Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1929:cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 21 Mar 2016 14:28:59 +0100 |
| parents | 84c7eaeb5244 |
| children | 72a2fd7fed8b |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 1900 | 3 * Copyright (C) 2012-2016 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 "OrthancInitialization.h" |
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84 #include "ServerToolbox.h" |
| 790 | 85 #include "FromDcmtkBridge.h" |
| 86 #include "ToDcmtkBridge.h" | |
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87 #include "Internals/DicomFrameIndex.h" |
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88 #include "../Core/Images/JpegReader.h" |
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89 #include "../Core/Images/PngReader.h" |
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90 #include "../Core/Logging.h" |
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91 #include "../Core/OrthancException.h" |
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92 #include "../Core/Toolbox.h" |
| 790 | 93 #include "../Core/Uuid.h" |
| 94 | |
| 95 #include <list> | |
| 96 #include <limits> | |
| 97 | |
| 98 #include <boost/lexical_cast.hpp> | |
| 99 | |
| 100 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 101 #include <dcmtk/dcmdata/dcdicent.h> | |
| 102 #include <dcmtk/dcmdata/dcdict.h> | |
| 103 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 104 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 105 #include <dcmtk/dcmdata/dcuid.h> | |
| 106 #include <dcmtk/dcmdata/dcmetinf.h> | |
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107 #include <dcmtk/dcmdata/dcdeftag.h> |
| 790 | 108 |
| 109 #include <dcmtk/dcmdata/dcvrae.h> | |
| 110 #include <dcmtk/dcmdata/dcvras.h> | |
| 111 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 112 #include <dcmtk/dcmdata/dcvrda.h> | |
| 113 #include <dcmtk/dcmdata/dcvrds.h> | |
| 114 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 115 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 116 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 117 #include <dcmtk/dcmdata/dcvris.h> | |
| 118 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 119 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 120 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 121 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 122 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 123 #include <dcmtk/dcmdata/dcvrss.h> | |
| 124 #include <dcmtk/dcmdata/dcvrst.h> | |
| 125 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 126 #include <dcmtk/dcmdata/dcvrui.h> | |
| 127 #include <dcmtk/dcmdata/dcvrul.h> | |
| 128 #include <dcmtk/dcmdata/dcvrus.h> | |
| 129 #include <dcmtk/dcmdata/dcvrut.h> | |
| 130 #include <dcmtk/dcmdata/dcpixel.h> | |
| 131 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 132 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 133 | |
| 134 | |
| 135 #include <boost/math/special_functions/round.hpp> | |
| 136 #include <dcmtk/dcmdata/dcostrmb.h> | |
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137 #include <boost/algorithm/string/predicate.hpp> |
| 790 | 138 |
| 139 | |
| 140 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 141 | |
| 142 | |
| 143 | |
| 144 namespace Orthanc | |
| 145 { | |
| 794 | 146 struct ParsedDicomFile::PImpl |
| 147 { | |
| 148 std::auto_ptr<DcmFileFormat> file_; | |
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149 std::auto_ptr<DicomFrameIndex> frameIndex_; |
| 794 | 150 }; |
| 151 | |
| 152 | |
| 153 // This method can only be called from the constructors! | |
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154 void ParsedDicomFile::Setup(const void* buffer, |
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155 size_t size) |
| 790 | 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(); | |
| 790 | 175 } |
| 176 | |
| 177 | |
| 178 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 179 DcmItem& dicom) | |
| 180 { | |
| 181 Json::Value v = Json::arrayValue; | |
| 182 | |
| 183 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 184 { | |
| 185 DcmElement* element = dicom.getElement(i); | |
| 186 if (element) | |
| 187 { | |
| 188 char buf[16]; | |
| 189 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 190 v.append(buf); | |
| 191 } | |
| 192 } | |
| 193 | |
| 194 output.AnswerJson(v); | |
| 195 } | |
| 196 | |
| 197 static inline uint16_t GetCharValue(char c) | |
| 198 { | |
| 199 if (c >= '0' && c <= '9') | |
| 200 return c - '0'; | |
| 201 else if (c >= 'a' && c <= 'f') | |
| 202 return c - 'a' + 10; | |
| 203 else if (c >= 'A' && c <= 'F') | |
| 204 return c - 'A' + 10; | |
| 205 else | |
| 206 return 0; | |
| 207 } | |
| 208 | |
| 209 static inline uint16_t GetTagValue(const char* c) | |
| 210 { | |
| 211 return ((GetCharValue(c[0]) << 12) + | |
| 212 (GetCharValue(c[1]) << 8) + | |
| 213 (GetCharValue(c[2]) << 4) + | |
| 214 GetCharValue(c[3])); | |
| 215 } | |
| 216 | |
| 217 static void ParseTagAndGroup(DcmTagKey& key, | |
| 218 const std::string& tag) | |
| 219 { | |
| 220 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 221 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 222 } | |
| 223 | |
| 224 | |
| 225 static void SendSequence(RestApiOutput& output, | |
| 226 DcmSequenceOfItems& sequence) | |
| 227 { | |
| 228 // This element is a sequence | |
| 229 Json::Value v = Json::arrayValue; | |
| 230 | |
| 231 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 232 { | |
| 233 v.append(boost::lexical_cast<std::string>(i)); | |
| 234 } | |
| 235 | |
| 236 output.AnswerJson(v); | |
| 237 } | |
| 238 | |
| 239 | |
| 240 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 241 E_TransferSyntax transferSyntax) | |
| 242 { | |
| 243 DcmPixelSequence* pixelSequence = NULL; | |
| 244 if (pixelData.getEncapsulatedRepresentation | |
| 245 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 246 { | |
| 247 return pixelSequence->card(); | |
| 248 } | |
| 249 else | |
| 250 { | |
| 251 return 1; | |
| 252 } | |
| 253 } | |
| 254 | |
| 255 | |
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256 namespace |
| 790 | 257 { |
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258 class DicomFieldStream : public IHttpStreamAnswer |
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259 { |
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260 private: |
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261 DcmElement& element_; |
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262 uint32_t length_; |
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263 uint32_t offset_; |
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264 std::string chunk_; |
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265 size_t chunkSize_; |
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266 |
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267 public: |
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268 DicomFieldStream(DcmElement& element, |
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269 E_TransferSyntax transferSyntax) : |
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270 element_(element), |
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271 length_(element.getLength(transferSyntax)), |
| 1616 | 272 offset_(0), |
| 273 chunkSize_(0) | |
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274 { |
| 1521 | 275 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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276 chunk_.resize(CHUNK_SIZE); |
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277 } |
| 790 | 278 |
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279 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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280 bool /*deflateAllowed*/) |
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281 { |
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282 // No support for compression |
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283 return HttpCompression_None; |
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284 } |
| 790 | 285 |
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286 virtual bool HasContentFilename(std::string& filename) |
| 790 | 287 { |
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288 return false; |
| 790 | 289 } |
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290 |
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291 virtual std::string GetContentType() |
| 790 | 292 { |
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293 return ""; |
| 790 | 294 } |
| 295 | |
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296 virtual uint64_t GetContentLength() |
| 790 | 297 { |
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298 return length_; |
| 790 | 299 } |
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300 |
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301 virtual bool ReadNextChunk() |
| 790 | 302 { |
| 1520 | 303 assert(offset_ <= length_); |
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304 |
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305 if (offset_ == length_) |
