Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 831:84513f2ee1f3
pch for unit tests and server
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 02 Jun 2014 12:15:45 +0200 |
| parents | a811bdf8b8eb |
| children | 839be3022203 |
| 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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pch for unit tests and server
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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" | |
| 85 #include "../Core/Toolbox.h" | |
| 86 #include "../Core/OrthancException.h" | |
| 799 | 87 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 88 #include "../Core/Uuid.h" |
| 89 #include "../Core/DicomFormat/DicomString.h" | |
| 90 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 91 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
|
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92 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 93 |
| 94 #include <list> | |
| 95 #include <limits> | |
| 96 | |
| 97 #include <boost/lexical_cast.hpp> | |
| 98 | |
| 99 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 100 #include <dcmtk/dcmdata/dcdicent.h> | |
| 101 #include <dcmtk/dcmdata/dcdict.h> | |
| 102 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 103 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 104 #include <dcmtk/dcmdata/dcuid.h> | |
| 105 #include <dcmtk/dcmdata/dcmetinf.h> | |
| 106 | |
| 107 #include <dcmtk/dcmdata/dcvrae.h> | |
| 108 #include <dcmtk/dcmdata/dcvras.h> | |
| 109 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 110 #include <dcmtk/dcmdata/dcvrda.h> | |
| 111 #include <dcmtk/dcmdata/dcvrds.h> | |
| 112 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 113 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 114 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 115 #include <dcmtk/dcmdata/dcvris.h> | |
| 116 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 117 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 118 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 119 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 120 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 121 #include <dcmtk/dcmdata/dcvrss.h> | |
| 122 #include <dcmtk/dcmdata/dcvrst.h> | |
| 123 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 124 #include <dcmtk/dcmdata/dcvrui.h> | |
| 125 #include <dcmtk/dcmdata/dcvrul.h> | |
| 126 #include <dcmtk/dcmdata/dcvrus.h> | |
| 127 #include <dcmtk/dcmdata/dcvrut.h> | |
| 128 #include <dcmtk/dcmdata/dcpixel.h> | |
| 129 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 130 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 131 | |
| 132 | |
| 133 #include <boost/math/special_functions/round.hpp> | |
| 134 #include <glog/logging.h> | |
| 135 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 136 | |
| 137 | |
| 138 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 139 | |
| 140 | |
| 141 | |
| 142 namespace Orthanc | |
| 143 { | |
| 794 | 144 struct ParsedDicomFile::PImpl |
| 145 { | |
| 146 std::auto_ptr<DcmFileFormat> file_; | |
| 147 }; | |
| 148 | |
| 149 | |
| 150 // This method can only be called from the constructors! | |
| 790 | 151 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 152 { | |
| 153 DcmInputBufferStream is; | |
| 154 if (size > 0) | |
| 155 { | |
| 156 is.setBuffer(buffer, size); | |
| 157 } | |
| 158 is.setEos(); | |
| 159 | |
| 794 | 160 pimpl_->file_.reset(new DcmFileFormat); |
| 161 pimpl_->file_->transferInit(); | |
| 162 if (!pimpl_->file_->read(is).good()) | |
| 790 | 163 { |
| 794 | 164 delete pimpl_; // Avoid a memory leak due to exception |
| 165 // throwing, as we are in the constructor | |
| 166 | |
| 790 | 167 throw OrthancException(ErrorCode_BadFileFormat); |
| 168 } | |
| 794 | 169 pimpl_->file_->loadAllDataIntoMemory(); |
| 170 pimpl_->file_->transferEnd(); | |
| 790 | 171 } |
| 172 | |
| 173 | |
| 174 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 175 DcmItem& dicom) | |
| 176 { | |
| 177 Json::Value v = Json::arrayValue; | |
| 178 | |
| 179 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 180 { | |
| 181 DcmElement* element = dicom.getElement(i); | |
| 182 if (element) | |
| 183 { | |
| 184 char buf[16]; | |
| 185 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 186 v.append(buf); | |
| 187 } | |
| 188 } | |
| 189 | |
| 190 output.AnswerJson(v); | |
| 191 } | |
| 192 | |
| 193 static inline uint16_t GetCharValue(char c) | |
| 194 { | |
| 195 if (c >= '0' && c <= '9') | |
| 196 return c - '0'; | |
| 197 else if (c >= 'a' && c <= 'f') | |
| 198 return c - 'a' + 10; | |
| 199 else if (c >= 'A' && c <= 'F') | |
| 200 return c - 'A' + 10; | |
| 201 else | |
| 202 return 0; | |
| 203 } | |
| 204 | |
| 205 static inline uint16_t GetTagValue(const char* c) | |
| 206 { | |
| 207 return ((GetCharValue(c[0]) << 12) + | |
| 208 (GetCharValue(c[1]) << 8) + | |
| 209 (GetCharValue(c[2]) << 4) + | |
| 210 GetCharValue(c[3])); | |
| 211 } | |
| 212 | |
| 213 static void ParseTagAndGroup(DcmTagKey& key, | |
| 214 const std::string& tag) | |
| 215 { | |
| 216 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 217 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 218 } | |
| 219 | |
| 220 | |
| 221 static void SendSequence(RestApiOutput& output, | |
| 222 DcmSequenceOfItems& sequence) | |
| 223 { | |
| 224 // This element is a sequence | |
| 225 Json::Value v = Json::arrayValue; | |
| 226 | |
