Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1800:30e97a1f4093 worklists
callback for handling worklists with plugins
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 20 Nov 2015 13:53:20 +0100 |
| parents | 6a2d507ef064 |
| children | f08978b1f45b |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
|
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
| 790 | 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" |
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87 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" |
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88 #include "../Core/Images/ImageBuffer.h" |
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89 #include "../Core/Images/JpegWriter.h" |
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90 #include "../Core/Images/JpegReader.h" |
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91 #include "../Core/Images/PngReader.h" |
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92 #include "../Core/Images/PngWriter.h" |
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93 #include "../Core/Logging.h" |
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94 #include "../Core/OrthancException.h" |
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95 #include "../Core/Toolbox.h" |
| 790 | 96 #include "../Core/Uuid.h" |
| 97 | |
| 98 #include <list> | |
| 99 #include <limits> | |
| 100 | |
| 101 #include <boost/lexical_cast.hpp> | |
| 102 | |
| 103 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 104 #include <dcmtk/dcmdata/dcdicent.h> | |
| 105 #include <dcmtk/dcmdata/dcdict.h> | |
| 106 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 107 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 108 #include <dcmtk/dcmdata/dcuid.h> | |
| 109 #include <dcmtk/dcmdata/dcmetinf.h> | |
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110 #include <dcmtk/dcmdata/dcdeftag.h> |
| 790 | 111 |
| 112 #include <dcmtk/dcmdata/dcvrae.h> | |
| 113 #include <dcmtk/dcmdata/dcvras.h> | |
| 114 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 115 #include <dcmtk/dcmdata/dcvrda.h> | |
| 116 #include <dcmtk/dcmdata/dcvrds.h> | |
| 117 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 118 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 119 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 120 #include <dcmtk/dcmdata/dcvris.h> | |
| 121 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 122 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 123 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 124 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 125 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 126 #include <dcmtk/dcmdata/dcvrss.h> | |
| 127 #include <dcmtk/dcmdata/dcvrst.h> | |
| 128 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 129 #include <dcmtk/dcmdata/dcvrui.h> | |
| 130 #include <dcmtk/dcmdata/dcvrul.h> | |
| 131 #include <dcmtk/dcmdata/dcvrus.h> | |
| 132 #include <dcmtk/dcmdata/dcvrut.h> | |
| 133 #include <dcmtk/dcmdata/dcpixel.h> | |
| 134 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 135 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 136 | |
| 137 | |
| 138 #include <boost/math/special_functions/round.hpp> | |
| 139 #include <dcmtk/dcmdata/dcostrmb.h> | |
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140 #include <boost/algorithm/string/predicate.hpp> |
| 790 | 141 |
| 142 | |
| 143 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 144 | |
| 145 | |
| 146 | |
| 147 namespace Orthanc | |
| 148 { | |
| 794 | 149 struct ParsedDicomFile::PImpl |
| 150 { | |
| 151 std::auto_ptr<DcmFileFormat> file_; | |
| 152 }; | |
| 153 | |
| 154 | |
| 155 // This method can only be called from the constructors! | |
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156 void ParsedDicomFile::Setup(const void* buffer, |
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157 size_t size) |
| 790 | 158 { |
| 159 DcmInputBufferStream is; | |
| 160 if (size > 0) | |
| 161 { | |
| 162 is.setBuffer(buffer, size); | |
| 163 } | |
| 164 is.setEos(); | |
| 165 | |
| 794 | 166 pimpl_->file_.reset(new DcmFileFormat); |
| 167 pimpl_->file_->transferInit(); | |
| 168 if (!pimpl_->file_->read(is).good()) | |
| 790 | 169 { |
| 794 | 170 delete pimpl_; // Avoid a memory leak due to exception |
| 171 // throwing, as we are in the constructor | |
| 172 | |
| 790 | 173 throw OrthancException(ErrorCode_BadFileFormat); |
| 174 } | |
| 794 | 175 pimpl_->file_->loadAllDataIntoMemory(); |
| 176 pimpl_->file_->transferEnd(); | |
| 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 | |
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258 namespace |
| 790 | 259 { |
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260 class DicomFieldStream : public IHttpStreamAnswer |
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261 { |
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262 private: |
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263 DcmElement& element_; |
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264 uint32_t length_; |
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265 uint32_t offset_; |
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266 std::string chunk_; |
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267 size_t chunkSize_; |
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268 |
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269 public: |
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270 DicomFieldStream(DcmElement& element, |
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271 E_TransferSyntax transferSyntax) : |
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272 element_(element), |
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273 length_(element.getLength(transferSyntax)), |
| 1616 | 274 offset_(0), |
| 275 chunkSize_(0) | |
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276 { |
| 1521 | 277 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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278 chunk_.resize(CHUNK_SIZE); |
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279 } |
| 790 | 280 |
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281 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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282 bool /*deflateAllowed*/) |
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283 { |
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284 // No support for compression |
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285 return HttpCompression_None; |
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286 } |
| 790 | 287 |
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288 virtual bool HasContentFilename(std::string& filename) |
| 790 | 289 { |
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290 return false; |
| 790 | 291 } |
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292 |
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293 virtual std::string GetContentType() |
| 790 | 294 { |
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295 return ""; |
| 790 | 296 } |
| 297 | |
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298 virtual uint64_t GetContentLength() |
| 790 | 299 { |
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300 return length_; |
| 790 | 301 } |
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302 |
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303 virtual bool ReadNextChunk() |
| 790 | 304 { |
| 1520 | 305 assert(offset_ <= length_); |
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306 |
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307 if (offset_ == length_) |
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308 { |
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309 return false; |
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310 } |
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311 else |
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312 { |
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313 if (length_ - offset_ < chunk_.size()) |
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314 { |
