Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1190:851a55d183c9
fix issue #22
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 16 Oct 2014 11:23:09 +0200 |
| parents | 80671157d051 |
| children | 6e7e5ed91c2d |
| 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 | |
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83 #include "ServerToolbox.h" |
| 790 | 84 #include "FromDcmtkBridge.h" |
| 85 #include "ToDcmtkBridge.h" | |
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86 #include "Internals/DicomImageDecoder.h" |
| 790 | 87 #include "../Core/Toolbox.h" |
| 88 #include "../Core/OrthancException.h" | |
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89 #include "../Core/ImageFormats/ImageBuffer.h" |
| 799 | 90 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 91 #include "../Core/Uuid.h" |
| 92 #include "../Core/DicomFormat/DicomString.h" | |
| 93 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 94 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
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95 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 96 |
| 97 #include <list> | |
| 98 #include <limits> | |
| 99 | |
| 100 #include <boost/lexical_cast.hpp> | |
| 101 | |
| 102 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 103 #include <dcmtk/dcmdata/dcdicent.h> | |
| 104 #include <dcmtk/dcmdata/dcdict.h> | |
| 105 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 106 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 107 #include <dcmtk/dcmdata/dcuid.h> | |
| 108 #include <dcmtk/dcmdata/dcmetinf.h> | |
| 109 | |
| 110 #include <dcmtk/dcmdata/dcvrae.h> | |
| 111 #include <dcmtk/dcmdata/dcvras.h> | |
| 112 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 113 #include <dcmtk/dcmdata/dcvrda.h> | |
| 114 #include <dcmtk/dcmdata/dcvrds.h> | |
| 115 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 116 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 117 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 118 #include <dcmtk/dcmdata/dcvris.h> | |
| 119 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 120 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 121 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 122 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 123 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 124 #include <dcmtk/dcmdata/dcvrss.h> | |
| 125 #include <dcmtk/dcmdata/dcvrst.h> | |
| 126 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 127 #include <dcmtk/dcmdata/dcvrui.h> | |
| 128 #include <dcmtk/dcmdata/dcvrul.h> | |
| 129 #include <dcmtk/dcmdata/dcvrus.h> | |
| 130 #include <dcmtk/dcmdata/dcvrut.h> | |
| 131 #include <dcmtk/dcmdata/dcpixel.h> | |
| 132 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 133 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 134 | |
| 135 | |
| 136 #include <boost/math/special_functions/round.hpp> | |
| 137 #include <glog/logging.h> | |
| 138 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 139 | |
| 140 | |
| 141 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 142 | |
| 143 | |
| 144 | |
| 145 namespace Orthanc | |
| 146 { | |
| 794 | 147 struct ParsedDicomFile::PImpl |
| 148 { | |
| 149 std::auto_ptr<DcmFileFormat> file_; | |
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150 Encoding encoding_; |
| 794 | 151 }; |
| 152 | |
| 153 | |
| 154 // This method can only be called from the constructors! | |
| 790 | 155 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 156 { | |
| 157 DcmInputBufferStream is; | |
| 158 if (size > 0) | |
| 159 { | |
| 160 is.setBuffer(buffer, size); | |
| 161 } | |
| 162 is.setEos(); | |
| 163 | |
| 794 | 164 pimpl_->file_.reset(new DcmFileFormat); |
| 165 pimpl_->file_->transferInit(); | |
| 166 if (!pimpl_->file_->read(is).good()) | |
| 790 | 167 { |
| 794 | 168 delete pimpl_; // Avoid a memory leak due to exception |
| 169 // throwing, as we are in the constructor | |
| 170 | |
| 790 | 171 throw OrthancException(ErrorCode_BadFileFormat); |
| 172 } | |
| 794 | 173 pimpl_->file_->loadAllDataIntoMemory(); |
| 174 pimpl_->file_->transferEnd(); | |
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175 |
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176 pimpl_->encoding_ = FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
| 790 | 177 } |
| 178 | |
| 179 | |
| 180 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 181 DcmItem& dicom) | |
| 182 { | |
| 183 Json::Value v = Json::arrayValue; | |
| 184 | |
| 185 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 186 { | |
| 187 DcmElement* element = dicom.getElement(i); | |
| 188 if (element) | |
| 189 { | |
| 190 char buf[16]; | |
| 191 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 192 v.append(buf); | |
| 193 } | |
| 194 } | |
| 195 | |
| 196 output.AnswerJson(v); | |
| 197 } | |
| 198 | |
| 199 static inline uint16_t GetCharValue(char c) | |
| 200 { | |
| 201 if (c >= '0' && c <= '9') | |
| 202 return c - '0'; | |
| 203 else if (c >= 'a' && c <= 'f') | |
| 204 return c - 'a' + 10; | |
| 205 else if (c >= 'A' && c <= 'F') | |
| 206 return c - 'A' + 10; | |
| 207 else | |
| 208 return 0; | |
| 209 } | |
| 210 | |
| 211 static inline uint16_t GetTagValue(const char* c) | |
| 212 { | |
| 213 return ((GetCharValue(c[0]) << 12) + | |
| 214 (GetCharValue(c[1]) << 8) + | |
| 215 (GetCharValue(c[2]) << 4) + | |
| 216 GetCharValue(c[3])); | |
| 217 } | |
| 218 | |
| 219 static void ParseTagAndGroup(DcmTagKey& key, | |
| 220 const std::string& tag) | |
| 221 { | |
| 222 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 223 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 224 } | |
| 225 | |
| 226 | |
| 227 static void SendSequence(RestApiOutput& output, | |
| 228 DcmSequenceOfItems& sequence) | |
| 229 { | |
| 230 // This element is a sequence | |
| 231 Json::Value v = Json::arrayValue; | |
| 232 | |
| 233 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 234 { | |
| 235 v.append(boost::lexical_cast<std::string>(i)); | |
| 236 } | |
| 237 | |
| 238 output.AnswerJson(v); | |
| 239 } | |
| 240 | |
| 241 | |
| 242 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 243 E_TransferSyntax transferSyntax) | |
| 244 { | |
| 245 DcmPixelSequence* pixelSequence = NULL; | |
| 246 if (pixelData.getEncapsulatedRepresentation | |
| 247 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 248 { | |
| 249 return pixelSequence->card(); | |
| 250 } | |
| 251 else | |
| 252 { | |
| 253 return 1; | |
| 254 } | |
| 255 } | |
| 256 | |
| 257 | |
| 258 static void AnswerDicomField(RestApiOutput& output, | |
| 259 DcmElement& element, | |
| 260 E_TransferSyntax transferSyntax) | |
| 261 { | |
| 262 // This element is nor a sequence, neither a pixel-data | |
| 263 std::string buffer; | |
| 264 buffer.resize(65536); | |
| 265 Uint32 length = element.getLength(transferSyntax); | |
| 266 Uint32 offset = 0; | |
| 267 | |