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306 { |
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307 return false; |
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308 } |
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309 else |
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310 { |
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311 if (length_ - offset_ < chunk_.size()) |
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312 { |
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313 chunkSize_ = length_ - offset_; |
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314 } |
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315 else |
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316 { |
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317 chunkSize_ = chunk_.size(); |
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318 } |
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319 |
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320 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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321 |
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322 offset_ += chunkSize_; |
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323 |
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324 if (!cond.good()) |
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325 { |
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326 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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327 throw OrthancException(ErrorCode_InternalError); |
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328 } |
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329 |
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330 return true; |
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331 } |
| 790 | 332 } |
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333 |
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334 virtual const char *GetChunkContent() |
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335 { |
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336 return chunk_.c_str(); |
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337 } |
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338 |
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339 virtual size_t GetChunkSize() |
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340 { |
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341 return chunkSize_; |
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342 } |
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343 }; |
| 790 | 344 } |
| 345 | |
| 346 | |
| 347 static bool AnswerPixelData(RestApiOutput& output, | |
| 348 DcmItem& dicom, | |
| 349 E_TransferSyntax transferSyntax, | |
| 350 const std::string* blockUri) | |
| 351 { | |
| 352 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 353 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 354 | |
| 355 DcmElement *element = NULL; | |
| 356 if (!dicom.findAndGetElement(k, element).good() || | |
| 357 element == NULL) | |
| 358 { | |
| 359 return false; | |
| 360 } | |
| 361 | |
| 362 try | |
| 363 { | |
| 364 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 365 if (blockUri == NULL) | |
| 366 { | |
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367 // The user asks how many blocks are present in this pixel data |
| 790 | 368 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); |
| 369 | |
| 370 Json::Value result(Json::arrayValue); | |
| 371 for (unsigned int i = 0; i < blocks; i++) | |
| 372 { | |
| 373 result.append(boost::lexical_cast<std::string>(i)); | |
| 374 } | |
| 375 | |
| 376 output.AnswerJson(result); | |
| 377 return true; | |
| 378 } | |
| 379 | |
| 380 | |
| 381 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 382 | |
| 383 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 384 { | |
| 385 DcmPixelSequence* pixelSequence = NULL; | |
| 386 if (pixelData.getEncapsulatedRepresentation | |
| 387 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 388 { | |
| 389 // This is the case for JPEG transfer syntaxes | |
| 390 if (block < pixelSequence->card()) | |
| 391 { | |
| 392 DcmPixelItem* pixelItem = NULL; | |
| 393 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 394 { | |
| 395 if (pixelItem->getLength() == 0) | |
| 396 { | |
| 397 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 398 return true; | |
| 399 } | |
| 400 | |
| 401 Uint8* buffer = NULL; | |
| 402 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 403 { | |
| 404 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 405 return true; | |
| 406 } | |
| 407 } | |
| 408 } | |
| 409 } | |
| 410 else | |
| 411 { | |
| 412 // This is the case for raw, uncompressed image buffers | |
| 413 assert(*blockUri == "0"); | |
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414 DicomFieldStream stream(*element, transferSyntax); |
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415 output.AnswerStream(stream); |
| 790 | 416 } |
| 417 } | |
| 418 } | |
| 419 catch (boost::bad_lexical_cast&) | |
| 420 { | |
| 421 // The URI entered by the user is not a number | |
| 422 } | |
| 423 catch (std::bad_cast&) | |
| 424 { | |
| 425 // This should never happen | |
| 426 } | |
| 427 | |
| 428 return false; | |
| 429 } | |
| 430 | |
| 431 | |
| 432 | |
| 433 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 434 const std::string& tag, | |
| 435 DcmItem& dicom, | |
| 436 E_TransferSyntax transferSyntax) | |
| 437 { | |
| 438 DcmTagKey k; | |
| 439 ParseTagAndGroup(k, tag); | |
| 440 | |
| 441 DcmSequenceOfItems* sequence = NULL; | |
| 442 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 443 sequence != NULL && | |
| 444 sequence->getVR() == EVR_SQ) | |
| 445 { | |
| 446 SendSequence(output, *sequence); | |
| 447 return; | |
| 448 } | |
| 449 | |
| 450 DcmElement* element = NULL; | |
| 451 if (dicom.findAndGetElement(k, element).good() && | |
| 452 element != NULL && | |
| 453 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 454 element->getVR() != EVR_SQ) | |
| 455 { | |
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456 DicomFieldStream stream(*element, transferSyntax); |
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457 output.AnswerStream(stream); |
| 790 | 458 } |
| 459 } | |
| 460 | |
| 461 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 462 const UriComponents& uri) | |
| 463 { | |
| 794 | 464 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 465 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 466 |
| 467 // Special case: Accessing the pixel data | |
| 468 if (uri.size() == 1 || | |
| 469 uri.size() == 2) | |
| 470 { | |
| 471 DcmTagKey tag; | |
| 472 ParseTagAndGroup(tag, uri[0]); | |
| 473 | |
| 474 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 475 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 476 { | |
| 477 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 478 return; | |
| 479 } | |
| 480 } | |
| 481 | |
| 482 // Go down in the tag hierarchy according to the URI | |
| 483 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 484 { | |
| 485 size_t index; | |
| 486 try | |
| 487 { | |
| 488 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 489 } | |
| 490 catch (boost::bad_lexical_cast&) | |
| 491 { | |
| 492 return; | |
| 493 } | |
| 494 | |
| 495 DcmTagKey k; | |
| 496 DcmItem *child = NULL; | |
| 497 ParseTagAndGroup(k, uri[2 * pos]); | |
| 498 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 499 child == NULL) | |
| 500 { | |
| 501 return; | |
| 502 } | |
| 503 | |
| 504 dicom = child; | |
| 505 } | |
| 506 | |
| 507 // We have reached the end of the URI | |
| 508 if (uri.size() % 2 == 0) | |
| 509 { | |
| 510 SendPathValueForDictionary(output, *dicom); | |
| 511 } | |
| 512 else | |
| 513 { | |
| 514 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 515 } | |
| 516 } | |
| 517 | |
| 518 | |
| 519 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 520 { | |
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521 InvalidateCache(); |
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522 |
| 790 | 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 InvalidateCache(); |
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536 |
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537 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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538 |
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539 // Loop over the dataset to detect its private tags |
| 790 | 540 typedef std::list<DcmElement*> Tags; |
| 541 Tags privateTags; | |
| 542 | |
| 543 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 544 { | |
| 545 DcmElement* element = dataset.getElement(i); | |
| 546 DcmTag tag(element->getTag()); | |
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547 |
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548 // Is this a private tag? |
| 1694 | 549 if (tag.isPrivate()) |
| 790 | 550 { |
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551 bool remove = true; |
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552 |
