Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 910:28a52982196e plugins
refactoring
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 20 Jun 2014 13:38:19 +0200 |
| parents | e078ea944089 |
| children | 509e146c3cb3 |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, | |
| 4 * Belgium | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 | |
| 34 /*========================================================================= | |
| 35 | |
| 36 This file is based on portions of the following project: | |
| 37 | |
| 38 Program: GDCM (Grassroots DICOM). A DICOM library | |
| 39 Module: http://gdcm.sourceforge.net/Copyright.html | |
| 40 | |
| 41 Copyright (c) 2006-2011 Mathieu Malaterre | |
| 42 Copyright (c) 1993-2005 CREATIS | |
| 43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
| 44 All rights reserved. | |
| 45 | |
| 46 Redistribution and use in source and binary forms, with or without | |
| 47 modification, are permitted provided that the following conditions are met: | |
| 48 | |
| 49 * Redistributions of source code must retain the above copyright notice, | |
| 50 this list of conditions and the following disclaimer. | |
| 51 | |
| 52 * Redistributions in binary form must reproduce the above copyright notice, | |
| 53 this list of conditions and the following disclaimer in the documentation | |
| 54 and/or other materials provided with the distribution. | |
| 55 | |
| 56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
| 57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
| 58 endorse or promote products derived from this software without specific | |
| 59 prior written permission. | |
| 60 | |
| 61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
| 62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| 63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
| 65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
| 66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
| 67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
| 68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
| 69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| 70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 71 | |
| 72 =========================================================================*/ | |
| 73 | |
| 74 | |
|
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75 #include "PrecompiledHeadersServer.h" |
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76 |
| 790 | 77 #ifndef NOMINMAX |
| 78 #define NOMINMAX | |
| 79 #endif | |
| 80 | |
| 81 #include "ParsedDicomFile.h" | |
| 82 | |
| 83 #include "FromDcmtkBridge.h" | |
| 84 #include "ToDcmtkBridge.h" | |
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85 #include "Internals/DicomImageDecoder.h" |
| 790 | 86 #include "../Core/Toolbox.h" |
| 87 #include "../Core/OrthancException.h" | |
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88 #include "../Core/ImageFormats/ImageBuffer.h" |
| 799 | 89 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 90 #include "../Core/Uuid.h" |
| 91 #include "../Core/DicomFormat/DicomString.h" | |
| 92 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 93 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
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94 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 95 |
| 96 #include <list> | |
| 97 #include <limits> | |
| 98 | |
| 99 #include <boost/lexical_cast.hpp> | |
| 100 | |
| 101 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 102 #include <dcmtk/dcmdata/dcdicent.h> | |
| 103 #include <dcmtk/dcmdata/dcdict.h> | |
| 104 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 105 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 106 #include <dcmtk/dcmdata/dcuid.h> | |
| 107 #include <dcmtk/dcmdata/dcmetinf.h> | |
| 108 | |
| 109 #include <dcmtk/dcmdata/dcvrae.h> | |
| 110 #include <dcmtk/dcmdata/dcvras.h> | |
| 111 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 112 #include <dcmtk/dcmdata/dcvrda.h> | |
| 113 #include <dcmtk/dcmdata/dcvrds.h> | |
| 114 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 115 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 116 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 117 #include <dcmtk/dcmdata/dcvris.h> | |
| 118 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 119 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 120 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 121 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 122 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 123 #include <dcmtk/dcmdata/dcvrss.h> | |
| 124 #include <dcmtk/dcmdata/dcvrst.h> | |
| 125 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 126 #include <dcmtk/dcmdata/dcvrui.h> | |
| 127 #include <dcmtk/dcmdata/dcvrul.h> | |
| 128 #include <dcmtk/dcmdata/dcvrus.h> | |
| 129 #include <dcmtk/dcmdata/dcvrut.h> | |
| 130 #include <dcmtk/dcmdata/dcpixel.h> | |
| 131 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 132 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 133 | |
| 134 | |
| 135 #include <boost/math/special_functions/round.hpp> | |
| 136 #include <glog/logging.h> | |
| 137 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 138 | |
| 139 | |
| 140 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 141 | |
| 142 | |
| 143 | |
| 144 namespace Orthanc | |
| 145 { | |
| 794 | 146 struct ParsedDicomFile::PImpl |
| 147 { | |
| 148 std::auto_ptr<DcmFileFormat> file_; | |
| 149 }; | |
| 150 | |
| 151 | |
| 152 // This method can only be called from the constructors! | |
| 790 | 153 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 154 { | |
| 155 DcmInputBufferStream is; | |
| 156 if (size > 0) | |
| 157 { | |
| 158 is.setBuffer(buffer, size); | |
| 159 } | |
| 160 is.setEos(); | |
| 161 | |
| 794 | 162 pimpl_->file_.reset(new DcmFileFormat); |
| 163 pimpl_->file_->transferInit(); | |
| 164 if (!pimpl_->file_->read(is).good()) | |
| 790 | 165 { |
| 794 | 166 delete pimpl_; // Avoid a memory leak due to exception |
| 167 // throwing, as we are in the constructor | |
| 168 | |
| 790 | 169 throw OrthancException(ErrorCode_BadFileFormat); |
| 170 } | |
| 794 | 171 pimpl_->file_->loadAllDataIntoMemory(); |
| 172 pimpl_->file_->transferEnd(); | |
| 790 | 173 } |
| 174 | |
| 175 | |
| 176 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 177 DcmItem& dicom) | |