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268 output.GetLowLevelOutput().SetContentType(CONTENT_TYPE_OCTET_STREAM); |
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269 output.GetLowLevelOutput().SetContentLength(length); |
| 790 | 270 |
| 271 while (offset < length) | |
| 272 { | |
| 273 Uint32 nbytes; | |
| 274 if (length - offset < buffer.size()) | |
| 275 { | |
| 276 nbytes = length - offset; | |
| 277 } | |
| 278 else | |
| 279 { | |
| 280 nbytes = buffer.size(); | |
| 281 } | |
| 282 | |
| 283 OFCondition cond = element.getPartialValue(&buffer[0], offset, nbytes); | |
| 284 | |
| 285 if (cond.good()) | |
| 286 { | |
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287 output.GetLowLevelOutput().SendBody(&buffer[0], nbytes); |
| 790 | 288 offset += nbytes; |
| 289 } | |
| 290 else | |
| 291 { | |
| 292 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); | |
| 293 return; | |
| 294 } | |
| 295 } | |
| 296 | |
| 297 output.MarkLowLevelOutputDone(); | |
| 298 } | |
| 299 | |
| 300 | |
| 301 static bool AnswerPixelData(RestApiOutput& output, | |
| 302 DcmItem& dicom, | |
| 303 E_TransferSyntax transferSyntax, | |
| 304 const std::string* blockUri) | |
| 305 { | |
| 306 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 307 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 308 | |
| 309 DcmElement *element = NULL; | |
| 310 if (!dicom.findAndGetElement(k, element).good() || | |
| 311 element == NULL) | |
| 312 { | |
| 313 return false; | |
| 314 } | |
| 315 | |
| 316 try | |
| 317 { | |
| 318 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 319 if (blockUri == NULL) | |
| 320 { | |
| 321 // The user asks how many blocks are presents in this pixel data | |
| 322 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 323 | |
| 324 Json::Value result(Json::arrayValue); | |
| 325 for (unsigned int i = 0; i < blocks; i++) | |
| 326 { | |
| 327 result.append(boost::lexical_cast<std::string>(i)); | |
| 328 } | |
| 329 | |
| 330 output.AnswerJson(result); | |
| 331 return true; | |
| 332 } | |
| 333 | |
| 334 | |
| 335 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 336 | |
| 337 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 338 { | |
| 339 DcmPixelSequence* pixelSequence = NULL; | |
| 340 if (pixelData.getEncapsulatedRepresentation | |
| 341 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 342 { | |
| 343 // This is the case for JPEG transfer syntaxes | |
| 344 if (block < pixelSequence->card()) | |
| 345 { | |
| 346 DcmPixelItem* pixelItem = NULL; | |
| 347 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 348 { | |
| 349 if (pixelItem->getLength() == 0) | |
| 350 { | |
| 351 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 352 return true; | |
| 353 } | |
| 354 | |
| 355 Uint8* buffer = NULL; | |
| 356 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 357 { | |
| 358 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 359 return true; | |
| 360 } | |
| 361 } | |
| 362 } | |
| 363 } | |
| 364 else | |
| 365 { | |
| 366 // This is the case for raw, uncompressed image buffers | |
| 367 assert(*blockUri == "0"); | |
| 368 AnswerDicomField(output, *element, transferSyntax); | |
| 369 } | |
| 370 } | |
| 371 } | |
| 372 catch (boost::bad_lexical_cast&) | |
| 373 { | |
| 374 // The URI entered by the user is not a number | |
| 375 } | |
| 376 catch (std::bad_cast&) | |
| 377 { | |
| 378 // This should never happen | |
| 379 } | |
| 380 | |
| 381 return false; | |
| 382 } | |
| 383 | |
| 384 | |
| 385 | |
| 386 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 387 const std::string& tag, | |
| 388 DcmItem& dicom, | |
| 389 E_TransferSyntax transferSyntax) | |
| 390 { | |
| 391 DcmTagKey k; | |
| 392 ParseTagAndGroup(k, tag); | |
| 393 | |
| 394 DcmSequenceOfItems* sequence = NULL; | |
| 395 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 396 sequence != NULL && | |
| 397 sequence->getVR() == EVR_SQ) | |
| 398 { | |
| 399 SendSequence(output, *sequence); | |
| 400 return; | |
| 401 } | |
| 402 | |
| 403 DcmElement* element = NULL; | |
| 404 if (dicom.findAndGetElement(k, element).good() && | |
| 405 element != NULL && | |
| 406 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 407 element->getVR() != EVR_SQ) | |
| 408 { | |
| 409 AnswerDicomField(output, *element, transferSyntax); | |
| 410 } | |
| 411 } | |
| 412 | |
| 413 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 414 const UriComponents& uri) | |
| 415 { | |
| 794 | 416 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 417 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 418 |
| 419 // Special case: Accessing the pixel data | |
| 420 if (uri.size() == 1 || | |
| 421 uri.size() == 2) | |
| 422 { | |
| 423 DcmTagKey tag; | |
| 424 ParseTagAndGroup(tag, uri[0]); | |
| 425 | |
| 426 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 427 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 428 { | |
| 429 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 430 return; | |
| 431 } | |
| 432 } | |
| 433 | |
| 434 // Go down in the tag hierarchy according to the URI | |
| 435 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 436 { | |
| 437 size_t index; | |
| 438 try | |
| 439 { | |
| 440 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 441 } | |
| 442 catch (boost::bad_lexical_cast&) | |
| 443 { | |
| 444 return; | |
| 445 } | |
| 446 | |
| 447 DcmTagKey k; | |
| 448 DcmItem *child = NULL; | |
| 449 ParseTagAndGroup(k, uri[2 * pos]); | |
| 450 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 451 child == NULL) | |
| 452 { | |
| 453 return; | |
| 454 } | |
| 455 | |
| 456 dicom = child; | |
| 457 } | |
| 458 | |
| 459 // We have reached the end of the URI | |
| 460 if (uri.size() % 2 == 0) | |
| 461 { | |
| 462 SendPathValueForDictionary(output, *dicom); | |
| 463 } | |
| 464 else | |
| 465 { | |
| 466 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 467 } | |
| 468 } | |
| 469 | |
| 470 | |
| 471 | |
| 472 | |
| 473 | |
| 474 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 475 { | |
| 476 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 477 | |
| 478 switch (key.getEVR()) | |
| 479 { | |
| 480 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 481 | |
| 482 /** | |
| 483 * TODO. | |
| 484 **/ | |
| 485 | |
| 486 case EVR_OB: // other byte | |
| 487 case EVR_OF: // other float | |
| 488 case EVR_OW: // other word | |
| 489 case EVR_AT: // attribute tag | |
| 490 throw OrthancException(ErrorCode_NotImplemented); | |
| 491 | |
| 492 case EVR_UN: // unknown value representation | |
| 493 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 494 | |
| 495 | |
| 496 /** | |
| 497 * String types. | |
| 498 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 499 **/ | |
| 500 | |
| 501 case EVR_AS: // age string | |
| 502 return new DcmAgeString(key); | |
| 503 | |
| 504 case EVR_AE: // application entity title | |