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553 // Check whether this private tag is to be kept |
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554 if (toKeep != NULL) |
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555 { |
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556 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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557 if (toKeep->find(tmp) != toKeep->end()) |
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558 { |
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559 remove = false; // Keep it |
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560 } |
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561 } |
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562 |
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563 if (remove) |
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564 { |
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565 privateTags.push_back(element); |
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566 } |
| 790 | 567 } |
| 568 } | |
| 569 | |
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570 // Loop over the detected private tags to remove them |
| 790 | 571 for (Tags::iterator it = privateTags.begin(); |
| 572 it != privateTags.end(); ++it) | |
| 573 { | |
| 574 DcmElement* tmp = dataset.remove(*it); | |
| 575 if (tmp != NULL) | |
| 576 { | |
| 577 delete tmp; | |
| 578 } | |
| 579 } | |
| 580 } | |
| 581 | |
| 582 | |
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583 static void InsertInternal(DcmDataset& dicom, |
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584 DcmElement* element) |
| 790 | 585 { |
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586 OFCondition cond = dicom.insert(element, false, false); |
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587 if (!cond.good()) |
| 790 | 588 { |
| 589 // This field already exists | |
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590 delete element; |
| 790 | 591 throw OrthancException(ErrorCode_InternalError); |
| 592 } | |
| 593 } | |
| 594 | |
| 595 | |
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596 void ParsedDicomFile::Insert(const DicomTag& tag, |
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597 const Json::Value& value, |
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598 bool decodeDataUriScheme) |
| 790 | 599 { |
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600 InvalidateCache(); |
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601 |
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602 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
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603 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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604 } |
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605 |
| 790 | 606 |
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607 static void ReplaceInternal(DcmDataset& dicom, |
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608 std::auto_ptr<DcmElement>& element, |
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609 DicomReplaceMode mode) |
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610 { |
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611 const DcmTagKey& tag = element->getTag(); |
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612 |
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613 if (!dicom.findAndDeleteElement(tag).good()) |
| 790 | 614 { |
| 615 // This field does not exist, act wrt. the specified "mode" | |
| 616 switch (mode) | |
| 617 { | |
| 618 case DicomReplaceMode_InsertIfAbsent: | |
| 619 break; | |
| 620 | |
| 621 case DicomReplaceMode_ThrowIfAbsent: | |
| 622 throw OrthancException(ErrorCode_InexistentItem); | |
| 623 | |
| 624 case DicomReplaceMode_IgnoreIfAbsent: | |
| 625 return; | |
| 626 } | |
| 627 } | |
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628 |
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629 // Either the tag was not existing, or the replace mode was set to |
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630 // "InsertIfAbsent" |
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631 InsertInternal(dicom, element.release()); |
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632 } |
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633 |
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634 |
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635 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
| 1695 | 636 const std::string& utf8Value, |
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637 bool decodeDataUriScheme) |
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638 { |
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639 if (tag != DICOM_TAG_SOP_CLASS_UID && |
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640 tag != DICOM_TAG_SOP_INSTANCE_UID) |
| 790 | 641 { |
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642 return; |
| 790 | 643 } |
| 644 | |
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645 std::string binary; |
| 1695 | 646 const std::string* decoded = &utf8Value; |
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647 |
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648 if (decodeDataUriScheme && |
| 1695 | 649 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
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650 { |
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651 std::string mime; |
| 1695 | 652 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value); |
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653 decoded = &binary; |
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654 } |
| 1695 | 655 else |
| 656 { | |
| 657 Encoding encoding = GetEncoding(); | |
| 658 if (GetEncoding() != Encoding_Utf8) | |
| 659 { | |
| 660 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
| 661 decoded = &binary; | |
| 662 } | |
| 663 } | |
| 790 | 664 |
| 665 /** | |
| 666 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 667 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 668 * you make changes to the related tags in the dataset ('SOP Class | |
| 669 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 670 * options. You can disable this behaviour by using the -nmu | |
| 671 * option. | |
| 672 **/ | |
| 673 | |
| 674 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 675 { | |
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676 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
| 790 | 677 } |
| 678 | |
| 679 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 680 { | |
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681 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
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682 } |
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683 } |
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684 |
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685 |
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686 void ParsedDicomFile::Replace(const DicomTag& tag, |
| 1695 | 687 const std::string& utf8Value, |
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688 DicomReplaceMode mode) |
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689 { |
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690 InvalidateCache(); |
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691 |
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692 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
| 1695 | 693 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, false, GetEncoding()); |
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694 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
| 1695 | 695 UpdateStorageUid(tag, utf8Value, false); |
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696 } |
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697 |
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698 |
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699 void ParsedDicomFile::Replace(const DicomTag& tag, |
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700 const Json::Value& value, |
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701 bool decodeDataUriScheme, |
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702 DicomReplaceMode mode) |
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703 { |
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704 InvalidateCache(); |
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705 |
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706 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
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707 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
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708 |
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709 if (tag == DICOM_TAG_SOP_CLASS_UID || |
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710 tag == DICOM_TAG_SOP_INSTANCE_UID) |
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711 { |
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712 if (value.type() != Json::stringValue) |