| 178 { | |
| 179 Json::Value v = Json::arrayValue; | |
| 180 | |
| 181 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 182 { | |
| 183 DcmElement* element = dicom.getElement(i); | |
| 184 if (element) | |
| 185 { | |
| 186 char buf[16]; | |
| 187 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 188 v.append(buf); | |
| 189 } | |
| 190 } | |
| 191 | |
| 192 output.AnswerJson(v); | |
| 193 } | |
| 194 | |
| 195 static inline uint16_t GetCharValue(char c) | |
| 196 { | |
| 197 if (c >= '0' && c <= '9') | |
| 198 return c - '0'; | |
| 199 else if (c >= 'a' && c <= 'f') | |
| 200 return c - 'a' + 10; | |
| 201 else if (c >= 'A' && c <= 'F') | |
| 202 return c - 'A' + 10; | |
| 203 else | |
| 204 return 0; | |
| 205 } | |
| 206 | |
| 207 static inline uint16_t GetTagValue(const char* c) | |
| 208 { | |
| 209 return ((GetCharValue(c[0]) << 12) + | |
| 210 (GetCharValue(c[1]) << 8) + | |
| 211 (GetCharValue(c[2]) << 4) + | |
| 212 GetCharValue(c[3])); | |
| 213 } | |
| 214 | |
| 215 static void ParseTagAndGroup(DcmTagKey& key, | |
| 216 const std::string& tag) | |
| 217 { | |
| 218 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 219 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 220 } | |
| 221 | |
| 222 | |
| 223 static void SendSequence(RestApiOutput& output, | |
| 224 DcmSequenceOfItems& sequence) | |
| 225 { | |
| 226 // This element is a sequence | |
| 227 Json::Value v = Json::arrayValue; | |
| 228 | |
| 229 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 230 { | |
| 231 v.append(boost::lexical_cast<std::string>(i)); | |
| 232 } | |
| 233 | |
| 234 output.AnswerJson(v); | |
| 235 } | |
| 236 | |
| 237 | |
| 238 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 239 E_TransferSyntax transferSyntax) | |
| 240 { | |
| 241 DcmPixelSequence* pixelSequence = NULL; | |
| 242 if (pixelData.getEncapsulatedRepresentation | |
| 243 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 244 { | |
| 245 return pixelSequence->card(); | |
| 246 } | |
| 247 else | |
| 248 { | |
| 249 return 1; | |
| 250 } | |
| 251 } | |
| 252 | |
| 253 | |
| 254 static void AnswerDicomField(RestApiOutput& output, | |
| 255 DcmElement& element, | |
| 256 E_TransferSyntax transferSyntax) | |
| 257 { | |
| 258 // This element is nor a sequence, neither a pixel-data | |
| 259 std::string buffer; | |
| 260 buffer.resize(65536); | |
| 261 Uint32 length = element.getLength(transferSyntax); | |
| 262 Uint32 offset = 0; | |
| 263 | |
| 264 output.GetLowLevelOutput().SendOkHeader(CONTENT_TYPE_OCTET_STREAM, true, length, NULL); | |
| 265 | |
| 266 while (offset < length) | |
| 267 { | |
| 268 Uint32 nbytes; | |
| 269 if (length - offset < buffer.size()) | |
| 270 { | |
| 271 nbytes = length - offset; | |
| 272 } | |
| 273 else | |
| 274 { | |
| 275 nbytes = buffer.size(); | |
| 276 } | |
| 277 | |
| 278 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); | |
| 279 | |
| 280 if (cond.good()) | |
| 281 { | |
|
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282 output.GetLowLevelOutput().SendBodyData(&buffer[0], nbytes); |
| 790 | 283 offset += nbytes; |
| 284 } | |
| 285 else | |
| 286 { | |
| 287 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); | |
| 288 return; | |
| 289 } | |
| 290 } | |
| 291 | |
| 292 output.MarkLowLevelOutputDone(); | |
| 293 } | |
| 294 | |
| 295 | |
| 296 static bool AnswerPixelData(RestApiOutput& output, | |
| 297 DcmItem& dicom, | |
| 298 E_TransferSyntax transferSyntax, | |
| 299 const std::string* blockUri) | |
| 300 { | |
| 301 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 302 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 303 | |
| 304 DcmElement *element = NULL; | |
| 305 if (!dicom.findAndGetElement(k, element).good() || | |
| 306 element == NULL) | |
| 307 { | |
| 308 return false; | |
| 309 } | |
| 310 | |
| 311 try | |
| 312 { | |
| 313 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 314 if (blockUri == NULL) | |
| 315 { | |
| 316 // The user asks how many blocks are presents in this pixel data | |
| 317 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 318 | |
| 319 Json::Value result(Json::arrayValue); | |
| 320 for (unsigned int i = 0; i < blocks; i++) | |
| 321 { | |
| 322 result.append(boost::lexical_cast<std::string>(i)); | |
| 323 } | |
| 324 | |
| 325 output.AnswerJson(result); | |
| 326 return true; | |
| 327 } | |
| 328 | |
| 329 | |
| 330 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 331 | |
| 332 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 333 { | |
| 334 DcmPixelSequence* pixelSequence = NULL; | |
| 335 if (pixelData.getEncapsulatedRepresentation | |
| 336 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 337 { | |
| 338 // This is the case for JPEG transfer syntaxes | |
| 339 if (block < pixelSequence->card()) | |
| 340 { | |
| 341 DcmPixelItem* pixelItem = NULL; | |
| 342 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 343 { | |
| 344 if (pixelItem->getLength() == 0) | |
| 345 { | |
| 346 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 347 return true; | |
| 348 } | |
| 349 | |
| 350 Uint8* buffer = NULL; | |
| 351 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 352 { | |
| 353 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 354 return true; | |
| 355 } | |
| 356 } | |
| 357 } | |
| 358 } | |
| 359 else | |
| 360 { | |
| 361 // This is the case for raw, uncompressed image buffers | |
| 362 assert(*blockUri == "0"); | |
| 363 AnswerDicomField(output, *element, transferSyntax); | |
| 364 } | |
| 365 } | |
| 366 } | |
| 367 catch (boost::bad_lexical_cast&) | |
| 368 { | |
| 369 // The URI entered by the user is not a number | |
| 370 } | |
| 371 catch (std::bad_cast&) | |
| 372 { | |
| 373 // This should never happen | |
| 374 } | |
| 375 | |
| 376 return false; | |
| 377 } | |
| 378 | |
| 379 | |
| 380 | |
| 381 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 382 const std::string& tag, | |
| 383 DcmItem& dicom, | |
| 384 E_TransferSyntax transferSyntax) | |
| 385 { | |
| 386 DcmTagKey k; | |
| 387 ParseTagAndGroup(k, tag); | |
| 388 | |
| 389 DcmSequenceOfItems* sequence = NULL; | |
| 390 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 391 sequence != NULL && | |
| 392 sequence->getVR() == EVR_SQ) | |
| 393 { | |
| 394 SendSequence(output, *sequence); | |
| 395 return; | |
| 396 } | |
| 397 | |