| 227 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 228 { | |
| 229 v.append(boost::lexical_cast<std::string>(i)); | |
| 230 } | |
| 231 | |
| 232 output.AnswerJson(v); | |
| 233 } | |
| 234 | |
| 235 | |
| 236 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 237 E_TransferSyntax transferSyntax) | |
| 238 { | |
| 239 DcmPixelSequence* pixelSequence = NULL; | |
| 240 if (pixelData.getEncapsulatedRepresentation | |
| 241 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 242 { | |
| 243 return pixelSequence->card(); | |
| 244 } | |
| 245 else | |
| 246 { | |
| 247 return 1; | |
| 248 } | |
| 249 } | |
| 250 | |
| 251 | |
| 252 static void AnswerDicomField(RestApiOutput& output, | |
| 253 DcmElement& element, | |
| 254 E_TransferSyntax transferSyntax) | |
| 255 { | |
| 256 // This element is nor a sequence, neither a pixel-data | |
| 257 std::string buffer; | |
| 258 buffer.resize(65536); | |
| 259 Uint32 length = element.getLength(transferSyntax); | |
| 260 Uint32 offset = 0; | |
| 261 | |
| 262 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL); | |
| 263 | |
| 264 while (offset < length) | |
| 265 { | |
| 266 Uint32 nbytes; | |
| 267 if (length - offset < buffer.size()) | |
| 268 { | |
| 269 nbytes = length - offset; | |
| 270 } | |
| 271 else | |
| 272 { | |
| 273 nbytes = buffer.size(); | |
| 274 } | |
| 275 | |
| 276 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); | |
| 277 | |
| 278 if (cond.good()) | |
| 279 { | |
| 280 output.GetLowLevelOutput().Send(&buffer[0], nbytes); | |
| 281 offset += nbytes; | |
| 282 } | |
| 283 else | |
| 284 { | |
| 285 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); | |
| 286 return; | |
| 287 } | |
| 288 } | |
| 289 | |
| 290 output.MarkLowLevelOutputDone(); | |
| 291 } | |
| 292 | |
| 293 | |
| 294 static bool AnswerPixelData(RestApiOutput& output, | |
| 295 DcmItem& dicom, | |
| 296 E_TransferSyntax transferSyntax, | |
| 297 const std::string* blockUri) | |
| 298 { | |
| 299 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 300 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 301 | |
| 302 DcmElement *element = NULL; | |
| 303 if (!dicom.findAndGetElement(k, element).good() || | |
| 304 element == NULL) | |
| 305 { | |
| 306 return false; | |
| 307 } | |
| 308 | |
| 309 try | |
| 310 { | |
| 311 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 312 if (blockUri == NULL) | |
| 313 { | |
| 314 // The user asks how many blocks are presents in this pixel data | |
| 315 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 316 | |
| 317 Json::Value result(Json::arrayValue); | |
| 318 for (unsigned int i = 0; i < blocks; i++) | |
| 319 { | |
| 320 result.append(boost::lexical_cast<std::string>(i)); | |
| 321 } | |
| 322 | |
| 323 output.AnswerJson(result); | |
| 324 return true; | |
| 325 } | |
| 326 | |
| 327 | |
| 328 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 329 | |
| 330 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 331 { | |
| 332 DcmPixelSequence* pixelSequence = NULL; | |
| 333 if (pixelData.getEncapsulatedRepresentation | |
| 334 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 335 { | |
| 336 // This is the case for JPEG transfer syntaxes | |
| 337 if (block < pixelSequence->card()) | |
| 338 { | |
| 339 DcmPixelItem* pixelItem = NULL; | |
| 340 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 341 { | |
| 342 if (pixelItem->getLength() == 0) | |
| 343 { | |
| 344 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 345 return true; | |
| 346 } | |
| 347 | |
| 348 Uint8* buffer = NULL; | |
| 349 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 350 { | |
| 351 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 352 return true; | |
| 353 } | |
| 354 } | |
| 355 } | |
| 356 } | |
| 357 else | |
| 358 { | |
| 359 // This is the case for raw, uncompressed image buffers | |
| 360 assert(*blockUri == "0"); | |
| 361 AnswerDicomField(output, *element, transferSyntax); | |
| 362 } | |
| 363 } | |
| 364 } | |
| 365 catch (boost::bad_lexical_cast&) | |
| 366 { | |
| 367 // The URI entered by the user is not a number | |
| 368 } | |
| 369 catch (std::bad_cast&) | |
| 370 { | |
| 371 // This should never happen | |
| 372 } | |
| 373 | |
| 374 return false; | |
| 375 } | |
| 376 | |
| 377 | |
| 378 | |
| 379 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 380 const std::string& tag, | |
| 381 DcmItem& dicom, | |
| 382 E_TransferSyntax transferSyntax) | |
| 383 { | |
| 384 DcmTagKey k; | |
| 385 ParseTagAndGroup(k, tag); | |
| 386 | |
| 387 DcmSequenceOfItems* sequence = NULL; | |
| 388 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 389 sequence != NULL && | |
| 390 sequence->getVR() == EVR_SQ) | |
| 391 { | |
| 392 SendSequence(output, *sequence); | |
| 393 return; | |
| 394 } | |
| 395 | |
| 396 DcmElement* element = NULL; | |
| 397 if (dicom.findAndGetElement(k, element).good() && | |
| 398 element != NULL && | |
| 399 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 400 element->getVR() != EVR_SQ) | |
| 401 { | |
| 402 AnswerDicomField(output, *element, transferSyntax); | |
| 403 } | |
| 404 } | |
| 405 | |
| 406 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 407 const UriComponents& uri) | |
| 408 { | |
| 794 | 409 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 410 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 411 |
| 412 // Special case: Accessing the pixel data | |
| 413 if (uri.size() == 1 || | |
| 414 uri.size() == 2) | |