| 505 return new DcmApplicationEntity(key); | |
| 506 | |
| 507 case EVR_CS: // code string | |
| 508 return new DcmCodeString(key); | |
| 509 | |
| 510 case EVR_DA: // date string | |
| 511 return new DcmDate(key); | |
| 512 | |
| 513 case EVR_DT: // date time string | |
| 514 return new DcmDateTime(key); | |
| 515 | |
| 516 case EVR_DS: // decimal string | |
| 517 return new DcmDecimalString(key); | |
| 518 | |
| 519 case EVR_IS: // integer string | |
| 520 return new DcmIntegerString(key); | |
| 521 | |
| 522 case EVR_TM: // time string | |
| 523 return new DcmTime(key); | |
| 524 | |
| 525 case EVR_UI: // unique identifier | |
| 526 return new DcmUniqueIdentifier(key); | |
| 527 | |
| 528 case EVR_ST: // short text | |
| 529 return new DcmShortText(key); | |
| 530 | |
| 531 case EVR_LO: // long string | |
| 532 return new DcmLongString(key); | |
| 533 | |
| 534 case EVR_LT: // long text | |
| 535 return new DcmLongText(key); | |
| 536 | |
| 537 case EVR_UT: // unlimited text | |
| 538 return new DcmUnlimitedText(key); | |
| 539 | |
| 540 case EVR_SH: // short string | |
| 541 return new DcmShortString(key); | |
| 542 | |
| 543 case EVR_PN: // person name | |
| 544 return new DcmPersonName(key); | |
| 545 | |
| 546 | |
| 547 /** | |
| 548 * Numerical types | |
| 549 **/ | |
| 550 | |
| 551 case EVR_SL: // signed long | |
| 552 return new DcmSignedLong(key); | |
| 553 | |
| 554 case EVR_SS: // signed short | |
| 555 return new DcmSignedShort(key); | |
| 556 | |
| 557 case EVR_UL: // unsigned long | |
| 558 return new DcmUnsignedLong(key); | |
| 559 | |
| 560 case EVR_US: // unsigned short | |
| 561 return new DcmUnsignedShort(key); | |
| 562 | |
| 563 case EVR_FL: // float single-precision | |
| 564 return new DcmFloatingPointSingle(key); | |
| 565 | |
| 566 case EVR_FD: // float double-precision | |
| 567 return new DcmFloatingPointDouble(key); | |
| 568 | |
| 569 | |
| 570 /** | |
| 571 * Sequence types, should never occur at this point. | |
| 572 **/ | |
| 573 | |
| 574 case EVR_SQ: // sequence of items | |
| 575 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 576 | |
| 577 | |
| 578 /** | |
| 579 * Internal to DCMTK. | |
| 580 **/ | |
| 581 | |
| 582 case EVR_ox: // OB or OW depending on context | |
| 583 case EVR_xs: // SS or US depending on context | |
| 584 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 585 case EVR_na: // na="not applicable", for data which has no VR | |
| 586 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 587 case EVR_item: // used internally for items | |
| 588 case EVR_metainfo: // used internally for meta info datasets | |
| 589 case EVR_dataset: // used internally for datasets | |
| 590 case EVR_fileFormat: // used internally for DICOM files | |
| 591 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 592 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 593 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 594 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 595 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 596 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 597 case EVR_OverlayData: // used internally for overlay data | |
| 598 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 599 default: | |
| 600 break; | |
| 601 } | |
| 602 | |
| 603 throw OrthancException(ErrorCode_InternalError); | |
| 604 } | |
| 605 | |
| 606 | |
| 607 | |
| 608 static void FillElementWithString(DcmElement& element, | |
| 609 const DicomTag& tag, | |
| 610 const std::string& value) | |
| 611 { | |
| 612 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 613 bool ok = false; | |
| 614 | |
| 615 try | |
| 616 { | |
| 617 switch (key.getEVR()) | |
| 618 { | |
| 619 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 620 | |
| 621 /** | |
| 622 * TODO. | |
| 623 **/ | |
| 624 | |
| 625 case EVR_OB: // other byte | |
| 626 case EVR_OF: // other float | |
| 627 case EVR_OW: // other word | |
| 628 case EVR_AT: // attribute tag | |
| 629 throw OrthancException(ErrorCode_NotImplemented); | |
| 630 | |
| 631 case EVR_UN: // unknown value representation | |
| 632 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 633 | |
| 634 | |
| 635 /** | |
| 636 * String types. | |
| 637 **/ | |
| 638 | |
| 639 case EVR_DS: // decimal string | |
| 640 case EVR_IS: // integer string | |
| 641 case EVR_AS: // age string | |
| 642 case EVR_DA: // date string | |
| 643 case EVR_DT: // date time string | |
| 644 case EVR_TM: // time string | |
| 645 case EVR_AE: // application entity title | |
| 646 case EVR_CS: // code string | |
| 647 case EVR_SH: // short string | |
| 648 case EVR_LO: // long string | |
| 649 case EVR_ST: // short text | |
| 650 case EVR_LT: // long text | |
| 651 case EVR_UT: // unlimited text | |
| 652 case EVR_PN: // person name | |
| 653 case EVR_UI: // unique identifier | |
| 654 { | |
| 655 ok = element.putString(value.c_str()).good(); | |
| 656 break; | |
| 657 } | |
| 658 | |
| 659 | |
| 660 /** | |
| 661 * Numerical types | |
| 662 **/ | |
| 663 | |
| 664 case EVR_SL: // signed long | |
| 665 { | |
| 666 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 667 break; | |
| 668 } | |
| 669 | |
| 670 case EVR_SS: // signed short | |
| 671 { | |
| 672 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 673 break; | |
| 674 } | |
| 675 | |
| 676 case EVR_UL: // unsigned long | |
| 677 { | |
| 678 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 679 break; | |
| 680 } | |
| 681 | |
| 682 case EVR_US: // unsigned short | |
| 683 { | |
| 684 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 685 break; | |
| 686 } | |
| 687 | |
| 688 case EVR_FL: // float single-precision | |
| 689 { | |
| 690 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 691 break; | |
| 692 } | |
| 693 | |
| 694 case EVR_FD: // float double-precision | |
| 695 { | |
| 696 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 697 break; | |
| 698 } | |
| 699 | |
| 700 | |
| 701 /** | |
| 702 * Sequence types, should never occur at this point. | |
| 703 **/ | |
| 704 | |
| 705 case EVR_SQ: // sequence of items | |
| 706 { | |
| 707 ok = false; | |
| 708 break; | |
| 709 } | |
| 710 | |
| 711 | |
| 712 /** | |
| 713 * Internal to DCMTK. | |
| 714 **/ | |
| 715 | |
| 716 case EVR_ox: // OB or OW depending on context | |
| 717 case EVR_xs: // SS or US depending on context | |
| 718 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 719 case EVR_na: // na="not applicable", for data which has no VR | |
| 720 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 721 case EVR_item: // used internally for items | |
| 722 case EVR_metainfo: // used internally for meta info datasets | |
| 723 case EVR_dataset: // used internally for datasets | |
| 724 case EVR_fileFormat: // used internally for DICOM files | |