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315 chunkSize_ = length_ - offset_; |
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316 } |
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317 else |
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318 { |
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319 chunkSize_ = chunk_.size(); |
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320 } |
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321 |
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322 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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323 |
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324 offset_ += chunkSize_; |
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325 |
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326 if (!cond.good()) |
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327 { |
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328 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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329 throw OrthancException(ErrorCode_InternalError); |
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330 } |
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331 |
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332 return true; |
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333 } |
| 790 | 334 } |
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335 |
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336 virtual const char *GetChunkContent() |
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337 { |
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338 return chunk_.c_str(); |
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339 } |
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340 |
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341 virtual size_t GetChunkSize() |
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342 { |
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343 return chunkSize_; |
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344 } |
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345 }; |
| 790 | 346 } |
| 347 | |
| 348 | |
| 349 static bool AnswerPixelData(RestApiOutput& output, | |
| 350 DcmItem& dicom, | |
| 351 E_TransferSyntax transferSyntax, | |
| 352 const std::string* blockUri) | |
| 353 { | |
| 354 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 355 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 356 | |
| 357 DcmElement *element = NULL; | |
| 358 if (!dicom.findAndGetElement(k, element).good() || | |
| 359 element == NULL) | |
| 360 { | |
| 361 return false; | |
| 362 } | |
| 363 | |
| 364 try | |
| 365 { | |
| 366 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 367 if (blockUri == NULL) | |
| 368 { | |
| 369 // The user asks how many blocks are presents in this pixel data | |
| 370 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 371 | |
| 372 Json::Value result(Json::arrayValue); | |
| 373 for (unsigned int i = 0; i < blocks; i++) | |
| 374 { | |
| 375 result.append(boost::lexical_cast<std::string>(i)); | |
| 376 } | |
| 377 | |
| 378 output.AnswerJson(result); | |
| 379 return true; | |
| 380 } | |
| 381 | |
| 382 | |
| 383 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 384 | |
| 385 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 386 { | |
| 387 DcmPixelSequence* pixelSequence = NULL; | |
| 388 if (pixelData.getEncapsulatedRepresentation | |
| 389 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 390 { | |
| 391 // This is the case for JPEG transfer syntaxes | |
| 392 if (block < pixelSequence->card()) | |
| 393 { | |
| 394 DcmPixelItem* pixelItem = NULL; | |
| 395 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 396 { | |
| 397 if (pixelItem->getLength() == 0) | |
| 398 { | |
| 399 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 400 return true; | |
| 401 } | |
| 402 | |
| 403 Uint8* buffer = NULL; | |
| 404 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 405 { | |
| 406 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 407 return true; | |
| 408 } | |
| 409 } | |
| 410 } | |
| 411 } | |
| 412 else | |
| 413 { | |
| 414 // This is the case for raw, uncompressed image buffers | |
| 415 assert(*blockUri == "0"); | |
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416 DicomFieldStream stream(*element, transferSyntax); |
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417 output.AnswerStream(stream); |
| 790 | 418 } |
| 419 } | |
| 420 } | |
| 421 catch (boost::bad_lexical_cast&) | |
| 422 { | |
| 423 // The URI entered by the user is not a number | |
| 424 } | |
| 425 catch (std::bad_cast&) | |
| 426 { | |
| 427 // This should never happen | |
| 428 } | |
| 429 | |
| 430 return false; | |
| 431 } | |
| 432 | |
| 433 | |
| 434 | |
| 435 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 436 const std::string& tag, | |
| 437 DcmItem& dicom, | |
| 438 E_TransferSyntax transferSyntax) | |
| 439 { | |
| 440 DcmTagKey k; | |
| 441 ParseTagAndGroup(k, tag); | |
| 442 | |
| 443 DcmSequenceOfItems* sequence = NULL; | |
| 444 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 445 sequence != NULL && | |
| 446 sequence->getVR() == EVR_SQ) | |
| 447 { | |
| 448 SendSequence(output, *sequence); | |
| 449 return; | |
| 450 } | |
| 451 | |
| 452 DcmElement* element = NULL; | |
| 453 if (dicom.findAndGetElement(k, element).good() && | |
| 454 element != NULL && | |
| 455 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 456 element->getVR() != EVR_SQ) | |
| 457 { | |
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458 DicomFieldStream stream(*element, transferSyntax); |
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459 output.AnswerStream(stream); |
| 790 | 460 } |
| 461 } | |
| 462 | |
| 463 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 464 const UriComponents& uri) | |
| 465 { | |
| 794 | 466 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 467 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 468 |
| 469 // Special case: Accessing the pixel data | |
| 470 if (uri.size() == 1 || | |
| 471 uri.size() == 2) | |
| 472 { | |
| 473 DcmTagKey tag; | |
| 474 ParseTagAndGroup(tag, uri[0]); | |
| 475 | |
| 476 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 477 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 478 { | |
| 479 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 480 return; | |
| 481 } | |
| 482 } | |
| 483 | |
| 484 // Go down in the tag hierarchy according to the URI | |
| 485 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 486 { | |
| 487 size_t index; | |
| 488 try | |
| 489 { | |
| 490 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 491 } | |
| 492 catch (boost::bad_lexical_cast&) | |
| 493 { | |
| 494 return; | |
| 495 } | |
| 496 | |
| 497 DcmTagKey k; | |
| 498 DcmItem *child = NULL; | |
| 499 ParseTagAndGroup(k, uri[2 * pos]); | |
| 500 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 501 child == NULL) | |
| 502 { | |
| 503 return; | |
| 504 } | |
| 505 | |
| 506 dicom = child; | |
| 507 } | |
| 508 | |
| 509 // We have reached the end of the URI | |
| 510 if (uri.size() % 2 == 0) | |
| 511 { | |
| 512 SendPathValueForDictionary(output, *dicom); | |
| 513 } | |
| 514 else | |
| 515 { | |
| 516 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 517 } | |
| 518 } | |
| 519 | |
| 520 | |
| 521 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 522 { | |
| 523 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 524 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 525 if (element != NULL) |
| 526 { | |
| 527 delete element; | |
| 528 } | |
| 529 } | |
| 530 | |
| 531 | |
| 532 | |
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533 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 534 { |
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535 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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536 |
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537 // Loop over the dataset to detect its private tags |
| 790 | 538 typedef std::list<DcmElement*> Tags; |
| 539 Tags privateTags; | |
| 540 | |