| 398 DcmElement* element = NULL; | |
| 399 if (dicom.findAndGetElement(k, element).good() && | |
| 400 element != NULL && | |
| 401 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 402 element->getVR() != EVR_SQ) | |
| 403 { | |
| 404 AnswerDicomField(output, *element, transferSyntax); | |
| 405 } | |
| 406 } | |
| 407 | |
| 408 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 409 const UriComponents& uri) | |
| 410 { | |
| 794 | 411 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 412 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 413 |
| 414 // Special case: Accessing the pixel data | |
| 415 if (uri.size() == 1 || | |
| 416 uri.size() == 2) | |
| 417 { | |
| 418 DcmTagKey tag; | |
| 419 ParseTagAndGroup(tag, uri[0]); | |
| 420 | |
| 421 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 422 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 423 { | |
| 424 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 425 return; | |
| 426 } | |
| 427 } | |
| 428 | |
| 429 // Go down in the tag hierarchy according to the URI | |
| 430 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 431 { | |
| 432 size_t index; | |
| 433 try | |
| 434 { | |
| 435 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 436 } | |
| 437 catch (boost::bad_lexical_cast&) | |
| 438 { | |
| 439 return; | |
| 440 } | |
| 441 | |
| 442 DcmTagKey k; | |
| 443 DcmItem *child = NULL; | |
| 444 ParseTagAndGroup(k, uri[2 * pos]); | |
| 445 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 446 child == NULL) | |
| 447 { | |
| 448 return; | |
| 449 } | |
| 450 | |
| 451 dicom = child; | |
| 452 } | |
| 453 | |
| 454 // We have reached the end of the URI | |
| 455 if (uri.size() % 2 == 0) | |
| 456 { | |
| 457 SendPathValueForDictionary(output, *dicom); | |
| 458 } | |
| 459 else | |
| 460 { | |
| 461 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 462 } | |
| 463 } | |
| 464 | |
| 465 | |
| 466 | |
| 467 | |
| 468 | |
| 469 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 470 { | |
| 471 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 472 | |
| 473 switch (key.getEVR()) | |
| 474 { | |
| 475 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 476 | |
| 477 /** | |
| 478 * TODO. | |
| 479 **/ | |
| 480 | |
| 481 case EVR_OB: // other byte | |
| 482 case EVR_OF: // other float | |
| 483 case EVR_OW: // other word | |
| 484 case EVR_AT: // attribute tag | |
| 485 throw OrthancException(ErrorCode_NotImplemented); | |
| 486 | |
| 487 case EVR_UN: // unknown value representation | |
| 488 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 489 | |
| 490 | |
| 491 /** | |
| 492 * String types. | |
| 493 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 494 **/ | |
| 495 | |
| 496 case EVR_AS: // age string | |
| 497 return new DcmAgeString(key); | |
| 498 | |
| 499 case EVR_AE: // application entity title | |
| 500 return new DcmApplicationEntity(key); | |
| 501 | |
| 502 case EVR_CS: // code string | |
| 503 return new DcmCodeString(key); | |
| 504 | |
| 505 case EVR_DA: // date string | |
| 506 return new DcmDate(key); | |
| 507 | |
| 508 case EVR_DT: // date time string | |
| 509 return new DcmDateTime(key); | |
| 510 | |
| 511 case EVR_DS: // decimal string | |
| 512 return new DcmDecimalString(key); | |
| 513 | |
| 514 case EVR_IS: // integer string | |
| 515 return new DcmIntegerString(key); | |
| 516 | |
| 517 case EVR_TM: // time string | |
| 518 return new DcmTime(key); | |
| 519 | |
| 520 case EVR_UI: // unique identifier | |
| 521 return new DcmUniqueIdentifier(key); | |
| 522 | |
| 523 case EVR_ST: // short text | |
| 524 return new DcmShortText(key); | |
| 525 | |
| 526 case EVR_LO: // long string | |
| 527 return new DcmLongString(key); | |
| 528 | |
| 529 case EVR_LT: // long text | |
| 530 return new DcmLongText(key); | |
| 531 | |
| 532 case EVR_UT: // unlimited text | |
| 533 return new DcmUnlimitedText(key); | |
| 534 | |
| 535 case EVR_SH: // short string | |
| 536 return new DcmShortString(key); | |
| 537 | |
| 538 case EVR_PN: // person name | |
| 539 return new DcmPersonName(key); | |
| 540 | |
| 541 | |
| 542 /** | |
| 543 * Numerical types | |
| 544 **/ | |
| 545 | |
| 546 case EVR_SL: // signed long | |
| 547 return new DcmSignedLong(key); | |
| 548 | |
| 549 case EVR_SS: // signed short | |
| 550 return new DcmSignedShort(key); | |
| 551 | |
| 552 case EVR_UL: // unsigned long | |
| 553 return new DcmUnsignedLong(key); | |
| 554 | |
| 555 case EVR_US: // unsigned short | |
| 556 return new DcmUnsignedShort(key); | |
| 557 | |
| 558 case EVR_FL: // float single-precision | |
| 559 return new DcmFloatingPointSingle(key); | |
| 560 | |
| 561 case EVR_FD: // float double-precision | |
| 562 return new DcmFloatingPointDouble(key); | |
| 563 | |
| 564 | |
| 565 /** | |
| 566 * Sequence types, should never occur at this point. | |
| 567 **/ | |
| 568 | |
| 569 case EVR_SQ: // sequence of items | |
| 570 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 571 | |
| 572 | |
| 573 /** | |
| 574 * Internal to DCMTK. | |
| 575 **/ | |
| 576 | |
| 577 case EVR_ox: // OB or OW depending on context | |
| 578 case EVR_xs: // SS or US depending on context | |
| 579 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 580 case EVR_na: // na="not applicable", for data which has no VR | |
| 581 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 582 case EVR_item: // used internally for items | |
| 583 case EVR_metainfo: // used internally for meta info datasets | |
| 584 case EVR_dataset: // used internally for datasets | |
| 585 case EVR_fileFormat: // used internally for DICOM files | |
| 586 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 587 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 588 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 589 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 590 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 591 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 592 case EVR_OverlayData: // used internally for overlay data | |
| 593 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 594 default: | |
| 595 break; | |
| 596 } | |
| 597 | |
| 598 throw OrthancException(ErrorCode_InternalError); | |
| 599 } | |
| 600 | |
| 601 | |
| 602 | |
| 603 static void FillElementWithString(DcmElement& element, | |
| 604 const DicomTag& tag, | |