| 725 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 726 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 727 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 728 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 729 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 730 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 731 case EVR_OverlayData: // used internally for overlay data | |
| 732 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 733 default: | |
| 734 break; | |
| 735 } | |
| 736 } | |
| 737 catch (boost::bad_lexical_cast&) | |
| 738 { | |
| 739 ok = false; | |
| 740 } | |
| 741 | |
| 742 if (!ok) | |
| 743 { | |
| 744 throw OrthancException(ErrorCode_InternalError); | |
| 745 } | |
| 746 } | |
| 747 | |
| 748 | |
| 749 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 750 { | |
| 751 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 752 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 753 if (element != NULL) |
| 754 { | |
| 755 delete element; | |
| 756 } | |
| 757 } | |
| 758 | |
| 759 | |
| 760 | |
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761 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 762 { |
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763 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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764 |
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765 // Loop over the dataset to detect its private tags |
| 790 | 766 typedef std::list<DcmElement*> Tags; |
| 767 Tags privateTags; | |
| 768 | |
| 769 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 770 { | |
| 771 DcmElement* element = dataset.getElement(i); | |
| 772 DcmTag tag(element->getTag()); | |
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773 |
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774 // Is this a private tag? |
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775 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 776 { |
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777 bool remove = true; |
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778 |
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779 // Check whether this private tag is to be kept |
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780 if (toKeep != NULL) |
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781 { |
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782 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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783 if (toKeep->find(tmp) != toKeep->end()) |
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784 { |
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785 remove = false; // Keep it |
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786 } |
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787 } |
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788 |
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789 if (remove) |
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790 { |
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791 privateTags.push_back(element); |
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792 } |
| 790 | 793 } |
| 794 } | |
| 795 | |
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796 // Loop over the detected private tags to remove them |
| 790 | 797 for (Tags::iterator it = privateTags.begin(); |
| 798 it != privateTags.end(); ++it) | |
| 799 { | |
| 800 DcmElement* tmp = dataset.remove(*it); | |
| 801 if (tmp != NULL) | |
| 802 { | |
| 803 delete tmp; | |
| 804 } | |
| 805 } | |
| 806 } | |
| 807 | |
| 808 | |
| 809 | |
| 810 void ParsedDicomFile::Insert(const DicomTag& tag, | |
| 811 const std::string& value) | |
| 812 { | |
| 813 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); | |
| 814 FillElementWithString(*element, tag, value); | |
| 815 | |
| 794 | 816 if (!pimpl_->file_->getDataset()->insert(element.release(), false, false).good()) |
| 790 | 817 { |
| 818 // This field already exists | |
| 819 throw OrthancException(ErrorCode_InternalError); | |
| 820 } | |
| 821 } | |
| 822 | |
| 823 | |
| 824 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 825 const std::string& value, | |
| 826 DicomReplaceMode mode) | |
| 827 { | |
| 828 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 829 DcmElement* element = NULL; | |
| 830 | |
| 794 | 831 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 832 element == NULL) |
| 833 { | |
| 834 // This field does not exist, act wrt. the specified "mode" | |
| 835 switch (mode) | |
| 836 { | |
| 837 case DicomReplaceMode_InsertIfAbsent: | |
| 838 Insert(tag, value); | |
| 839 break; | |
| 840 | |
| 841 case DicomReplaceMode_ThrowIfAbsent: | |
| 842 throw OrthancException(ErrorCode_InexistentItem); | |
| 843 | |
| 844 case DicomReplaceMode_IgnoreIfAbsent: | |
| 845 return; | |
| 846 } | |
| 847 } | |
| 848 else | |
| 849 { | |
| 850 FillElementWithString(*element, tag, value); | |
| 851 } | |
| 852 | |
| 853 | |
| 854 /** | |
| 855 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 856 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 857 * you make changes to the related tags in the dataset ('SOP Class | |
| 858 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 859 * options. You can disable this behaviour by using the -nmu | |
| 860 * option. | |
| 861 **/ | |
| 862 | |
| 863 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 864 { | |
| 865 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 866 } | |
| 867 | |
| 868 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 869 { | |
| 870 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 871 } | |
| 872 } | |
| 873 | |
| 874 | |
| 875 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 876 { | |
| 877 std::string serialized; | |
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878 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 879 { |
| 880 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 881 } | |
| 882 } | |
| 883 | |
| 884 | |
| 885 | |
| 886 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 887 const DicomTag& tag) | |
| 888 { | |
| 889 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 890 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
| 790 | 891 DcmElement* element = NULL; |
| 892 if (!dataset.findAndGetElement(k, element).good() || | |
| 893 element == NULL) | |
| 894 { | |
| 895 return false; | |
| 896 } | |
| 897 | |
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898 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
| 790 | 899 |
| 900 if (v.get() == NULL) | |
| 901 { | |
| 902 value = ""; | |
| 903 } | |
| 904 else | |
| 905 { | |
| 906 value = v->AsString(); | |
| 907 } | |
| 908 | |
| 909 return true; | |
| 910 } | |
| 911 | |
| 912 | |
| 913 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 914 { | |
| 915 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 916 | |
| 917 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 918 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 919 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 920 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 921 { | |