| 541 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 542 { | |
| 543 DcmElement* element = dataset.getElement(i); | |
| 544 DcmTag tag(element->getTag()); | |
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545 |
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546 // Is this a private tag? |
| 1694 | 547 if (tag.isPrivate()) |
| 790 | 548 { |
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549 bool remove = true; |
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550 |
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551 // Check whether this private tag is to be kept |
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552 if (toKeep != NULL) |
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553 { |
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554 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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555 if (toKeep->find(tmp) != toKeep->end()) |
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556 { |
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557 remove = false; // Keep it |
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558 } |
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559 } |
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560 |
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561 if (remove) |
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562 { |
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563 privateTags.push_back(element); |
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564 } |
| 790 | 565 } |
| 566 } | |
| 567 | |
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568 // Loop over the detected private tags to remove them |
| 790 | 569 for (Tags::iterator it = privateTags.begin(); |
| 570 it != privateTags.end(); ++it) | |
| 571 { | |
| 572 DcmElement* tmp = dataset.remove(*it); | |
| 573 if (tmp != NULL) | |
| 574 { | |
| 575 delete tmp; | |
| 576 } | |
| 577 } | |
| 578 } | |
| 579 | |
| 580 | |
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581 static void InsertInternal(DcmDataset& dicom, |
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582 DcmElement* element) |
| 790 | 583 { |
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584 OFCondition cond = dicom.insert(element, false, false); |
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585 if (!cond.good()) |
| 790 | 586 { |
| 587 // This field already exists | |
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588 delete element; |
| 790 | 589 throw OrthancException(ErrorCode_InternalError); |
| 590 } | |
| 591 } | |
| 592 | |
| 593 | |
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594 void ParsedDicomFile::Insert(const DicomTag& tag, |
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595 const Json::Value& value, |
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596 bool decodeBinaryTags) |
| 790 | 597 { |
| 1695 | 598 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeBinaryTags, GetEncoding())); |
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599 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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600 } |
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601 |
| 790 | 602 |
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603 static void ReplaceInternal(DcmDataset& dicom, |
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604 std::auto_ptr<DcmElement>& element, |
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605 DicomReplaceMode mode) |
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606 { |
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607 const DcmTagKey& tag = element->getTag(); |
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608 |
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609 if (!dicom.findAndDeleteElement(tag).good()) |
| 790 | 610 { |
| 611 // This field does not exist, act wrt. the specified "mode" | |
| 612 switch (mode) | |
| 613 { | |
| 614 case DicomReplaceMode_InsertIfAbsent: | |
| 615 break; | |
| 616 | |
| 617 case DicomReplaceMode_ThrowIfAbsent: | |
| 618 throw OrthancException(ErrorCode_InexistentItem); | |
| 619 | |
| 620 case DicomReplaceMode_IgnoreIfAbsent: | |
| 621 return; | |
| 622 } | |
| 623 } | |
|
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624 |
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625 // Either the tag was not existing, or the replace mode was set to |
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626 // "InsertIfAbsent" |
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627 InsertInternal(dicom, element.release()); |
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628 } |
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629 |
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630 |
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631 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
| 1695 | 632 const std::string& utf8Value, |
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633 bool decodeBinaryTags) |
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634 { |
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635 if (tag != DICOM_TAG_SOP_CLASS_UID && |
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636 tag != DICOM_TAG_SOP_INSTANCE_UID) |
| 790 | 637 { |
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638 return; |
| 790 | 639 } |
| 640 | |
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641 std::string binary; |
| 1695 | 642 const std::string* decoded = &utf8Value; |
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643 |
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644 if (decodeBinaryTags && |
| 1695 | 645 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
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646 { |
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647 std::string mime; |
| 1695 | 648 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value); |
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649 decoded = &binary; |
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650 } |
| 1695 | 651 else |
| 652 { | |
| 653 Encoding encoding = GetEncoding(); | |
| 654 if (GetEncoding() != Encoding_Utf8) | |
| 655 { | |
| 656 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
| 657 decoded = &binary; | |
| 658 } | |
| 659 } | |
| 790 | 660 |
| 661 /** | |
| 662 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 663 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 664 * you make changes to the related tags in the dataset ('SOP Class | |
| 665 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 666 * options. You can disable this behaviour by using the -nmu | |
| 667 * option. | |
| 668 **/ | |
| 669 | |
| 670 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 671 { | |
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672 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
| 790 | 673 } |
| 674 | |
| 675 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 676 { | |
|
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677 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
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678 } |
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679 } |
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680 |
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681 |
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682 void ParsedDicomFile::Replace(const DicomTag& tag, |
| 1695 | 683 const std::string& utf8Value, |
|
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684 DicomReplaceMode mode) |
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685 { |
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686 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
| 1695 | 687 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, false, GetEncoding()); |
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688 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
| 1695 | 689 UpdateStorageUid(tag, utf8Value, false); |
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690 } |
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691 |
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692 |