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713 { |
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714 throw OrthancException(ErrorCode_BadParameterType); |
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715 } |
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716 |
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717 UpdateStorageUid(tag, value.asString(), decodeDataUriScheme); |
| 790 | 718 } |
| 719 } | |
| 720 | |
| 721 | |
| 722 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 723 { | |
| 724 std::string serialized; | |
|
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725 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 726 { |
| 727 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 728 } | |
| 729 } | |
| 730 | |
| 731 | |
| 732 | |
| 733 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 734 const DicomTag& tag) | |
| 735 { | |
| 736 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 737 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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738 |
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739 if (tag.IsPrivate() || |
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740 FromDcmtkBridge::IsUnknownTag(tag) || |
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741 tag == DICOM_TAG_PIXEL_DATA || |
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742 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 743 { |
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744 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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745 long unsigned int count = 0; |
| 790 | 746 |
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747 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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748 { |
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749 if (count > 0) |
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750 { |
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751 assert(data != NULL); |
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752 value.assign(reinterpret_cast<const char*>(data), count); |
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753 } |
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754 else |
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755 { |
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756 value.clear(); |
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757 } |
| 790 | 758 |
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759 return true; |
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760 } |
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761 else |
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762 { |
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763 return false; |
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764 } |
| 790 | 765 } |
| 766 else | |
| 767 { | |
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768 DcmElement* element = NULL; |
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769 if (!dataset.findAndGetElement(k, element).good() || |
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770 element == NULL) |
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771 { |
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772 return false; |
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773 } |
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774 |
|
1736
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changeset
|
775 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
|
1929
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
776 (*element, DicomToJsonFlags_Default, |
|
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
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parents:
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diff
changeset
|
777 ORTHANC_MAXIMUM_TAG_LENGTH, GetEncoding())); |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
778 |
|
1737
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
779 if (v.get() == NULL || |
|
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
780 v->IsNull()) |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
781 { |
|
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Fix replacement and insertion of private DICOM tags
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|
782 value = ""; |
|
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parents:
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diff
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|
783 } |
|
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parents:
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diff
changeset
|
784 else |
|
f796207e3df1
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parents:
1288
diff
changeset
|
785 { |
|
1737
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
786 // TODO v->IsBinary() |
|
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
787 value = v->GetContent(); |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
788 } |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
789 |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
790 return true; |
| 790 | 791 } |
| 792 } | |
| 793 | |
| 794 | |
| 795 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 796 { | |
| 797 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 798 | |
| 799 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 800 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 801 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 802 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 803 { | |
| 804 throw OrthancException(ErrorCode_BadFileFormat); | |
| 805 } | |
| 806 | |
| 807 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 808 } | |
| 809 | |
| 810 | |
| 811 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 812 { | |
|
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
991
diff
changeset
|
813 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 814 } |
| 815 | |
| 816 | |
| 817 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 818 { | |
| 819 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 820 std::string content; | |
| 821 SaveToMemoryBuffer(content); | |
| 822 Toolbox::WriteFile(content, path); | |
| 823 } | |
| 824 | |
| 825 | |
|
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
826 ParsedDicomFile::ParsedDicomFile(bool createIdentifiers) : pimpl_(new PImpl) |
| 790 | 827 { |
| 794 | 828 pimpl_->file_.reset(new DcmFileFormat); |
|
1805
f08978b1f45b
c-find scu for modality worklists
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parents:
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diff
changeset
|
829 |
|
f08978b1f45b
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parents:
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diff
changeset
|
830 if (createIdentifiers) |
|
f08978b1f45b
c-find scu for modality worklists
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parents:
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diff
changeset
|
831 { |
|
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
832 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
|
f08978b1f45b
c-find scu for modality worklists
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parents:
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diff
changeset
|
833 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); |
|
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
834 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); |
|
f08978b1f45b
c-find scu for modality worklists
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parents:
1800
diff
changeset
|
835 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
|
f08978b1f45b
c-find scu for modality worklists
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parents:
1800
diff
changeset
|
836 } |
| 790 | 837 } |
| 838 | |
| 791 | 839 |
|
1787
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
840 ParsedDicomFile::ParsedDicomFile(const DicomMap& map) : pimpl_(new PImpl) |
|
1786
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
841 { |
|
1787
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
842 std::auto_ptr<DcmDataset> dataset(ToDcmtkBridge::Convert(map)); |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
843 |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
844 // NOTE: This implies an unnecessary memory copy of the dataset, but no way to get around |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
845 // http://support.dcmtk.org/redmine/issues/544 |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
846 std::auto_ptr<DcmFileFormat> fileFormat(new DcmFileFormat(dataset.get())); |
|
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
847 |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
1786
diff
changeset
|
848 pimpl_->file_.reset(fileFormat.release()); |
|
1786
164d78911382
primitives to handle dicom worklists
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parents:
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diff
changeset
|
849 } |
|
164d78911382