| 922 throw OrthancException(ErrorCode_BadFileFormat); | |
| 923 } | |
| 924 | |
| 925 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 926 } | |
| 927 | |
| 928 | |
| 929 template <typename T> | |
| 930 static void ExtractPngImageTruncate(std::string& result, | |
| 931 DicomIntegerPixelAccessor& accessor, | |
| 932 PixelFormat format) | |
| 933 { | |
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934 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 935 |
| 936 PngWriter w; | |
| 937 | |
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938 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 939 T* pixel = &image[0]; |
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940 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 941 { |
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942 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 943 { |
| 944 int32_t v = accessor.GetValue(x, y); | |
| 945 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 946 *pixel = std::numeric_limits<T>::min(); | |
| 947 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 948 *pixel = std::numeric_limits<T>::max(); | |
| 949 else | |
| 950 *pixel = static_cast<T>(v); | |
| 951 } | |
| 952 } | |
| 953 | |
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954 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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955 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 956 } |
| 957 | |
| 958 | |
| 959 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 960 { | |
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961 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 962 } |
| 963 | |
| 964 | |
| 965 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 966 { | |
| 967 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 968 std::string content; | |
| 969 SaveToMemoryBuffer(content); | |
| 970 Toolbox::WriteFile(content, path); | |
| 971 } | |
| 972 | |
| 973 | |
| 794 | 974 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 975 { |
| 794 | 976 pimpl_->file_.reset(new DcmFileFormat); |
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977 pimpl_->encoding_ = Encoding_Ascii; |
| 790 | 978 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 979 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 980 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 981 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 982 } | |
| 983 | |
| 791 | 984 |
| 794 | 985 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 986 { |
| 987 Setup(content, size); | |
| 988 } | |
| 989 | |
| 794 | 990 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 991 { |
| 992 if (content.size() == 0) | |
| 993 { | |
| 994 Setup(NULL, 0); | |
| 995 } | |
| 996 else | |
| 997 { | |
| 998 Setup(&content[0], content.size()); | |
| 999 } | |
| 1000 } | |
| 792 | 1001 |
| 1002 | |
| 794 | 1003 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1004 pimpl_(new PImpl) | |
| 792 | 1005 { |
| 794 | 1006 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
956
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1007 |
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1008 pimpl_->encoding_ = other.pimpl_->encoding_; |
| 792 | 1009 } |
| 1010 | |
| 1011 | |
| 1012 ParsedDicomFile::~ParsedDicomFile() | |
| 1013 { | |
| 794 | 1014 delete pimpl_; |
| 792 | 1015 } |
| 1016 | |
| 793 | 1017 |
| 1018 void* ParsedDicomFile::GetDcmtkObject() | |
| 1019 { | |
| 794 | 1020 return pimpl_->file_.get(); |
| 793 | 1021 } |
| 1022 | |
| 1023 | |
| 1024 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1025 { | |
| 794 | 1026 return new ParsedDicomFile(*this); |
| 793 | 1027 } |
|
800
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1028 |
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1029 |
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1030 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
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1031 { |
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1032 std::string mime, content; |
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1033 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
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1034 |
|
809
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1035 std::string decoded; |
|
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1036 Toolbox::DecodeBase64(decoded, content); |
|
800
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1037 |
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1038 if (mime == "image/png") |
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1039 { |
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1040 PngReader reader; |
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1041 reader.ReadFromMemory(decoded); |
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1042 EmbedImage(reader); |
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1043 } |
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1044 else |
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1045 { |
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1046 throw OrthancException(ErrorCode_NotImplemented); |
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1047 } |
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1048 } |
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1049 |
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1050 |
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1051 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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1052 { |
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1053 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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1054 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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1055 accessor.GetFormat() != PixelFormat_RGB24 && |
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1056 accessor.GetFormat() != PixelFormat_RGBA32) |
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1057 { |
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1058 throw OrthancException(ErrorCode_NotImplemented); |
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1059 } |
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1060 |
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1061 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1062 { |
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1063 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1064 } |
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1065 |
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1066 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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1067 |