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693 void ParsedDicomFile::Replace(const DicomTag& tag, |
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694 const Json::Value& value, |
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695 bool decodeBinaryTags, |
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696 DicomReplaceMode mode) |
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697 { |
| 1695 | 698 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeBinaryTags, GetEncoding())); |
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699 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
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700 |
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701 if (tag == DICOM_TAG_SOP_CLASS_UID || |
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702 tag == DICOM_TAG_SOP_INSTANCE_UID) |
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703 { |
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704 if (value.type() != Json::stringValue) |
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705 { |
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706 throw OrthancException(ErrorCode_BadParameterType); |
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707 } |
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708 |
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709 UpdateStorageUid(tag, value.asString(), decodeBinaryTags); |
| 790 | 710 } |
| 711 } | |
| 712 | |
| 713 | |
| 714 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 715 { | |
| 716 std::string serialized; | |
|
1004
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diff
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|
717 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 718 { |
| 719 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 720 } | |
| 721 } | |
| 722 | |
| 723 | |
| 724 | |
| 725 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 726 const DicomTag& tag) | |
| 727 { | |
| 728 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 729 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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730 |
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731 if (FromDcmtkBridge::IsPrivateTag(tag) || |
|
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732 FromDcmtkBridge::IsUnknownTag(tag) || |
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733 tag == DICOM_TAG_PIXEL_DATA || |
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734 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 735 { |
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736 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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737 long unsigned int count = 0; |
| 790 | 738 |
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739 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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740 { |
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741 if (count > 0) |
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742 { |
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743 assert(data != NULL); |
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744 value.assign(reinterpret_cast<const char*>(data), count); |
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745 } |
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746 else |
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747 { |
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748 value.clear(); |
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749 } |
| 790 | 750 |
|
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751 return true; |
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752 } |
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753 else |
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754 { |
|
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755 return false; |
|
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756 } |
| 790 | 757 } |
| 758 else | |
| 759 { | |
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760 DcmElement* element = NULL; |
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761 if (!dataset.findAndGetElement(k, element).good() || |
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762 element == NULL) |
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763 { |
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764 return false; |
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765 } |
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|
766 |
|
1736
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767 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
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768 (*element, DicomToJsonFlags_Default, GetEncoding())); |
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769 |
|
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770 if (v.get() == NULL || |
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771 v->IsNull()) |
|
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772 { |
|
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773 value = ""; |
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774 } |
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775 else |
|
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776 { |
|
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777 // TODO v->IsBinary() |
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778 value = v->GetContent(); |
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779 } |
|
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780 |
|
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781 return true; |
| 790 | 782 } |
| 783 } | |
| 784 | |
| 785 | |
| 786 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 787 { | |
| 788 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 789 | |
| 790 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 791 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 792 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 793 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 794 { | |
| 795 throw OrthancException(ErrorCode_BadFileFormat); | |
| 796 } | |
| 797 | |
| 798 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 799 } | |
| 800 | |
| 801 | |
| 802 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 803 { | |
|
1004
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804 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 805 } |
| 806 | |
| 807 | |
| 808 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 809 { | |
| 810 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 811 std::string content; | |
| 812 SaveToMemoryBuffer(content); | |
| 813 Toolbox::WriteFile(content, path); | |
| 814 } | |
| 815 | |
| 816 | |
| 794 | 817 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 818 { |
| 794 | 819 pimpl_->file_.reset(new DcmFileFormat); |
| 790 | 820 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 821 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 822 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 823 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 824 } | |
| 825 | |
| 791 | 826 |
|
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827 ParsedDicomFile::ParsedDicomFile(const DicomMap& map) : pimpl_(new PImpl) |
|
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828 { |
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829 std::auto_ptr<DcmDataset> dataset(ToDcmtkBridge::Convert(map)); |
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830 |
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831 // NOTE: This implies an unnecessary memory copy of the dataset, but no way to get around |
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832 // http://support.dcmtk.org/redmine/issues/544 |
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833 std::auto_ptr<DcmFileFormat> fileFormat(new DcmFileFormat(dataset.get())); |
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834 |
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835 pimpl_->file_.reset(fileFormat.release()); |
|
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836 } |