| 605 const std::string& value) | |
| 606 { | |
| 607 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 608 bool ok = false; | |
| 609 | |
| 610 try | |
| 611 { | |
| 612 switch (key.getEVR()) | |
| 613 { | |
| 614 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 615 | |
| 616 /** | |
| 617 * TODO. | |
| 618 **/ | |
| 619 | |
| 620 case EVR_OB: // other byte | |
| 621 case EVR_OF: // other float | |
| 622 case EVR_OW: // other word | |
| 623 case EVR_AT: // attribute tag | |
| 624 throw OrthancException(ErrorCode_NotImplemented); | |
| 625 | |
| 626 case EVR_UN: // unknown value representation | |
| 627 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 628 | |
| 629 | |
| 630 /** | |
| 631 * String types. | |
| 632 **/ | |
| 633 | |
| 634 case EVR_DS: // decimal string | |
| 635 case EVR_IS: // integer string | |
| 636 case EVR_AS: // age string | |
| 637 case EVR_DA: // date string | |
| 638 case EVR_DT: // date time string | |
| 639 case EVR_TM: // time string | |
| 640 case EVR_AE: // application entity title | |
| 641 case EVR_CS: // code string | |
| 642 case EVR_SH: // short string | |
| 643 case EVR_LO: // long string | |
| 644 case EVR_ST: // short text | |
| 645 case EVR_LT: // long text | |
| 646 case EVR_UT: // unlimited text | |
| 647 case EVR_PN: // person name | |
| 648 case EVR_UI: // unique identifier | |
| 649 { | |
| 650 ok = element.putString(value.c_str()).good(); | |
| 651 break; | |
| 652 } | |
| 653 | |
| 654 | |
| 655 /** | |
| 656 * Numerical types | |
| 657 **/ | |
| 658 | |
| 659 case EVR_SL: // signed long | |
| 660 { | |
| 661 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 662 break; | |
| 663 } | |
| 664 | |
| 665 case EVR_SS: // signed short | |
| 666 { | |
| 667 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 668 break; | |
| 669 } | |
| 670 | |
| 671 case EVR_UL: // unsigned long | |
| 672 { | |
| 673 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 674 break; | |
| 675 } | |
| 676 | |
| 677 case EVR_US: // unsigned short | |
| 678 { | |
| 679 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 680 break; | |
| 681 } | |
| 682 | |
| 683 case EVR_FL: // float single-precision | |
| 684 { | |
| 685 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 686 break; | |
| 687 } | |
| 688 | |
| 689 case EVR_FD: // float double-precision | |
| 690 { | |
| 691 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 692 break; | |
| 693 } | |
| 694 | |
| 695 | |
| 696 /** | |
| 697 * Sequence types, should never occur at this point. | |
| 698 **/ | |
| 699 | |
| 700 case EVR_SQ: // sequence of items | |
| 701 { | |
| 702 ok = false; | |
| 703 break; | |
| 704 } | |
| 705 | |
| 706 | |
| 707 /** | |
| 708 * Internal to DCMTK. | |
| 709 **/ | |
| 710 | |
| 711 case EVR_ox: // OB or OW depending on context | |
| 712 case EVR_xs: // SS or US depending on context | |
| 713 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 714 case EVR_na: // na="not applicable", for data which has no VR | |
| 715 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 716 case EVR_item: // used internally for items | |
| 717 case EVR_metainfo: // used internally for meta info datasets | |
| 718 case EVR_dataset: // used internally for datasets | |
| 719 case EVR_fileFormat: // used internally for DICOM files | |
| 720 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 721 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 722 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 723 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 724 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 725 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 726 case EVR_OverlayData: // used internally for overlay data | |
| 727 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 728 default: | |
| 729 break; | |
| 730 } | |
| 731 } | |
| 732 catch (boost::bad_lexical_cast&) | |
| 733 { | |
| 734 ok = false; | |
| 735 } | |
| 736 | |
| 737 if (!ok) | |
| 738 { | |
| 739 throw OrthancException(ErrorCode_InternalError); | |
| 740 } | |
| 741 } | |
| 742 | |
| 743 | |
| 744 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 745 { | |
| 746 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 747 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 748 if (element != NULL) |
| 749 { | |
| 750 delete element; | |
| 751 } | |
| 752 } | |
| 753 | |
| 754 | |
| 755 | |
| 756 void ParsedDicomFile::RemovePrivateTags() | |
| 757 { | |
| 758 typedef std::list<DcmElement*> Tags; | |
| 759 | |
| 760 Tags privateTags; | |
| 761 | |
| 794 | 762 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 763 for (unsigned long i = 0; i < dataset.card(); i++) |
| 764 { | |
| 765 DcmElement* element = dataset.getElement(i); | |
| 766 DcmTag tag(element->getTag()); | |
| 767 if (!strcmp("PrivateCreator", tag.getTagName()) || // TODO - This may change with future versions of DCMTK | |
| 768 tag.getPrivateCreator() != NULL) | |
| 769 { | |
| 770 privateTags.push_back(element); | |
| 771 } | |
| 772 } | |
| 773 | |
| 774 for (Tags::iterator it = privateTags.begin(); | |
| 775 it != privateTags.end(); ++it) | |
| 776 { | |
| 777 DcmElement* tmp = dataset.remove(*it); | |
| 778 if (tmp != NULL) | |
| 779 { | |
| 780 delete tmp; | |
| 781 } | |
| 782 } | |
| 783 } | |
| 784 | |
| 785 | |
| 786 | |
| 787 void ParsedDicomFile::Insert(const DicomTag& tag, | |
| 788 const std::string& value) | |
| 789 { | |
| 790 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); | |
| 791 FillElementWithString(*element, tag, value); | |
| 792 | |
| 794 | 793 if (!pimpl_->file_->getDataset()->insert(element.release(), false, false).good()) |
| 790 | 794 { |
| 795 // This field already exists | |
| 796 throw OrthancException(ErrorCode_InternalError); | |
| 797 } | |
| 798 } | |
| 799 | |
| 800 | |
| 801 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 802 const std::string& value, | |
| 803 DicomReplaceMode mode) | |
| 804 { | |
| 805 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 806 DcmElement* element = NULL; | |
| 807 | |
| 794 | 808 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 809 element == NULL) |
| 810 { | |
| 811 // This field does not exist, act wrt. the specified "mode" | |
| 812 switch (mode) | |
| 813 { | |
| 814 case DicomReplaceMode_InsertIfAbsent: | |
| 815 Insert(tag, value); | |
| 816 break; | |