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1068 Remove(DICOM_TAG_PIXEL_DATA); |
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1069 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
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1070 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
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1071 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
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1072 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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1073 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
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1074 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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1075 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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1076 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
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1077 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1078 Replace(DICOM_TAG_HIGH_BIT, "7"); |
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1079 |
|
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1080 unsigned int bytesPerPixel = 1; |
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1081 |
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1082 switch (accessor.GetFormat()) |
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1083 { |
|
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1084 case PixelFormat_RGB24: |
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1085 case PixelFormat_RGBA32: |
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1086 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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1087 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
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1088 bytesPerPixel = 3; |
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1089 break; |
|
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1090 |
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1091 case PixelFormat_Grayscale8: |
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1092 break; |
|
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1093 |
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1094 case PixelFormat_Grayscale16: |
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1095 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
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1096 Replace(DICOM_TAG_BITS_STORED, "16"); |
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1097 Replace(DICOM_TAG_HIGH_BIT, "15"); |
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1098 bytesPerPixel = 2; |
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1099 break; |
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1100 |
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1101 default: |
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1102 throw OrthancException(ErrorCode_NotImplemented); |
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1103 } |
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1104 |
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1105 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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1106 DICOM_TAG_PIXEL_DATA.GetElement()); |
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1107 |
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1108 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
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1109 |
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1110 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
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1111 Uint8* target = NULL; |
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1112 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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1113 |
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1114 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1115 { |
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1116 switch (accessor.GetFormat()) |
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1117 { |
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1118 case PixelFormat_RGB24: |
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1119 case PixelFormat_Grayscale8: |
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1120 case PixelFormat_Grayscale16: |
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1121 case PixelFormat_SignedGrayscale16: |
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1122 { |
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1123 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
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|
1124 target += pitch; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1125 break; |
|
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|
1126 } |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1127 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1128 case PixelFormat_RGBA32: |
|
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|
1129 { |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1130 // The alpha channel is not supported by the DICOM standard |
|
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|
1131 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
|
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|
1132 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
|
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|
1133 { |
|
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generation of DICOM images from PNG files
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|
1134 target[0] = source[0]; |
|
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|
1135 target[1] = source[1]; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1136 target[2] = source[2]; |
|
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|
1137 } |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1138 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1139 break; |
|
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|
1140 } |
|
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|
1141 |
|
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|
1142 default: |
|
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|
1143 throw OrthancException(ErrorCode_NotImplemented); |
|
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|
1144 } |
|
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|
1145 } |
|
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|
1146 |
|
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|
1147 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
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|
1148 { |
|