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837 |
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838 |
|
1800
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839 ParsedDicomFile::ParsedDicomFile(const void* content, |
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840 size_t size) : pimpl_(new PImpl) |
| 791 | 841 { |
| 842 Setup(content, size); | |
| 843 } | |
| 844 | |
| 794 | 845 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 846 { |
| 847 if (content.size() == 0) | |
| 848 { | |
| 849 Setup(NULL, 0); | |
| 850 } | |
| 851 else | |
| 852 { | |
| 853 Setup(&content[0], content.size()); | |
| 854 } | |
| 855 } | |
| 792 | 856 |
| 857 | |
| 794 | 858 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 859 pimpl_(new PImpl) | |
| 792 | 860 { |
| 794 | 861 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
956
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862 |
|
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863 // Create a new instance-level identifier |
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864 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 865 } |
| 866 | |
| 867 | |
|
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868 ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl) |
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869 { |
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870 pimpl_->file_.reset(new DcmFileFormat(&dicom)); |
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871 } |
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872 |
|
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873 |
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874 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl) |
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875 { |
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876 pimpl_->file_.reset(new DcmFileFormat(dicom)); |
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877 } |
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878 |
|
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879 |
| 792 | 880 ParsedDicomFile::~ParsedDicomFile() |
| 881 { | |
| 794 | 882 delete pimpl_; |
| 792 | 883 } |
| 884 | |
| 793 | 885 |
|
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886 DcmFileFormat& ParsedDicomFile::GetDcmtkObject() |
| 793 | 887 { |
|
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888 return *pimpl_->file_.get(); |
| 793 | 889 } |
| 890 | |
| 891 | |
| 892 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 893 { | |
| 794 | 894 return new ParsedDicomFile(*this); |
| 793 | 895 } |
|
800
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896 |
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897 |
| 1562 | 898 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
800
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899 { |
|
1641
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900 std::string mime, content; |
|
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901 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
| 1562 | 902 Toolbox::ToLowerCase(mime); |
|
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903 |
|
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904 if (mime == "image/png" || |
|
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905 mime == "image/jpeg") |
| 1562 | 906 { |
| 907 EmbedImage(mime, content); | |
| 908 } | |
| 909 else if (mime == "application/pdf") | |
| 910 { | |
| 911 EmbedPdf(content); | |
| 912 } | |
| 913 else | |
| 914 { | |
|
1693
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915 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
| 1562 | 916 throw OrthancException(ErrorCode_NotImplemented); |
| 917 } | |
|
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918 } |
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919 |
|
800
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920 |
|
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921 void ParsedDicomFile::EmbedImage(const std::string& mime, |
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922 const std::string& content) |
|
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923 { |
|
800
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924 if (mime == "image/png") |
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925 { |
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926 PngReader reader; |
|
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927 reader.ReadFromMemory(content); |
|
800
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928 EmbedImage(reader); |
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929 } |
|
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930 else if (mime == "image/jpeg") |
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931 { |
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932 JpegReader reader; |
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933 reader.ReadFromMemory(content); |
|
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934 EmbedImage(reader); |
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935 } |
|
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936 else |
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937 { |
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938 throw OrthancException(ErrorCode_NotImplemented); |
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939 } |
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940 } |
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941 |
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942 |
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943 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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944 { |
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945 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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946 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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947 accessor.GetFormat() != PixelFormat_RGB24 && |
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948 accessor.GetFormat() != PixelFormat_RGBA32) |
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949 { |
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950 throw OrthancException(ErrorCode_NotImplemented); |
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951 } |
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952 |
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953 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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954 { |
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955 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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956 } |
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957 |
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958 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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959 |
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960 Remove(DICOM_TAG_PIXEL_DATA); |
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961 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
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962 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
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963 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
964 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
965 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
966 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
967 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
968 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
969 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
970 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
971 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
972 unsigned int bytesPerPixel = 1; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
973 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
974 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
975 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