| 817 | |
| 818 case DicomReplaceMode_ThrowIfAbsent: | |
| 819 throw OrthancException(ErrorCode_InexistentItem); | |
| 820 | |
| 821 case DicomReplaceMode_IgnoreIfAbsent: | |
| 822 return; | |
| 823 } | |
| 824 } | |
| 825 else | |
| 826 { | |
| 827 FillElementWithString(*element, tag, value); | |
| 828 } | |
| 829 | |
| 830 | |
| 831 /** | |
| 832 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 833 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 834 * you make changes to the related tags in the dataset ('SOP Class | |
| 835 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 836 * options. You can disable this behaviour by using the -nmu | |
| 837 * option. | |
| 838 **/ | |
| 839 | |
| 840 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 841 { | |
| 842 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 843 } | |
| 844 | |
| 845 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 846 { | |
| 847 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 848 } | |
| 849 } | |
| 850 | |
| 851 | |
| 852 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 853 { | |
| 854 std::string serialized; | |
| 794 | 855 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, pimpl_->file_->getDataset())) |
| 790 | 856 { |
| 857 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 858 } | |
| 859 } | |
| 860 | |
| 861 | |
| 862 | |
| 863 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 864 const DicomTag& tag) | |
| 865 { | |
| 866 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 867 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 868 DcmElement* element = NULL; |
| 869 if (!dataset.findAndGetElement(k, element).good() || | |
| 870 element == NULL) | |
| 871 { | |
| 872 return false; | |
| 873 } | |
| 874 | |
| 875 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element)); | |
| 876 | |
| 877 if (v.get() == NULL) | |
| 878 { | |
| 879 value = ""; | |
| 880 } | |
| 881 else | |
| 882 { | |
| 883 value = v->AsString(); | |
| 884 } | |
| 885 | |
| 886 return true; | |
| 887 } | |
| 888 | |
| 889 | |
| 890 | |
| 891 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 892 { | |
| 893 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 894 | |
| 895 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 896 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 897 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 898 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 899 { | |
| 900 throw OrthancException(ErrorCode_BadFileFormat); | |
| 901 } | |
| 902 | |
| 903 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 904 } | |
| 905 | |
| 906 | |
| 907 static void StoreElement(Json::Value& target, | |
| 908 DcmElement& element, | |
| 909 unsigned int maxStringLength); | |
| 910 | |
| 911 static void StoreItem(Json::Value& target, | |
| 912 DcmItem& item, | |
| 913 unsigned int maxStringLength) | |
| 914 { | |
| 915 target = Json::Value(Json::objectValue); | |
| 916 | |
| 917 for (unsigned long i = 0; i < item.card(); i++) | |
| 918 { | |
| 919 DcmElement* element = item.getElement(i); | |
| 920 StoreElement(target, *element, maxStringLength); | |
| 921 } | |
| 922 } | |
| 923 | |
| 924 | |
| 925 static void StoreElement(Json::Value& target, | |
| 926 DcmElement& element, | |
| 927 unsigned int maxStringLength) | |
| 928 { | |
| 929 assert(target.type() == Json::objectValue); | |
| 930 | |
| 931 DicomTag tag(FromDcmtkBridge::GetTag(element)); | |
| 932 const std::string formattedTag = tag.Format(); | |
| 933 | |
| 934 #if 0 | |
| 935 const std::string tagName = FromDcmtkBridge::GetName(tag); | |
| 936 #else | |
| 937 // This version of the code gives access to the name of the private tags | |
| 938 DcmTag tagbis(element.getTag()); | |
| 939 const std::string tagName(tagbis.getTagName()); | |
| 940 #endif | |
| 941 | |
| 942 if (element.isLeaf()) | |
| 943 { | |
| 944 Json::Value value(Json::objectValue); | |
| 945 value["Name"] = tagName; | |
| 946 | |
| 947 if (tagbis.getPrivateCreator() != NULL) | |
| 948 { | |
| 949 value["PrivateCreator"] = tagbis.getPrivateCreator(); | |
| 950 } | |
| 951 | |
| 952 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(element)); | |
| 953 if (v->IsNull()) | |
| 954 { | |
| 955 value["Type"] = "Null"; | |
| 956 value["Value"] = Json::nullValue; | |
| 957 } | |
| 958 else | |
| 959 { | |
| 960 std::string s = v->AsString(); | |
| 961 if (maxStringLength == 0 || | |
| 962 s.size() <= maxStringLength) | |
| 963 { | |
| 964 value["Type"] = "String"; | |
| 965 value["Value"] = s; | |
| 966 } | |
| 967 else | |
| 968 { | |
| 969 value["Type"] = "TooLong"; | |
| 970 value["Value"] = Json::nullValue; | |
| 971 } | |
| 972 } | |
| 973 | |
| 974 target[formattedTag] = value; | |
| 975 } | |
| 976 else | |
| 977 { | |
| 978 Json::Value children(Json::arrayValue); | |
| 979 | |
| 980 // "All subclasses of DcmElement except for DcmSequenceOfItems | |
| 981 // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset | |
| 982 // etc. are not." The following cast is thus OK. | |
| 983 DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); | |
| 984 | |
| 985 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 986 { | |
| 987 DcmItem* child = sequence.getItem(i); | |
| 988 Json::Value& v = children.append(Json::objectValue); | |
| 989 StoreItem(v, *child, maxStringLength); | |
| 990 } | |
| 991 | |
| 992 target[formattedTag]["Name"] = tagName; | |
| 993 target[formattedTag]["Type"] = "Sequence"; | |
| 994 target[formattedTag]["Value"] = children; | |
| 995 } | |
| 996 } | |
| 997 | |
| 998 | |
| 999 template <typename T> | |
| 1000 static void ExtractPngImageTruncate(std::string& result, | |
| 1001 DicomIntegerPixelAccessor& accessor, | |
| 1002 PixelFormat format) | |
| 1003 { | |
|
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1004 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 1005 |
| 1006 PngWriter w; | |
| 1007 | |
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1008 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 1009 T* pixel = &image[0]; |
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1010 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 1011 { |
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1012 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 1013 { |
| 1014 int32_t v = accessor.GetValue(x, y); | |