primitives to handle dicom worklists
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parents:
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diff
changeset
|
850 |
|
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
851 |
|
1800
30e97a1f4093
callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1788
diff
changeset
|
852 ParsedDicomFile::ParsedDicomFile(const void* content, |
|
30e97a1f4093
callback for handling worklists with plugins
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parents:
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diff
changeset
|
853 size_t size) : pimpl_(new PImpl) |
| 791 | 854 { |
| 855 Setup(content, size); | |
| 856 } | |
| 857 | |
| 794 | 858 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 859 { |
| 860 if (content.size() == 0) | |
| 861 { | |
| 862 Setup(NULL, 0); | |
| 863 } | |
| 864 else | |
| 865 { | |
| 866 Setup(&content[0], content.size()); | |
| 867 } | |
| 868 } | |
| 792 | 869 |
| 870 | |
| 794 | 871 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 872 pimpl_(new PImpl) | |
| 792 | 873 { |
| 794 | 874 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
875 |
|
1564
1b7def486e62
creation of DICOM series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1562
diff
changeset
|
876 // Create a new instance-level identifier |
|
1b7def486e62
creation of DICOM series
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parents:
1562
diff
changeset
|
877 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 878 } |
| 879 | |
| 880 | |
|
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
881 ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl) |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
882 { |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
883 pimpl_->file_.reset(new DcmFileFormat(&dicom)); |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
884 } |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
885 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
886 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
887 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl) |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
888 { |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
889 pimpl_->file_.reset(new DcmFileFormat(dicom)); |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
890 } |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
891 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
892 |
| 792 | 893 ParsedDicomFile::~ParsedDicomFile() |
| 894 { | |
| 794 | 895 delete pimpl_; |
| 792 | 896 } |
| 897 | |
| 793 | 898 |
|
1824
b530c3dfe2a6
refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1818
diff
changeset
|
899 DcmFileFormat& ParsedDicomFile::GetDcmtkObject() const |
| 793 | 900 { |
|
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
901 return *pimpl_->file_.get(); |
| 793 | 902 } |
| 903 | |
| 904 | |
| 905 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 906 { | |
| 794 | 907 return new ParsedDicomFile(*this); |
| 793 | 908 } |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
909 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
910 |
| 1562 | 911 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
912 { |
|
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1616
diff
changeset
|
913 std::string mime, content; |
|
4e56b5a206b7
Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1616
diff
changeset
|
914 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
| 1562 | 915 Toolbox::ToLowerCase(mime); |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
916 |
|
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
917 if (mime == "image/png" || |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
918 mime == "image/jpeg") |
| 1562 | 919 { |
| 920 EmbedImage(mime, content); | |
| 921 } | |
| 922 else if (mime == "application/pdf") | |
| 923 { | |
| 924 EmbedPdf(content); | |
| 925 } | |
| 926 else | |
| 927 { | |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
928 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
| 1562 | 929 throw OrthancException(ErrorCode_NotImplemented); |
| 930 } | |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
931 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
932 |
|
800
ecedd89055db
generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
933 |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
934 void ParsedDicomFile::EmbedImage(const std::string& mime, |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
935 const std::string& content) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
936 { |
|
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
937 InvalidateCache(); |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
938 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
939 if (mime == "image/png") |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
940 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
941 PngReader reader; |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
942 reader.ReadFromMemory(content); |
|
800
ecedd89055db
generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
943 EmbedImage(reader); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
944 } |
|
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
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parents:
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diff
changeset
|
945 else if (mime == "image/jpeg") |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
946 { |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
947 JpegReader reader; |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
948 reader.ReadFromMemory(content); |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
949 EmbedImage(reader); |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
950 } |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
951 else |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
952 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
953 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
954 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
955 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
956 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
957 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
958 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
959 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
960 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
961 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
962 accessor.GetFormat() != 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
|
963 accessor.GetFormat() != PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
964 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
965 throw OrthancException(ErrorCode_NotImplemented); |
|
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parents:
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diff
changeset
|
966 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
967 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
968 if (accessor.GetFormat() == PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
969 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
970 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
|
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
971 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
972 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
973 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
974 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
975 Remove(DICOM_TAG_PIXEL_DATA); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
976 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
977 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
ecedd89055db
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
978 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
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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_NUMBER_OF_FRAMES, "1"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
980 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
981 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:
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diff
changeset
|
982 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
983 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
984 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
985 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
986 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
987 unsigned int bytesPerPixel = 1; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
988 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
989 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
990 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
991 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
992 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
993 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
994 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:
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diff
changeset
|
995 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
996 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