| 415 { | |
| 416 DcmTagKey tag; | |
| 417 ParseTagAndGroup(tag, uri[0]); | |
| 418 | |
| 419 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 420 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 421 { | |
| 422 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 423 return; | |
| 424 } | |
| 425 } | |
| 426 | |
| 427 // Go down in the tag hierarchy according to the URI | |
| 428 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 429 { | |
| 430 size_t index; | |
| 431 try | |
| 432 { | |
| 433 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 434 } | |
| 435 catch (boost::bad_lexical_cast&) | |
| 436 { | |
| 437 return; | |
| 438 } | |
| 439 | |
| 440 DcmTagKey k; | |
| 441 DcmItem *child = NULL; | |
| 442 ParseTagAndGroup(k, uri[2 * pos]); | |
| 443 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 444 child == NULL) | |
| 445 { | |
| 446 return; | |
| 447 } | |
| 448 | |
| 449 dicom = child; | |
| 450 } | |
| 451 | |
| 452 // We have reached the end of the URI | |
| 453 if (uri.size() % 2 == 0) | |
| 454 { | |
| 455 SendPathValueForDictionary(output, *dicom); | |
| 456 } | |
| 457 else | |
| 458 { | |
| 459 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 460 } | |
| 461 } | |
| 462 | |
| 463 | |
| 464 | |
| 465 | |
| 466 | |
| 467 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 468 { | |
| 469 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 470 | |
| 471 switch (key.getEVR()) | |
| 472 { | |
| 473 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 474 | |
| 475 /** | |
| 476 * TODO. | |
| 477 **/ | |
| 478 | |
| 479 case EVR_OB: // other byte | |
| 480 case EVR_OF: // other float | |
| 481 case EVR_OW: // other word | |
| 482 case EVR_AT: // attribute tag | |
| 483 throw OrthancException(ErrorCode_NotImplemented); | |
| 484 | |
| 485 case EVR_UN: // unknown value representation | |
| 486 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 487 | |
| 488 | |
| 489 /** | |
| 490 * String types. | |
| 491 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 492 **/ | |
| 493 | |
| 494 case EVR_AS: // age string | |
| 495 return new DcmAgeString(key); | |
| 496 | |
| 497 case EVR_AE: // application entity title | |
| 498 return new DcmApplicationEntity(key); | |
| 499 | |
| 500 case EVR_CS: // code string | |
| 501 return new DcmCodeString(key); | |
| 502 | |
| 503 case EVR_DA: // date string | |
| 504 return new DcmDate(key); | |
| 505 | |
| 506 case EVR_DT: // date time string | |
| 507 return new DcmDateTime(key); | |
| 508 | |
| 509 case EVR_DS: // decimal string | |
| 510 return new DcmDecimalString(key); | |
| 511 | |
| 512 case EVR_IS: // integer string | |
| 513 return new DcmIntegerString(key); | |
| 514 | |
| 515 case EVR_TM: // time string | |
| 516 return new DcmTime(key); | |
| 517 | |
| 518 case EVR_UI: // unique identifier | |
| 519 return new DcmUniqueIdentifier(key); | |
| 520 | |
| 521 case EVR_ST: // short text | |
| 522 return new DcmShortText(key); | |
| 523 | |
| 524 case EVR_LO: // long string | |
| 525 return new DcmLongString(key); | |
| 526 | |
| 527 case EVR_LT: // long text | |
| 528 return new DcmLongText(key); | |
| 529 | |
| 530 case EVR_UT: // unlimited text | |
| 531 return new DcmUnlimitedText(key); | |
| 532 | |
| 533 case EVR_SH: // short string | |
| 534 return new DcmShortString(key); | |
| 535 | |
| 536 case EVR_PN: // person name | |
| 537 return new DcmPersonName(key); | |
| 538 | |
| 539 | |
| 540 /** | |
| 541 * Numerical types | |
| 542 **/ | |
| 543 | |
| 544 case EVR_SL: // signed long | |
| 545 return new DcmSignedLong(key); | |
| 546 | |
| 547 case EVR_SS: // signed short | |
| 548 return new DcmSignedShort(key); | |
| 549 | |
| 550 case EVR_UL: // unsigned long | |
| 551 return new DcmUnsignedLong(key); | |
| 552 | |
| 553 case EVR_US: // unsigned short | |
| 554 return new DcmUnsignedShort(key); | |
| 555 | |
| 556 case EVR_FL: // float single-precision | |
| 557 return new DcmFloatingPointSingle(key); | |
| 558 | |
| 559 case EVR_FD: // float double-precision | |
| 560 return new DcmFloatingPointDouble(key); | |
| 561 | |
| 562 | |
| 563 /** | |
| 564 * Sequence types, should never occur at this point. | |
| 565 **/ | |
| 566 | |
| 567 case EVR_SQ: // sequence of items | |
| 568 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 569 | |
| 570 | |
| 571 /** | |
| 572 * Internal to DCMTK. | |
| 573 **/ | |
| 574 | |
| 575 case EVR_ox: // OB or OW depending on context | |
| 576 case EVR_xs: // SS or US depending on context | |
| 577 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 578 case EVR_na: // na="not applicable", for data which has no VR | |
| 579 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 580 case EVR_item: // used internally for items | |
| 581 case EVR_metainfo: // used internally for meta info datasets | |
| 582 case EVR_dataset: // used internally for datasets | |
| 583 case EVR_fileFormat: // used internally for DICOM files | |
| 584 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 585 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 586 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 587 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 588 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 589 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 590 case EVR_OverlayData: // used internally for overlay data | |
| 591 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 592 default: | |
| 593 break; | |