| 1015 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 1016 *pixel = std::numeric_limits<T>::min(); | |
| 1017 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 1018 *pixel = std::numeric_limits<T>::max(); | |
| 1019 else | |
| 1020 *pixel = static_cast<T>(v); | |
| 1021 } | |
| 1022 } | |
| 1023 | |
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1024 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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1025 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 1026 } |
| 1027 | |
| 1028 | |
| 1029 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 1030 { | |
| 794 | 1031 FromDcmtkBridge::SaveToMemoryBuffer(buffer, pimpl_->file_->getDataset()); |
| 790 | 1032 } |
| 1033 | |
| 1034 | |
| 1035 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 1036 { | |
| 1037 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 1038 std::string content; | |
| 1039 SaveToMemoryBuffer(content); | |
| 1040 Toolbox::WriteFile(content, path); | |
| 1041 } | |
| 1042 | |
| 1043 | |
| 794 | 1044 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 1045 { |
| 794 | 1046 pimpl_->file_.reset(new DcmFileFormat); |
| 790 | 1047 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 1048 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 1049 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 1050 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 1051 } | |
| 1052 | |
| 791 | 1053 |
| 794 | 1054 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 1055 { |
| 1056 Setup(content, size); | |
| 1057 } | |
| 1058 | |
| 794 | 1059 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 1060 { |
| 1061 if (content.size() == 0) | |
| 1062 { | |
| 1063 Setup(NULL, 0); | |
| 1064 } | |
| 1065 else | |
| 1066 { | |
| 1067 Setup(&content[0], content.size()); | |
| 1068 } | |
| 1069 } | |
| 792 | 1070 |
| 1071 | |
| 794 | 1072 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1073 pimpl_(new PImpl) | |
| 792 | 1074 { |
| 794 | 1075 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
| 792 | 1076 } |
| 1077 | |
| 1078 | |
| 1079 ParsedDicomFile::~ParsedDicomFile() | |
| 1080 { | |
| 794 | 1081 delete pimpl_; |
| 792 | 1082 } |
| 1083 | |
| 793 | 1084 |
| 1085 void* ParsedDicomFile::GetDcmtkObject() | |
| 1086 { | |
| 794 | 1087 return pimpl_->file_.get(); |
| 793 | 1088 } |
| 1089 | |
| 1090 | |
| 1091 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1092 { | |
| 794 | 1093 return new ParsedDicomFile(*this); |
| 793 | 1094 } |
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1095 |
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1096 |
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1097 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
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1098 { |
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1099 std::string mime, content; |
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1100 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
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parents:
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diff
changeset
|
1101 |
|
809
8ce2f69436ca
do not return strings with base64
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
800
diff
changeset
|
1102 std::string decoded; |
|
8ce2f69436ca
do not return strings with base64
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
800
diff
changeset
|
1103 Toolbox::DecodeBase64(decoded, content); |
|
800
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1104 |
|
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1105 if (mime == "image/png") |
|
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parents:
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diff
changeset
|
1106 { |
|
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1107 PngReader reader; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1108 reader.ReadFromMemory(decoded); |
|
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1109 EmbedImage(reader); |
|
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diff
changeset
|
1110 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1111 else |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1112 { |
|
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diff
changeset
|
1113 throw OrthancException(ErrorCode_NotImplemented); |
|
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changeset
|
1114 } |
|
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generation of DICOM images from PNG files
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changeset
|
1115 } |
|
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changeset
|
1116 |
|
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diff
changeset
|
1117 |
|
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diff
changeset
|
1118 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
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changeset
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1119 { |
|
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diff
changeset
|
1120 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
|
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changeset
|
1121 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1122 accessor.GetFormat() != PixelFormat_RGB24 && |
|
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changeset
|
1123 accessor.GetFormat() != PixelFormat_RGBA32) |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1124 { |
|
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diff
changeset
|
1125 throw OrthancException(ErrorCode_NotImplemented); |
|
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changeset
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1126 } |
|
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diff
changeset
|
1127 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1128 if (accessor.GetFormat() == PixelFormat_RGBA32) |
|
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changeset
|
1129 { |
|
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changeset
|
1130 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
|
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changeset
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1131 } |
|
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changeset
|
1132 |
|