997 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
998 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
999 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1000 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1001 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
|
1002 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
|
1003 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1004 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1005 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1006 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1007 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1008 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1009 throw OrthancException(ErrorCode_NotImplemented); |
|
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generation of DICOM images from PNG files
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parents:
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diff
changeset
|
1010 } |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1011 |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1012 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1013 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1014 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1015 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1016 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1017 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1018 Uint8* target = NULL; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1019 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1020 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1021 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1022 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1023 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1024 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1025 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1026 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1027 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1028 case PixelFormat_SignedGrayscale16: |
|
ecedd89055db
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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 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1031 target += pitch; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1032 break; |
|
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 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1035 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1036 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1037 // The alpha channel is not supported by the DICOM standard |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1038 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:
799
diff
changeset
|
1039 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
|
1040 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1041 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1042 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1043 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1044 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1045 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1046 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1047 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1048 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1049 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1050 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1051 } |
|
ecedd89055db
generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
1052 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1053 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1054 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1055 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1056 throw OrthancException(ErrorCode_InternalError); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1057 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1058 } |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1059 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1060 |
|
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1061 Encoding ParsedDicomFile::GetEncoding() const |
|
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1062 { |
|
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1063 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset(), |
|
84c7eaeb5244
Configuration::GetDefaultEncoding
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1064 Configuration::GetDefaultEncoding()); |
|
956
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1065 } |
|
1090
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1066 |
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1067 |
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1068 void ParsedDicomFile::SetEncoding(Encoding encoding) |
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1069 { |
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1070 if (encoding == Encoding_Windows1251) |
|
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1071 { |
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1072 // This Cyrillic codepage is not officially supported by the |
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1073 // DICOM standard. Do not set the SpecificCharacterSet tag. |
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1074 return; |
|
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1075 } |
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1076 |
|
1565
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1077 std::string s = GetDicomSpecificCharacterSet(encoding); |
| 1091 | 1078 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
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1079 } |
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1080 |
| 1686 | 1081 void ParsedDicomFile::ToJson(Json::Value& target, |
| 1082 DicomToJsonFormat format, | |
|
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1083 DicomToJsonFlags flags, |
| 1686 | 1084 unsigned int maxStringLength) |
|
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1085 { |
|
1928
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1086 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), |
|
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1087 format, flags, maxStringLength, |
|
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1088 Configuration::GetDefaultEncoding()); |
|
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1089 } |
|
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1090 |
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1091 |
|
1831
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1092 void ParsedDicomFile::HeaderToJson(Json::Value& target, |
|
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|
1093 DicomToJsonFormat format) |
|
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1094 { |
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|
1095 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getMetaInfo(), format, DicomToJsonFlags_None, 0); |
|
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1096 } |
|
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|
1097 |
|
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|
1098 |
|
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1099 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
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1100 { |
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1101 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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1102 return pimpl_->file_->getDataset()->tagExists(key); |
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1103 } |
|
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|
1104 |
|
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1105 |
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|
1106 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
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|
1107 { |
|
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1108 if (pdf.size() < 5 || // (*) |
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1109 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
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1110 { |
|
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|
1111 LOG(ERROR) << "Not a PDF file"; |
|
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1112 throw OrthancException(ErrorCode_BadFileFormat); |
|
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|
1113 } |
|
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|
1114 |
|
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|
1115 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
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|
1116 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
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|
1117 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
|
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|
1118 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
| 1566 | 1119 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
|
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|