976 case PixelFormat_RGB24: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
977 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
978 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
979 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
980 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
981 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
982 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
983 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
984 break; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
985 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
986 case PixelFormat_Grayscale16: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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987 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
988 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
989 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
990 bytesPerPixel = 2; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
991 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
992 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
993 default: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
994 throw OrthancException(ErrorCode_NotImplemented); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
995 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
996 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
997 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
998 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
999 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1000 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1001 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1002 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1003 Uint8* target = NULL; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1004 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
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parents:
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diff
changeset
|
1005 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1006 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1007 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1008 switch (accessor.GetFormat()) |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1009 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1010 case PixelFormat_RGB24: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1011 case PixelFormat_Grayscale8: |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1012 case PixelFormat_Grayscale16: |
|
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generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
1013 case PixelFormat_SignedGrayscale16: |
|
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parents:
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diff
changeset
|
1014 { |
|
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parents:
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diff
changeset
|
1015 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
|
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parents:
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diff
changeset
|
1016 target += pitch; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1017 break; |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1018 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1019 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1020 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1021 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1022 // The alpha channel is not supported by the DICOM standard |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1023 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1024 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1025 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1026 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1027 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1028 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1029 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1030 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1031 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1032 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1033 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1034 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1035 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1036 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1037 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1038 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1039 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
ecedd89055db
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parents:
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diff
changeset
|
1040 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1041 throw OrthancException(ErrorCode_InternalError); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1042 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1043 } |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1044 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1045 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1046 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1047 unsigned int frame) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1048 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1049 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1050 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1051 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1052 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1053 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1054 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1055 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1056 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1057 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1058 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1059 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1060 ImageExtractionMode mode) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1061 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1062 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1063 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1064 bool ok = false; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1065 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1066 switch (mode) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1067 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1068 case ImageExtractionMode_UInt8: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1069 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1070 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1071 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1072 case ImageExtractionMode_UInt16: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1073 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1074 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1075 |
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|
1076 case ImageExtractionMode_Int16: |
|
1015
f009f7c75069
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|
1077 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
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|
1078 break; |
|
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|
1079 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1080 case ImageExtractionMode_Preview: |
|
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|
1081 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
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diff
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|
1082 break; |
|
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|
1083 |
|
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|
1084 default: |
|
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diff
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|
1085 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
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1086 } |
|
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1087 |
|
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1088 if (!ok) |