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changeset
|
1133 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
|
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changeset
|
1134 |
|
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changeset
|
1135 Remove(DICOM_TAG_PIXEL_DATA); |
|
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|
1136 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
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changeset
|
1137 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
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diff
changeset
|
1138 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
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diff
changeset
|
1139 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
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parents:
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diff
changeset
|
1140 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
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diff
changeset
|
1141 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
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diff
changeset
|
1142 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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changeset
|
1143 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
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diff
changeset
|
1144 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
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changeset
|
1145 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
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diff
changeset
|
1146 |
|
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diff
changeset
|
1147 unsigned int bytesPerPixel = 1; |
|
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changeset
|
1148 |
|
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changeset
|
1149 switch (accessor.GetFormat()) |
|
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changeset
|
1150 { |
|
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changeset
|
1151 case PixelFormat_RGB24: |
|
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changeset
|
1152 case PixelFormat_RGBA32: |
|
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changeset
|
1153 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
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changeset
|
1154 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
|
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changeset
|
1155 bytesPerPixel = 3; |
|
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changeset
|
1156 break; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1157 |
|
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changeset
|
1158 case PixelFormat_Grayscale8: |
|
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changeset
|
1159 break; |
|
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changeset
|
1160 |
|
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changeset
|
1161 case PixelFormat_Grayscale16: |
|
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changeset
|
1162 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
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changeset
|
1163 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
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changeset
|
1164 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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changeset
|
1165 bytesPerPixel = 2; |
|
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changeset
|
1166 break; |
|
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changeset
|
1167 |
|
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changeset
|
1168 default: |
|
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changeset
|
1169 throw OrthancException(ErrorCode_NotImplemented); |
|
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changeset
|
1170 } |
|
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changeset
|
1171 |
|
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changeset
|
1172 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
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changeset
|
1173 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
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changeset
|
1174 |
|
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changeset
|
1175 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
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changeset
|
1176 |
|
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changeset
|
1177 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
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changeset
|
1178 Uint8* target = NULL; |
|
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changeset
|
1179 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
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changeset
|
1180 |
|
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changeset
|
1181 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
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changeset
|
1182 { |
|
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changeset
|
1183 switch (accessor.GetFormat()) |
|
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changeset
|
1184 { |
|
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changeset
|
1185 case PixelFormat_RGB24: |
|
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changeset
|
1186 case PixelFormat_Grayscale8: |
|
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changeset
|
1187 case PixelFormat_Grayscale16: |
|
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changeset
|
1188 case PixelFormat_SignedGrayscale16: |
|
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changeset
|
1189 { |
|
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changeset
|
1190 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
|
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1191 target += pitch; |
|
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changeset
|
1192 break; |
|
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changeset
|
1193 } |
|
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changeset
|
1194 |
|