| 594 } | |
| 595 | |
| 596 throw OrthancException(ErrorCode_InternalError); | |
| 597 } | |
| 598 | |
| 599 | |
| 600 | |
| 601 static void FillElementWithString(DcmElement& element, | |
| 602 const DicomTag& tag, | |
| 603 const std::string& value) | |
| 604 { | |
| 605 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 606 bool ok = false; | |
| 607 | |
| 608 try | |
| 609 { | |
| 610 switch (key.getEVR()) | |
| 611 { | |
| 612 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 613 | |
| 614 /** | |
| 615 * TODO. | |
| 616 **/ | |
| 617 | |
| 618 case EVR_OB: // other byte | |
| 619 case EVR_OF: // other float | |
| 620 case EVR_OW: // other word | |
| 621 case EVR_AT: // attribute tag | |
| 622 throw OrthancException(ErrorCode_NotImplemented); | |
| 623 | |
| 624 case EVR_UN: // unknown value representation | |
| 625 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 626 | |
| 627 | |
| 628 /** | |
| 629 * String types. | |
| 630 **/ | |
| 631 | |
| 632 case EVR_DS: // decimal string | |
| 633 case EVR_IS: // integer string | |
| 634 case EVR_AS: // age string | |
| 635 case EVR_DA: // date string | |
| 636 case EVR_DT: // date time string | |
| 637 case EVR_TM: // time string | |
| 638 case EVR_AE: // application entity title | |
| 639 case EVR_CS: // code string | |
| 640 case EVR_SH: // short string | |
| 641 case EVR_LO: // long string | |
| 642 case EVR_ST: // short text | |
| 643 case EVR_LT: // long text | |
| 644 case EVR_UT: // unlimited text | |
| 645 case EVR_PN: // person name | |
| 646 case EVR_UI: // unique identifier | |
| 647 { | |
| 648 ok = element.putString(value.c_str()).good(); | |
| 649 break; | |
| 650 } | |
| 651 | |
| 652 | |
| 653 /** | |
| 654 * Numerical types | |
| 655 **/ | |
| 656 | |
| 657 case EVR_SL: // signed long | |
| 658 { | |
| 659 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 660 break; | |
| 661 } | |
| 662 | |
| 663 case EVR_SS: // signed short | |
| 664 { | |
| 665 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 666 break; | |
| 667 } | |
| 668 | |
| 669 case EVR_UL: // unsigned long | |
| 670 { | |
| 671 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 672 break; | |
| 673 } | |
| 674 | |
| 675 case EVR_US: // unsigned short | |
| 676 { | |
| 677 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 678 break; | |
| 679 } | |
| 680 | |
| 681 case EVR_FL: // float single-precision | |
| 682 { | |
| 683 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 684 break; | |
| 685 } | |
| 686 | |
| 687 case EVR_FD: // float double-precision | |
| 688 { | |
| 689 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 690 break; | |
| 691 } | |
| 692 | |
| 693 | |
| 694 /** | |
| 695 * Sequence types, should never occur at this point. | |
| 696 **/ | |
| 697 | |
| 698 case EVR_SQ: // sequence of items | |
| 699 { | |
| 700 ok = false; | |
| 701 break; | |
| 702 } | |
| 703 | |
| 704 | |
| 705 /** | |
| 706 * Internal to DCMTK. | |
| 707 **/ | |
| 708 | |
| 709 case EVR_ox: // OB or OW depending on context | |
| 710 case EVR_xs: // SS or US depending on context | |
| 711 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 712 case EVR_na: // na="not applicable", for data which has no VR | |
| 713 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 714 case EVR_item: // used internally for items | |
| 715 case EVR_metainfo: // used internally for meta info datasets | |
| 716 case EVR_dataset: // used internally for datasets | |
| 717 case EVR_fileFormat: // used internally for DICOM files | |
| 718 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 719 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 720 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 721 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 722 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 723 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 724 case EVR_OverlayData: // used internally for overlay data | |
| 725 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 726 default: | |
| 727 break; | |
| 728 } | |
| 729 } | |
| 730 catch (boost::bad_lexical_cast&) | |
| 731 { | |
| 732 ok = false; | |
| 733 } | |
| 734 | |
| 735 if (!ok) | |
| 736 { | |
| 737 throw OrthancException(ErrorCode_InternalError); | |
| 738 } | |
| 739 } | |
| 740 | |
| 741 | |
| 742 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 743 { | |
| 744 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 745 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 746 if (element != NULL) |
| 747 { | |
| 748 delete element; | |
| 749 } | |
| 750 } | |
| 751 | |
| 752 | |
| 753 | |
| 754 void ParsedDicomFile::RemovePrivateTags() | |
| 755 { | |
| 756 typedef std::list<DcmElement*> Tags; | |
| 757 | |
| 758 Tags privateTags; | |
| 759 | |
| 794 | 760 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 761 for (unsigned long i = 0; i < dataset.card(); i++) |
| 762 { | |
| 763 DcmElement* element = dataset.getElement(i); | |
| 764 DcmTag tag(element->getTag()); | |
| 765 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK | |
| 766 tag.getPrivateCreator() != NULL) | |
| 767 { | |
| 768 privateTags.push_back(element); | |
| 769 } | |
| 770 } | |
| 771 | |
| 772 for (Tags::iterator it = privateTags.begin(); | |
| 773 it != privateTags.end(); ++it) | |
| 774 { | |
| 775 DcmElement* tmp = dataset.remove(*it); | |
| 776 if (tmp != NULL) | |
| 777 { | |
| 778 delete tmp; | |
| 779 } | |
| 780 } | |
| 781 } | |
| 782 | |
| 783 | |