|
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|
1089 { |
|
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|
1090 throw OrthancException(ErrorCode_BadFileFormat); |
|
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1091 } |
|
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1092 } |
|
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1093 |
|
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diff
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|
1094 |
|
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|
1095 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
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1096 unsigned int frame, |
|
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|
1097 ImageExtractionMode mode) |
|
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|
1098 { |
|
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|
1099 ImageBuffer buffer; |
|
87791ebc1f50
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|
1100 ExtractImage(buffer, frame, mode); |
|
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1101 |
|
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|
1102 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
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|
1103 PngWriter writer; |
|
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|
1104 writer.WriteToMemory(result, accessor); |
|
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|
1105 } |
|
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1106 |
|
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|
1107 |
|
1781
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1108 void ParsedDicomFile::ExtractJpegImage(std::string& result, |
|
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|
1109 unsigned int frame, |
|
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|
1110 ImageExtractionMode mode, |
|
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|
1111 uint8_t quality) |
|
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|
1112 { |
|
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|
1113 if (mode != ImageExtractionMode_UInt8 && |
|
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|
1114 mode != ImageExtractionMode_Preview) |
|
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|
1115 { |
|
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|
1116 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
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1117 } |
|
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1118 |
|
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|
1119 ImageBuffer buffer; |
|
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|
1120 ExtractImage(buffer, frame, mode); |
|
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1121 |
|
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|
1122 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
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|
1123 JpegWriter writer; |
|
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|
1124 writer.SetQuality(quality); |
|
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|
1125 writer.WriteToMemory(result, accessor); |
|
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|
1126 } |
|
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|
1127 |
|
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|
1128 |
|
956
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|
1129 Encoding ParsedDicomFile::GetEncoding() const |
|
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|
1130 { |
| 1695 | 1131 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
|
956
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|
1132 } |
|
1090
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|
1133 |
|
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|
1134 |
|
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|
1135 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
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|
1136 { |
|
1558
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fix encodings of newly created dicom files
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|
1137 if (encoding == Encoding_Windows1251) |
|
1090
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|
1138 { |
|
1558
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1139 // This Cyrillic codepage is not officially supported by the |
|
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|
1140 // DICOM standard. Do not set the SpecificCharacterSet tag. |
|
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|
1141 return; |
|
1090
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|
1142 } |
|
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|
1143 |
|
1565
4b23310eb7e8
add tags per instances in a series
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|
1144 std::string s = GetDicomSpecificCharacterSet(encoding); |
| 1091 | 1145 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
1090
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|
1146 } |
|
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|
1147 |
| 1686 | 1148 void ParsedDicomFile::ToJson(Json::Value& target, |
| 1149 DicomToJsonFormat format, | |
|
1735
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|
1150 DicomToJsonFlags flags, |
| 1686 | 1151 unsigned int maxStringLength) |
|
1160
80671157d051
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diff
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|
1152 { |
|
1735
a001f6226c7c
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|
1153 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), format, flags, maxStringLength); |
|
1160
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diff
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|
1154 } |
|
1555
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|
1155 |
|
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|
1156 |
|
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changeset
|
1157 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
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|
1158 { |
|
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Creation of DICOM files with encapsulated PDF
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|
1159 DcmTag key(tag.GetGroup(), tag.GetElement()); |
|
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|
1160 return pimpl_->file_->getDataset()->tagExists(key); |
|
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|
1161 } |
|
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Creation of DICOM files with encapsulated PDF
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|
1162 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1163 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1164 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
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|
1165 { |
|
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Creation of DICOM files with encapsulated PDF
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|
1166 if (pdf.size() < 5 || // (*) |
|
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Creation of DICOM files with encapsulated PDF
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|
1167 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
|
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Creation of DICOM files with encapsulated PDF
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|
1168 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1169 LOG(ERROR) << "Not a PDF file"; |
|
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Creation of DICOM files with encapsulated PDF
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|
1170 throw OrthancException(ErrorCode_BadFileFormat); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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|
1171 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1172 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1173 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1174 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1175 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1176 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
