 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 837 { | |
| 838 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 839 } | |
| 840 | |
| 841 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 842 { | |
| 843 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 844 } | |
| 845 } | |
| 846 | |
| 847 | |
| 848 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 849 { | |
| 850 std::string serialized; | |
| 794 | 851 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, pimpl_->file_->getDataset())) |
| 790 | 852 { |
| 853 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 854 } | |
| 855 } | |
| 856 | |
| 857 | |
| 858 | |
| 859 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 860 const DicomTag& tag) | |
| 861 { | |
| 862 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 863 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 864 DcmElement* element = NULL; |
| 865 if (!dataset.findAndGetElement(k, element).good() || | |
| 866 element == NULL) | |
| 867 { | |
| 868 return false; | |
| 869 } | |
| 870 | |
| 871 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); | |
| 872 | |
| 873 if (v.get() == NULL) | |
| 874 { | |
| 875 value = ""; | |
| 876 } | |
| 877 else | |
| 878 { | |
| 879 value = v->AsString(); | |
| 880 } | |
| 881 | |
| 882 return true; | |
| 883 } | |
| 884 | |
| 885 | |
| 886 | |
| 887 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 888 { | |
| 889 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 890 | |
| 891 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 892 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 893 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 894 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 895 { | |
| 896 throw OrthancException(ErrorCode_BadFileFormat); | |
| 897 } | |
| 898 | |
| 899 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 900 } | |
| 901 | |
| 902 | |
| 903 static void StoreElement(Json::Value& target, | |
| 904 DcmElement& element, | |
| 905 unsigned int maxStringLength); | |
| 906 | |
| 907 static void StoreItem(Json::Value& target, | |
| 908 DcmItem& item, | |
| 909 unsigned int maxStringLength) | |
| 910 { | |
| 911 target = Json::Value(Json::objectValue); | |
| 912 | |
| 913 for (unsigned long i = 0; i < item.card(); i++) | |
| 914 { | |
| 915 DcmElement* element = item.getElement(i); | |
| 916 StoreElement(target, *element, maxStringLength); | |
| 917 } | |
| 918 } | |
| 919 | |
| 920 | |
| 921 static void StoreElement(Json::Value& target, | |
| 922 DcmElement& element, | |
| 923 unsigned int maxStringLength) | |
| 924 { | |
| 925 assert(target.type() == Json::objectValue); | |
| 926 | |
| 927 DicomTag tag(FromDcmtkBridge::GetTag(element)); | |
| 928 const std::string formattedTag = tag.Format(); | |
| 929 | |
| 930 #if 0 | |
| 931 const std::string tagName = FromDcmtkBridge::GetName(tag); | |
| 932 #else | |
| 933 // This version of the code gives access to the name of the private tags | |
| 934 DcmTag tagbis(element.getTag()); | |
| 935 const std::string tagName(tagbis.getTagName()); | |
| 936 #endif | |
| 937 | |
| 938 if (element.isLeaf()) | |
| 939 { | |
| 940 Json::Value value(Json::objectValue); | |
| 941 value["Name"] = tagName; | |
| 942 | |
| 943 if (tagbis.getPrivateCreator() != NULL) | |
| 944 { | |
| 945 value["PrivateCreator"] = tagbis.getPrivateCreator(); | |
| 946 } | |
| 947 | |
| 948 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); | |
| 949 if (v->IsNull()) | |
| 950 { | |
| 951 value["Type"] = "Null"; | |
| 952 value["Value"] = Json::nullValue; | |
| 953 } | |
| 954 else | |
| 955 { | |
| 956 std::string s = v->AsString(); | |
| 957 if (maxStringLength == 0 || | |
| 958 s.size() <= maxStringLength) | |
| 959 { | |
| 960 value["Type"] = "String"; | |
| 961 value["Value"] = s; | |
| 962 } | |
| 963 else | |
| 964 { | |
| 965 value["Type"] = "TooLong"; | |
| 966 value["Value"] = Json::nullValue; | |
| 967 } | |
| 968 } | |
| 969 | |
| 970 target[formattedTag] = value; | |
| 971 } | |
| 972 else | |
| 973 { | |
| 974 Json::Value children(Json::arrayValue); | |
| 975 | |
| 976 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 977 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 978 // etc. are not." The following cast is thus OK. | |
| 979 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 980 | |
| 981 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 982 { | |
| 983 DcmItem* child = sequence.getItem(i); | |
| 984 Json::Value& v = children.append(Json::objectValue); | |
| 985 StoreItem(v, *child, maxStringLength); | |
| 986 } | |
| 987 | |
| 988 target[formattedTag]["Name"] = tagName; | |
| 989 target[formattedTag]["Type"] = "Sequence"; | |
| 990 target[formattedTag]["Value"] = children; | |
| 991 } | |
| 992 } | |
| 993 | |
| 994 | |
| 995 template <typename T> | |
| 996 static void ExtractPngImageTruncate(std::string& result, | |
| 997 DicomIntegerPixelAccessor& accessor, | |
| 998 PixelFormat format) | |
| 999 { | |
| 1000 assert(accessor.GetChannelCount() == 1); | |
| 1001 | |
| 1002 PngWriter w; | |
| 1003 | |
| 1004 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); | |
| 1005 T* pixel = &image[0]; | |
| 1006 for (unsigned int y = 0; y < accessor.GetHeight(); y++) | |
| 1007 { | |
| 1008 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) | |
| 1009 { | |
| 1010 int32_t v = accessor.GetValue(x, y); | |
| 1011 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 1012 *pixel = std::numeric_limits<T>::min(); | |
| 1013 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 1014 *pixel = std::numeric_limits<T>::max(); | |
| 1015 else | |
| 1016 *pixel = static_cast<T>(v); | |
| 1017 } | |
| 1018 } | |
| 1019 | |
| 1020 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), | |
| 1021 accessor.GetWidth() * sizeof(T), format, &image[0]); | |
| 1022 } | |
| 1023 | |
| 1024 | |
| 1025 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 1026 { | |
| 794 | 1027 FromDcmtkBridge::SaveToMemoryBuffer(buffer, pimpl_->file_->getDataset()); |
| 790 | 1028 } |
| 1029 | |
| 1030 | |
| 1031 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 1032 { | |
| 1033 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 1034 std::string content; | |
| 1035 SaveToMemoryBuffer(content); | |
| 1036 Toolbox::WriteFile(content, path); | |
| 1037 } | |
| 1038 | |
| 1039 | |
| 794 | 1040 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 1041 { |
| 794 | 1042 pimpl_->file_.reset(new DcmFileFormat); |
| 790 | 1043 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 1044 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 1045 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 1046 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 1047 } | |