| 784 | |
| 785 void ParsedDicomFile::Insert(const DicomTag& tag, | |
| 786 const std::string& value) | |
| 787 { | |
| 788 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); | |
| 789 FillElementWithString(*element, tag, value); | |
| 790 | |
| 794 | 791 if (!pimpl_->file_->getDataset()->insert(element.release(), false, false).good()) |
| 790 | 792 { |
| 793 // This field already exists | |
| 794 throw OrthancException(ErrorCode_InternalError); | |
| 795 } | |
| 796 } | |
| 797 | |
| 798 | |
| 799 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 800 const std::string& value, | |
| 801 DicomReplaceMode mode) | |
| 802 { | |
| 803 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 804 DcmElement* element = NULL; | |
| 805 | |
| 794 | 806 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 807 element == NULL) |
| 808 { | |
| 809 // This field does not exist, act wrt. the specified "mode" | |
| 810 switch (mode) | |
| 811 { | |
| 812 case DicomReplaceMode_InsertIfAbsent: | |
| 813 Insert(tag, value); | |
| 814 break; | |
| 815 | |
| 816 case DicomReplaceMode_ThrowIfAbsent: | |
| 817 throw OrthancException(ErrorCode_InexistentItem); | |
| 818 | |
| 819 case DicomReplaceMode_IgnoreIfAbsent: | |
| 820 return; | |
| 821 } | |
| 822 } | |
| 823 else | |
| 824 { | |
| 825 FillElementWithString(*element, tag, value); | |
| 826 } | |
| 827 | |
| 828 | |
| 829 /** | |
| 830 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 831 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 832 * you make changes to the related tags in the dataset ('SOP Class | |
| 833 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 834 * options. You can disable this behaviour by using the -nmu | |
| 835 * option. | |
| 836 **/ | |
| 837 | |
| 838 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 839 { | |
| 840 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 841 } | |
| 842 | |
| 843 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 844 { | |
| 845 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 846 } | |
| 847 } | |
| 848 | |
| 849 | |
| 850 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 851 { | |
| 852 std::string serialized; | |
| 794 | 853 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, pimpl_->file_->getDataset())) |
| 790 | 854 { |
| 855 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 856 } | |
| 857 } | |
| 858 | |
| 859 | |
| 860 | |
| 861 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 862 const DicomTag& tag) | |
| 863 { | |
| 864 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 865 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 866 DcmElement* element = NULL; |
| 867 if (!dataset.findAndGetElement(k, element).good() || | |
| 868 element == NULL) | |
| 869 { | |
| 870 return false; | |
| 871 } | |
| 872 | |
| 873 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); | |
| 874 | |
| 875 if (v.get() == NULL) | |
| 876 { | |
| 877 value = ""; | |
| 878 } | |
| 879 else | |
| 880 { | |
| 881 value = v->AsString(); | |
| 882 } | |
| 883 | |
| 884 return true; | |
| 885 } | |
| 886 | |
| 887 | |
| 888 | |
| 889 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 890 { | |
| 891 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 892 | |
| 893 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 894 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 895 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 896 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 897 { | |
| 898 throw OrthancException(ErrorCode_BadFileFormat); | |
| 899 } | |
| 900 | |
| 901 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 902 } | |
| 903 | |
| 904 | |
| 905 static void StoreElement(Json::Value& target, | |
| 906 DcmElement& element, | |
| 907 unsigned int maxStringLength); | |
| 908 | |
| 909 static void StoreItem(Json::Value& target, | |
| 910 DcmItem& item, | |
| 911 unsigned int maxStringLength) | |
| 912 { | |
| 913 target = Json::Value(Json::objectValue); | |
| 914 | |
| 915 for (unsigned long i = 0; i < item.card(); i++) | |
| 916 { | |
| 917 DcmElement* element = item.getElement(i); | |
| 918 StoreElement(target, *element, maxStringLength); | |
| 919 } | |
| 920 } | |
| 921 | |
| 922 | |
| 923 static void StoreElement(Json::Value& target, | |
| 924 DcmElement& element, | |
| 925 unsigned int maxStringLength) | |
| 926 { | |
| 927 assert(target.type() == Json::objectValue); | |
| 928 | |
| 929 DicomTag tag(FromDcmtkBridge::GetTag(element)); | |
| 930 const std::string formattedTag = tag.Format(); | |
| 931 | |
| 932 #if 0 | |
| 933 const std::string tagName = FromDcmtkBridge::GetName(tag); | |
| 934 #else | |
| 935 // This version of the code gives access to the name of the private tags | |
| 936 DcmTag tagbis(element.getTag()); | |
| 937 const std::string tagName(tagbis.getTagName()); | |
| 938 #endif | |
| 939 | |
| 940 if (element.isLeaf()) | |
| 941 { | |
| 942 Json::Value value(Json::objectValue); | |
| 943 value["Name"] = tagName; | |
| 944 | |
| 945 if (tagbis.getPrivateCreator() != NULL) | |
| 946 { | |
| 947 value["PrivateCreator"] = tagbis.getPrivateCreator(); | |
| 948 } | |
| 949 | |
| 950 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); | |
| 951 if (v->IsNull()) | |
| 952 { | |
| 953 value["Type"] = "Null"; | |
| 954 value["Value"] = Json::nullValue; | |
| 955 } | |
| 956 else | |
| 957 { | |
| 958 std::string s = v->AsString(); | |
| 959 if (maxStringLength == 0 || | |