1120 |
|
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changeset
|
1121 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
|
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|
1122 |
|
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|
1123 size_t s = pdf.size(); |
|
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|
1124 if (s & 1) |
|
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|
1125 { |
|
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Creation of DICOM files with encapsulated PDF
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|
1126 // The size of the buffer must be even |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1127 s += 1; |
|
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Creation of DICOM files with encapsulated PDF
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|
1128 } |
|
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|
1129 |
|
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|
1130 Uint8* bytes = NULL; |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1131 OFCondition result = element->createUint8Array(s, bytes); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1132 if (!result.good() || bytes == NULL) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1133 { |
|
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Creation of DICOM files with encapsulated PDF
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|
1134 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
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Creation of DICOM files with encapsulated PDF
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|
1135 } |
|
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Creation of DICOM files with encapsulated PDF
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|
1136 |
|
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Creation of DICOM files with encapsulated PDF
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|
1137 // 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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|
1138 bytes[s - 1] = 0; |
|
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Creation of DICOM files with encapsulated PDF
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|
1139 |
|
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Creation of DICOM files with encapsulated PDF
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|
1140 memcpy(bytes, pdf.c_str(), pdf.size()); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1141 |
|
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|
1142 DcmPolymorphOBOW* obj = element.release(); |
|
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Creation of DICOM files with encapsulated PDF
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|
1143 result = pimpl_->file_->getDataset()->insert(obj); |
|
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Creation of DICOM files with encapsulated PDF
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|
1144 |
|
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Creation of DICOM files with encapsulated PDF
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|
1145 if (!result.good()) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1146 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1147 delete obj; |
|
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Creation of DICOM files with encapsulated PDF
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|
1148 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1149 } |
|
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Creation of DICOM files with encapsulated PDF
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|
1150 } |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1151 |
|
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|
1152 |
|
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changeset
|
1153 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
|
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|
1154 { |
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|
1155 std::string sop, mime; |
|
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|
1156 |
|
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|
1157 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
|
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|
1158 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
|
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|
1159 sop != UID_EncapsulatedPDFStorage || |
|
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|
1160 mime != "application/pdf") |
|
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|
1161 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1162 return false; |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1163 } |
|
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|
1164 |
|
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changeset
|
1165 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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|
1166 { |
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|
1167 return false; |
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1168 } |
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|
1169 |
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|
1170 // Strip the possible pad byte at the end of file, because the |
|
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1171 // encapsulated documents must always have an even length. The PDF |
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1172 // format expects files to end with %%EOF followed by CR/LF. If |
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1173 // the last character of the file is not a CR or LF, we assume it |
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|
1174 // is a pad byte and remove it. |
|
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1175 if (pdf.size() > 0) |
|
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1176 { |
|
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1177 char last = *pdf.rbegin(); |
|
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1178 |
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1179 if (last != 10 && last != 13) |
|
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1180 { |
|
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1181 pdf.resize(pdf.size() - 1); |
|
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1182 } |
|
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1183 } |
|
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1184 |
|
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1185 return true; |
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1186 } |
|
1662
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ParsedDicomFile::Convert()
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1187 |
|
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1188 |
|
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1189 void ParsedDicomFile::Convert(DicomMap& tags) |
|
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1190 { |
|
1929
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1191 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset(), |
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|
1192 ORTHANC_MAXIMUM_TAG_LENGTH, |
|
1928
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Configuration::GetDefaultEncoding
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1193 Configuration::GetDefaultEncoding()); |
|
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1194 } |
|
1818
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ParsedDicomFile::CreateFromJson
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1195 |
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1196 |
|
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1197 ParsedDicomFile* ParsedDicomFile::CreateFromJson(const Json::Value& json, |
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1198 DicomFromJsonFlags flags) |
|
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1199 { |
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1200 std::string tmp = Configuration::GetGlobalStringParameter("DefaultEncoding", "Latin1"); |
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1201 Encoding encoding = StringToEncoding(tmp.c_str()); |
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1202 |
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1203 Json::Value::Members tags = json.getMemberNames(); |
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1204 |
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1205 for (size_t i = 0; i < tags.size(); i++) |
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1206 { |
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1207 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); |
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1208 if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET) |
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1209 { |
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1210 const Json::Value& value = json[tags[i]]; |
|