| 1566 | 1177 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
|
1555
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Creation of DICOM files with encapsulated PDF
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changeset
|
1178 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1179 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
|
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changeset
|
1180 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1181 size_t s = pdf.size(); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1182 if (s & 1) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1183 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1184 // The size of the buffer must be even |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1185 s += 1; |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1186 } |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1187 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1188 Uint8* bytes = NULL; |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1189 OFCondition result = element->createUint8Array(s, bytes); |
|
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Creation of DICOM files with encapsulated PDF
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1190 if (!result.good() || bytes == NULL) |
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1191 { |
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Creation of DICOM files with encapsulated PDF
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1192 throw OrthancException(ErrorCode_NotEnoughMemory); |
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Creation of DICOM files with encapsulated PDF
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1193 } |
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Creation of DICOM files with encapsulated PDF
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1194 |
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Creation of DICOM files with encapsulated PDF
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1195 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
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Creation of DICOM files with encapsulated PDF
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1196 bytes[s - 1] = 0; |
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Creation of DICOM files with encapsulated PDF
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1197 |
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Creation of DICOM files with encapsulated PDF
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1198 memcpy(bytes, pdf.c_str(), pdf.size()); |
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Creation of DICOM files with encapsulated PDF
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1199 |
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Creation of DICOM files with encapsulated PDF
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1200 DcmPolymorphOBOW* obj = element.release(); |
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Creation of DICOM files with encapsulated PDF
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1201 result = pimpl_->file_->getDataset()->insert(obj); |
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Creation of DICOM files with encapsulated PDF
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1202 |
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Creation of DICOM files with encapsulated PDF
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1203 if (!result.good()) |
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Creation of DICOM files with encapsulated PDF
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1204 { |
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Creation of DICOM files with encapsulated PDF
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1205 delete obj; |
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Creation of DICOM files with encapsulated PDF
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1206 throw OrthancException(ErrorCode_NotEnoughMemory); |
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Creation of DICOM files with encapsulated PDF
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1207 } |
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Creation of DICOM files with encapsulated PDF
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1208 } |
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Creation of DICOM files with encapsulated PDF
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1209 |
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1556
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1210 |
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1211 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
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1212 { |
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1213 std::string sop, mime; |
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1214 |
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1215 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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1216 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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1217 sop != UID_EncapsulatedPDFStorage || |
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1218 mime != "application/pdf") |
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1219 { |
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1220 return false; |
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1221 } |
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1222 |
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1223 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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1224 { |
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1225 return false; |
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1226 } |
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1227 |
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1228 // Strip the possible pad byte at the end of file, because the |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1229 // encapsulated documents must always have an even length. The PDF |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1230 // format expects files to end with %%EOF followed by CR/LF. If |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1231 // the last character of the file is not a CR or LF, we assume it |
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1232 // is a pad byte and remove it. |
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1233 if (pdf.size() > 0) |
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1234 { |
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1235 char last = *pdf.rbegin(); |
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1236 |
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1237 if (last != 10 && last != 13) |
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1238 { |
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1239 pdf.resize(pdf.size() - 1); |
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1240 } |
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1241 } |
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1242 |
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1243 return true; |
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1244 } |
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1662
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1245 |
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ParsedDicomFile::Convert()
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1246 |
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1247 void ParsedDicomFile::Convert(DicomMap& tags) |
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ParsedDicomFile::Convert()
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1248 { |
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1249 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset()); |
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1250 } |
| 790 | 1251 } |