| 960 s.size() <= maxStringLength) | |
| 961 { | |
| 962 value["Type"] = "String"; | |
| 963 value["Value"] = s; | |
| 964 } | |
| 965 else | |
| 966 { | |
| 967 value["Type"] = "TooLong"; | |
| 968 value["Value"] = Json::nullValue; | |
| 969 } | |
| 970 } | |
| 971 | |
| 972 target[formattedTag] = value; | |
| 973 } | |
| 974 else | |
| 975 { | |
| 976 Json::Value children(Json::arrayValue); | |
| 977 | |
| 978 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 979 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 980 // etc. are not." The following cast is thus OK. | |
| 981 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 982 | |
| 983 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 984 { | |
| 985 DcmItem* child = sequence.getItem(i); | |
| 986 Json::Value& v = children.append(Json::objectValue); | |
| 987 StoreItem(v, *child, maxStringLength); | |
| 988 } | |
| 989 | |
| 990 target[formattedTag]["Name"] = tagName; | |
| 991 target[formattedTag]["Type"] = "Sequence"; | |
| 992 target[formattedTag]["Value"] = children; | |
| 993 } | |
| 994 } | |
| 995 | |
| 996 | |
| 997 template <typename T> | |
| 998 static void ExtractPngImageTruncate(std::string& result, | |
| 999 DicomIntegerPixelAccessor& accessor, | |
| 1000 PixelFormat format) | |
| 1001 { | |
| 1002 assert(accessor.GetChannelCount() == 1); | |
| 1003 | |
| 1004 PngWriter w; | |
| 1005 | |
| 1006 std::vector<T> image(accessor.GetWidth() * accessor.GetHeight(), 0); | |
| 1007 T* pixel = &image[0]; | |
| 1008 for (unsigned int y = 0; y < accessor.GetHeight(); y++) | |
| 1009 { | |
| 1010 for (unsigned int x = 0; x < accessor.GetWidth(); x++, pixel++) | |
| 1011 { | |
| 1012 int32_t v = accessor.GetValue(x, y); | |
| 1013 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 1014 *pixel = std::numeric_limits<T>::min(); | |
| 1015 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 1016 *pixel = std::numeric_limits<T>::max(); | |
| 1017 else | |
| 1018 *pixel = static_cast<T>(v); | |
| 1019 } | |
| 1020 } | |
| 1021 | |
| 1022 w.WriteToMemory(result, accessor.GetWidth(), accessor.GetHeight(), | |
| 1023 accessor.GetWidth() * sizeof(T), format, &image[0]); | |
| 1024 } | |
| 1025 | |
| 1026 | |
| 1027 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 1028 { | |
| 794 | 1029 FromDcmtkBridge::SaveToMemoryBuffer(buffer, pimpl_->file_->getDataset()); |
| 790 | 1030 } |
| 1031 | |
| 1032 | |
| 1033 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 1034 { | |
| 1035 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 1036 std::string content; | |
| 1037 SaveToMemoryBuffer(content); | |
| 1038 Toolbox::WriteFile(content, path); | |
| 1039 } | |
| 1040 | |
| 1041 | |
| 794 | 1042 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 1043 { |
| 794 | 1044 pimpl_->file_.reset(new DcmFileFormat); |
| 790 | 1045 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 1046 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 1047 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 1048 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 1049 } | |
| 1050 | |
| 791 | 1051 |
| 794 | 1052 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 1053 { |
| 1054 Setup(content, size); | |
| 1055 } | |
| 1056 | |
| 794 | 1057 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 1058 { |
| 1059 if (content.size() == 0) | |
| 1060 { | |
| 1061 Setup(NULL, 0); | |
| 1062 } | |
| 1063 else | |
| 1064 { | |
| 1065 Setup(&content[0], content.size()); | |
| 1066 } | |
| 1067 } | |
| 792 | 1068 |
| 1069 | |
| 794 | 1070 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1071 pimpl_(new PImpl) | |
| 792 | 1072 { |
| 794 | 1073 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
| 792 | 1074 } |
| 1075 | |
| 1076 | |
| 1077 ParsedDicomFile::~ParsedDicomFile() | |
| 1078 { | |
| 794 | 1079 delete pimpl_; |
| 792 | 1080 } |
| 1081 | |
| 793 | 1082 |
| 1083 void* ParsedDicomFile::GetDcmtkObject() | |
| 1084 { | |
| 794 | 1085 return pimpl_->file_.get(); |
| 793 | 1086 } |
| 1087 | |
| 1088 | |
| 1089 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1090 { | |
| 794 | 1091 return new ParsedDicomFile(*this); |
| 793 | 1092 } |
|
800
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1093 |
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1094 |
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1095 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
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1096 { |
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1097 std::string mime, content; |
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1098 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
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1099 |
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809
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1100 std::string decoded; |
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1101 Toolbox::DecodeBase64(decoded, content); |
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1102 |
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1103 if (mime == "image/png") |
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1104 { |
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1105 PngReader reader; |
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1106 reader.ReadFromMemory(decoded); |
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1107 EmbedImage(reader); |
|
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|