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changeset
|
1195 case PixelFormat_RGBA32: |
|
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changeset
|
1196 { |
|
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changeset
|
1197 // The alpha channel is not supported by the DICOM standard |
|
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changeset
|
1198 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
|
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1199 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
|
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changeset
|
1200 { |
|
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changeset
|
1201 target[0] = source[0]; |
|
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|
1202 target[1] = source[1]; |
|
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changeset
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1203 target[2] = source[2]; |
|
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changeset
|
1204 } |
|
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changeset
|
1205 |
|
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changeset
|
1206 break; |
|
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changeset
|
1207 } |
|
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changeset
|
1208 |
|
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|
1209 default: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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1210 throw OrthancException(ErrorCode_NotImplemented); |
|
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generation of DICOM images from PNG files
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|
1211 } |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1212 } |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1213 |
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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1214 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
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|
1215 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1216 throw OrthancException(ErrorCode_InternalError); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1217 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1218 } |
|
874
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1219 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1220 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1221 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1222 unsigned int frame) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1223 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1224 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1225 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1226 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1227 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1228 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1229 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1230 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1231 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1232 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
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|
1233 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1234 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1235 ImageExtractionMode mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1236 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1237 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1238 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1239 bool ok = false; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1240 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1241 switch (mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1242 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1243 case ImageExtractionMode_UInt8: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1244 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1245 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1246 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1247 case ImageExtractionMode_UInt16: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1248 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1249 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1250 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1251 case ImageExtractionMode_Int16: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1252 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1253 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1254 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1255 case ImageExtractionMode_Preview: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1256 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1257 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1258 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1259 default: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1260 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1261 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1262 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1263 if (!ok) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1264 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1265 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1266 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1267 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1268 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1269 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1270 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1271 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1272 ImageExtractionMode mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1273 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1274 ImageBuffer buffer; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1275 ExtractImage(buffer, frame, mode); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1276 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1277 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1278 PngWriter writer; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1279 writer.WriteToMemory(result, accessor); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1280 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1281 |
| 790 | 1282 } |