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1211 if (value.type() != Json::stringValue || |
|
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1212 !GetDicomEncoding(encoding, value.asCString())) |
|
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1213 { |
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1214 LOG(ERROR) << "Unknown encoding while creating DICOM from JSON: " << value; |
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ParsedDicomFile::CreateFromJson
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1215 throw OrthancException(ErrorCode_BadRequest); |
|
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1216 } |
|
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1217 } |
|
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1218 } |
|
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1219 |
|
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ParsedDicomFile::CreateFromJson
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1220 const bool generateIdentifiers = (flags & DicomFromJsonFlags_GenerateIdentifiers); |
|
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ParsedDicomFile::CreateFromJson
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1221 const bool decodeDataUriScheme = (flags & DicomFromJsonFlags_DecodeDataUriScheme); |
|
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ParsedDicomFile::CreateFromJson
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1222 |
|
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ParsedDicomFile::CreateFromJson
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1223 std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(generateIdentifiers)); |
|
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1224 result->SetEncoding(encoding); |
|
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ParsedDicomFile::CreateFromJson
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1225 |
|
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ParsedDicomFile::CreateFromJson
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1226 for (size_t i = 0; i < tags.size(); i++) |
|
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ParsedDicomFile::CreateFromJson
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1227 { |
|
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ParsedDicomFile::CreateFromJson
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1228 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); |
|
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ParsedDicomFile::CreateFromJson
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|
1229 const Json::Value& value = json[tags[i]]; |
|
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ParsedDicomFile::CreateFromJson
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1230 |
|
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ParsedDicomFile::CreateFromJson
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1231 if (tag == DICOM_TAG_PIXEL_DATA || |
|
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ParsedDicomFile::CreateFromJson
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1232 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
|
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ParsedDicomFile::CreateFromJson
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|
1233 { |
|
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ParsedDicomFile::CreateFromJson
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1234 if (value.type() != Json::stringValue) |
|
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ParsedDicomFile::CreateFromJson
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|
1235 { |
|
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ParsedDicomFile::CreateFromJson
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|
1236 throw OrthancException(ErrorCode_BadRequest); |
|
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ParsedDicomFile::CreateFromJson
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1237 } |
|
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ParsedDicomFile::CreateFromJson
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|
1238 else |
|
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ParsedDicomFile::CreateFromJson
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|
1239 { |
|
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ParsedDicomFile::CreateFromJson
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|
1240 result->EmbedContent(value.asString()); |
|
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ParsedDicomFile::CreateFromJson
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|
1241 } |
|
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ParsedDicomFile::CreateFromJson
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|
1242 } |
|
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ParsedDicomFile::CreateFromJson
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|
1243 else if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) |
|
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ParsedDicomFile::CreateFromJson
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|
1244 { |
|
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ParsedDicomFile::CreateFromJson
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|
1245 result->Replace(tag, value, decodeDataUriScheme); |
|
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ParsedDicomFile::CreateFromJson
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|
1246 } |
|
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ParsedDicomFile::CreateFromJson
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|
1247 } |
|
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ParsedDicomFile::CreateFromJson
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|
1248 |
|
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ParsedDicomFile::CreateFromJson
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|
1249 return result.release(); |
|
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ParsedDicomFile::CreateFromJson
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1250 } |
|
1924
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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|
1251 |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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1252 |
|
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|
1253 void ParsedDicomFile::GetRawFrame(std::string& target, |
|
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|
1254 std::string& mime, |
|
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|
1255 unsigned int frameId) |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1256 { |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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|
1257 if (pimpl_->frameIndex_.get() == NULL) |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1258 { |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1259 pimpl_->frameIndex_.reset(new DicomFrameIndex(*pimpl_->file_->getDataset())); |
|
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|
1260 } |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1261 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1262 pimpl_->frameIndex_->GetRawFrame(target, frameId); |
|
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changeset
|
1263 |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1264 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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|
1265 switch (transferSyntax) |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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|
1266 { |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1267 case EXS_JPEGProcess1TransferSyntax: |
|
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|
1268 mime = "image/jpeg"; |
|
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|
1269 break; |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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|
1270 |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1271 case EXS_JPEG2000LosslessOnly: |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1272 case EXS_JPEG2000: |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
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1273 mime = "image/jp2"; |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1274 |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1275 default: |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1276 mime = "application/octet-stream"; |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1277 break; |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1278 } |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1279 } |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1280 |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1281 |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1282 void ParsedDicomFile::InvalidateCache() |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1283 { |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1284 pimpl_->frameIndex_.reset(NULL); |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1285 } |
| 790 | 1286 } |