1108 } |
|
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changeset
|
1109 else |
|
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changeset
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1110 { |
|
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changeset
|
1111 throw OrthancException(ErrorCode_NotImplemented); |
|
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1112 } |
|
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1113 } |
|
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changeset
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1114 |
|
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changeset
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1115 |
|
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changeset
|
1116 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
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changeset
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1117 { |
|
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1118 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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changeset
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1119 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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1120 accessor.GetFormat() != PixelFormat_RGB24 && |
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1121 accessor.GetFormat() != PixelFormat_RGBA32) |
|
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changeset
|
1122 { |
|
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1123 throw OrthancException(ErrorCode_NotImplemented); |
|
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1124 } |
|
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changeset
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1125 |
|
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1126 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1127 { |
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1128 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1129 } |
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1130 |
|
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1131 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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changeset
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1132 |
|
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1133 Remove(DICOM_TAG_PIXEL_DATA); |
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1134 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
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1135 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
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1136 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
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1137 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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1138 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
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1139 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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1140 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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1141 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
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1142 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1143 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
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changeset
|
1144 |
|
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changeset
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1145 unsigned int bytesPerPixel = 1; |
|
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changeset
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1146 |
|
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changeset
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1147 switch (accessor.GetFormat()) |
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1148 { |
|
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1149 case PixelFormat_RGB24: |
|
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1150 case PixelFormat_RGBA32: |
|
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1151 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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1152 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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1153 bytesPerPixel = 3; |
|
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1154 break; |
|
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changeset
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1155 |
|
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changeset
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1156 case PixelFormat_Grayscale8: |
|
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changeset
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1157 break; |
|
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changeset
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1158 |
|
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changeset
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1159 case PixelFormat_Grayscale16: |
|
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changeset