| 1048 | |
| 791 | 1049 |
| 794 | 1050 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 1051 { |
| 1052 Setup(content, size); | |
| 1053 } | |
| 1054 | |
| 794 | 1055 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 1056 { |
| 1057 if (content.size() == 0) | |
| 1058 { | |
| 1059 Setup(NULL, 0); | |
| 1060 } | |
| 1061 else | |
| 1062 { | |
| 1063 Setup(&content[0], content.size()); | |
| 1064 } | |
| 1065 } | |
| 792 | 1066 |
| 1067 | |
| 794 | 1068 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1069 pimpl_(new PImpl) | |
| 792 | 1070 { |
| 794 | 1071 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
| 792 | 1072 } |
| 1073 | |
| 1074 | |
| 1075 ParsedDicomFile::~ParsedDicomFile() | |
| 1076 { | |
| 794 | 1077 delete pimpl_; |
| 792 | 1078 } |
| 1079 | |
| 793 | 1080 |
| 1081 void* ParsedDicomFile::GetDcmtkObject() | |
| 1082 { | |
| 794 | 1083 return pimpl_->file_.get(); |
| 793 | 1084 } |
| 1085 | |
| 1086 | |
| 1087 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1088 { | |
| 794 | 1089 return new ParsedDicomFile(*this); |
| 793 | 1090 } |
|
800
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1091 |
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1092 |
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1093 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
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1094 { |
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1095 std::string mime, content; |
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1096 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
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1097 |
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809
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1098 std::string decoded; |
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1099 Toolbox::DecodeBase64(decoded, content); |
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1100 |
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1101 if (mime == "image/png") |
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1102 { |
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1103 PngReader reader; |
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1104 reader.ReadFromMemory(decoded); |
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1105 EmbedImage(reader); |
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1106 } |
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1107 else |
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changeset
|
1108 { |
|
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changeset
|
1109 throw OrthancException(ErrorCode_NotImplemented); |
|
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changeset
|
1110 } |
|
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|
1111 } |
|
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diff
changeset
|
1112 |
|
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changeset
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1113 |
|
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changeset
|
1114 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
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changeset
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1115 { |
|
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1116 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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changeset
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1117 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
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changeset
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1118 accessor.GetFormat() != PixelFormat_RGB24 && |
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changeset
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1119 accessor.GetFormat() != PixelFormat_RGBA32) |
|
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changeset
|
1120 { |
|
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changeset
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1121 throw OrthancException(ErrorCode_NotImplemented); |
|
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changeset
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1122 } |
|
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changeset
|
1123 |
|
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1124 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1125 { |
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1126 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1127 } |
|
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changeset
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1128 |
|
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changeset
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1129 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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changeset
|
1130 |
|
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1131 Remove(DICOM_TAG_PIXEL_DATA); |
|
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1132 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
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1133 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
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1134 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
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1135 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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1136 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
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1137 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
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1138 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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1139 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
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1140 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1141 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
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changeset
|
1142 |
|
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changeset
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1143 unsigned int bytesPerPixel = 1; |
|
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1144 |
|
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changeset
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1145 switch (accessor.GetFormat()) |
|
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1146 { |
|
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1147 case PixelFormat_RGB24: |