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|
1149 throw OrthancException(ErrorCode_InternalError); |
|
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|
1150 } |
|
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|
1151 } |
|
874
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diff
changeset
|
1152 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1153 |
|
87791ebc1f50
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|
1154 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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|
1155 unsigned int frame) |
|
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diff
changeset
|
1156 { |
|
87791ebc1f50
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|
1157 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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|
1158 |
|
87791ebc1f50
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|
1159 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
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|
1160 { |
|
87791ebc1f50
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|
1161 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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parents:
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diff
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|
1162 } |
|
87791ebc1f50
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diff
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|
1163 } |
|
87791ebc1f50
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parents:
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diff
changeset
|
1164 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1165 |
|
87791ebc1f50
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parents:
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diff
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|
1166 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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changeset
|
1167 unsigned int frame, |
|
87791ebc1f50
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parents:
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diff
changeset
|
1168 ImageExtractionMode mode) |
|
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diff
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|
1169 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1170 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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diff
changeset
|
1171 |
|
87791ebc1f50
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diff
changeset
|
1172 bool ok = false; |
|
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parents:
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diff
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|
1173 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1174 switch (mode) |
|
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parents:
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diff
changeset
|
1175 { |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1176 case ImageExtractionMode_UInt8: |
|
1015
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|
1177 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
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parents:
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diff
changeset
|
1178 break; |
|
87791ebc1f50
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parents:
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diff
changeset
|
1179 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1180 case ImageExtractionMode_UInt16: |
|
1015
f009f7c75069
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1181 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
87791ebc1f50
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parents:
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diff
changeset
|
1182 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1183 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1184 case ImageExtractionMode_Int16: |
|
1015
f009f7c75069
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diff
changeset
|
1185 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1186 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1187 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1188 case ImageExtractionMode_Preview: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1189 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
87791ebc1f50
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parents:
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diff
changeset
|
1190 break; |
|
87791ebc1f50
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parents:
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diff
changeset
|
1191 |
|
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parents:
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diff
changeset
|
1192 default: |
|
87791ebc1f50
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parents:
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diff
changeset
|
1193 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
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parents:
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diff
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|
1194 } |
|
87791ebc1f50
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parents:
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diff
changeset
|
1195 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1196 if (!ok) |
|
87791ebc1f50
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parents:
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diff
changeset
|
1197 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1198 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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parents:
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diff
changeset
|
1199 } |
|
87791ebc1f50
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parents:
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diff
changeset
|
1200 } |
|
87791ebc1f50
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diff
changeset
|
1201 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1202 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1203 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
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diff
changeset
|
1204 unsigned int frame, |
|
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parents:
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diff
changeset
|
1205 ImageExtractionMode mode) |
|
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parents:
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diff
changeset
|
1206 { |
|
87791ebc1f50
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diff
changeset
|
1207 ImageBuffer buffer; |
|