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1160 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
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changeset
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1161 Replace(DICOM_TAG_BITS_STORED, "16"); |
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changeset
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1162 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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1163 bytesPerPixel = 2; |
|
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changeset
|
1164 break; |
|
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changeset
|
1165 |
|
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changeset
|
1166 default: |
|
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changeset
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1167 throw OrthancException(ErrorCode_NotImplemented); |
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1168 } |
|
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changeset
|
1169 |
|
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changeset
|
1170 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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1171 DICOM_TAG_PIXEL_DATA.GetElement()); |
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changeset
|
1172 |
|
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changeset
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1173 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
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changeset
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1174 |
|
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changeset
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1175 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
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1176 Uint8* target = NULL; |
|
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1177 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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changeset
|
1178 |
|
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changeset
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1179 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
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|
1180 { |
|
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changeset
|
1181 switch (accessor.GetFormat()) |
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|
1182 { |
|
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1183 case PixelFormat_RGB24: |
|
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1184 case PixelFormat_Grayscale8: |
|
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1185 case PixelFormat_Grayscale16: |
|
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1186 case PixelFormat_SignedGrayscale16: |
|
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1187 { |
|
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|
1188 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
|
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1189 target += pitch; |
|
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|
1190 break; |
|
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changeset
|
1191 } |
|
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|
1192 |
|
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1193 case PixelFormat_RGBA32: |
|
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1194 { |
|
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1195 // The alpha channel is not supported by the DICOM standard |
|
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1196 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
|
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1197 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
|
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changeset
|
1198 { |
|
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1199 target[0] = source[0]; |
|
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1200 target[1] = source[1]; |
|
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1201 target[2] = source[2]; |
|
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|
1202 } |
|
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changeset
|
1203 |
|
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changeset
|
1204 break; |
|
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changeset
|
1205 } |
|
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changeset
|
1206 |
|
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changeset
|
1207 default: |
|
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1208 throw OrthancException(ErrorCode_NotImplemented); |
|
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1209 } |
|
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1210 } |
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changeset
|
1211 |
|
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1212 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
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changeset
|
1213 { |
|
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1214 throw OrthancException(ErrorCode_InternalError); |
|
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1215 } |
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ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
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1216 } |
| 790 | 1217 } |