|
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1148 case PixelFormat_RGBA32: |
|
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1149 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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1150 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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1151 bytesPerPixel = 3; |
|
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1152 break; |
|
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changeset
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1153 |
|
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changeset
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1154 case PixelFormat_Grayscale8: |
|
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changeset
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1155 break; |
|
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changeset
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1156 |
|
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changeset
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1157 case PixelFormat_Grayscale16: |
|
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1158 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
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1159 Replace(DICOM_TAG_BITS_STORED, "16"); |
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1160 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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1161 bytesPerPixel = 2; |
|
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changeset
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1162 break; |
|
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changeset
|
1163 |
|
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changeset
|
1164 default: |
|
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1165 throw OrthancException(ErrorCode_NotImplemented); |
|
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1166 } |
|
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changeset
|
1167 |
|
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changeset
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1168 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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1169 DICOM_TAG_PIXEL_DATA.GetElement()); |
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changeset
|
1170 |
|
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changeset
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1171 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
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changeset
|
1172 |
|
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1173 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
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1174 Uint8* target = NULL; |
|
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1175 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
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changeset
|
1176 |
|
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1177 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1178 { |
|
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changeset
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1179 switch (accessor.GetFormat()) |
|
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changeset
|
1180 { |
|
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changeset
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1181 case PixelFormat_RGB24: |
|
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changeset
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1182 case PixelFormat_Grayscale8: |
|
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1183 case PixelFormat_Grayscale16: |
|
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1184 case PixelFormat_SignedGrayscale16: |
|
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1185 { |
|
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1186 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
|
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1187 target += pitch; |
|
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changeset
|
1188 break; |
|
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changeset
|
1189 } |
|
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changeset
|
1190 |
|
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changeset
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1191 case PixelFormat_RGBA32: |
|
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1192 { |
|
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1193 // The alpha channel is not supported by the DICOM standard |
|
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1194 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
|
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1195 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
|
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changeset
|
1196 { |
|
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1197 target[0] = source[0]; |
|
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1198 target[1] = source[1]; |
|
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1199 target[2] = source[2]; |
|
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changeset
|
1200 } |
|
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changeset
|
1201 |
|
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changeset
|
1202 break; |
|
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changeset
|
1203 } |
|
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changeset
|
1204 |
|
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changeset
|
1205 default: |
|
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changeset
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1206 throw OrthancException(ErrorCode_NotImplemented); |
|
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changeset
|
1207 } |
|
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|
1208 } |
|
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changeset
|
1209 |
|
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1210 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
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changeset
|
1211 { |
|
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changeset
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1212 throw OrthancException(ErrorCode_InternalError); |
|
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|
1213 } |
|
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changeset
|
1214 } |
| 790 | 1215 } |