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parents:
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diff
changeset
|
1208 ExtractImage(buffer, frame, mode); |
|
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diff
changeset
|
1209 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1210 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
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diff
changeset
|
1211 PngWriter writer; |
|
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changeset
|
1212 writer.WriteToMemory(result, accessor); |
|
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diff
changeset
|
1213 } |
|
87791ebc1f50
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diff
changeset
|
1214 |
|
956
2fd5a163776d
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|
1215 |
|
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|
1216 Encoding ParsedDicomFile::GetEncoding() const |
|
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|
1217 { |
|
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|
1218 return pimpl_->encoding_; |
|
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|
1219 } |
|
1090
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changeset
|
1220 |
|
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changeset
|
1221 |
|
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|
1222 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
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|
1223 { |
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|
1224 std::string s; |
|
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|
1225 |
|
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|
1226 // http://www.dabsoft.ch/dicom/3/C.12.1.1.2/ |
|
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|
1227 switch (encoding) |
|
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|
1228 { |
|
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|
1229 case Encoding_Utf8: |
|
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|
1230 case Encoding_Ascii: |
|
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|
1231 s = "ISO_IR 192"; |
|
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|
1232 break; |
|
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|
1233 |
|
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|
1234 case Encoding_Latin1: |
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|
1235 s = "ISO_IR 100"; |
|
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|
1236 break; |
|
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changeset
|
1237 |
|
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changeset
|
1238 case Encoding_Latin2: |
|
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|
1239 s = "ISO_IR 101"; |
|
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|
1240 break; |
|
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changeset
|
1241 |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1242 case Encoding_Latin3: |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1243 s = "ISO_IR 109"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1244 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
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|
1245 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1246 case Encoding_Latin4: |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1247 s = "ISO_IR 110"; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1248 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
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|
1249 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1250 case Encoding_Latin5: |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1251 s = "ISO_IR 148"; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1252 break; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1253 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1254 case Encoding_Cyrillic: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1255 s = "ISO_IR 144"; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1256 break; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1257 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1258 case Encoding_Arabic: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1259 s = "ISO_IR 127"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1260 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1261 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1262 case Encoding_Greek: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1263 s = "ISO_IR 126"; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1264 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1265 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1266 case Encoding_Hebrew: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1267 s = "ISO_IR 138"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1268 break; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1269 |
| 1091 | 1270 case Encoding_Japanese: |
| 1271 s = "ISO_IR 13"; | |
| 1272 break; | |
| 1273 | |
| 1274 case Encoding_Chinese: | |
| 1275 s = "GB18030"; | |
| 1276 break; | |
|
1090
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1277 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1278 case Encoding_Thai: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1279 s = "ISO_IR 166"; |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1280 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1281 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1282 default: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1283 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1284 } |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1285 |
| 1091 | 1286 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
1090
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1287 } |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1288 |
|
1160
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1289 void ParsedDicomFile::ToJson(Json::Value& target, bool simplify) |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1290 { |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1291 if (simplify) |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1292 { |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1293 Json::Value tmp; |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1294 FromDcmtkBridge::ToJson(tmp, *pimpl_->file_->getDataset()); |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1295 SimplifyTags(target, tmp); |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1296 } |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1297 else |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1298 { |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1299 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset()); |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1300 } |
|
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1301 } |
| 790 | 1302 } |