Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 2312:8700dcaa02e5 issue-46-anonymization
GenerateAnonymizationProfile.py
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 12 Jul 2017 16:44:33 +0200 |
| parents | b7fba68747f6 |
| children | 96b3ec054b69 |
| 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 |
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5 * Copyright (C) 2017 Osimis, Belgium |
| 790 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU General Public License as | |
| 9 * published by the Free Software Foundation, either version 3 of the | |
| 10 * License, or (at your option) any later version. | |
| 11 * | |
| 12 * In addition, as a special exception, the copyright holders of this | |
| 13 * program give permission to link the code of its release with the | |
| 14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 15 * that use the same license as the "OpenSSL" library), and distribute | |
| 16 * the linked executables. You must obey the GNU General Public License | |
| 17 * in all respects for all of the code used other than "OpenSSL". If you | |
| 18 * modify file(s) with this exception, you may extend this exception to | |
| 19 * your version of the file(s), but you are not obligated to do so. If | |
| 20 * you do not wish to do so, delete this exception statement from your | |
| 21 * version. If you delete this exception statement from all source files | |
| 22 * in the program, then also delete it here. | |
| 23 * | |
| 24 * This program is distributed in the hope that it will be useful, but | |
| 25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 27 * General Public License for more details. | |
| 28 * | |
| 29 * You should have received a copy of the GNU General Public License | |
| 30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 31 **/ | |
| 32 | |
| 33 | |
| 34 | |
| 35 /*========================================================================= | |
| 36 | |
| 37 This file is based on portions of the following project: | |
| 38 | |
| 39 Program: GDCM (Grassroots DICOM). A DICOM library | |
| 40 Module: http://gdcm.sourceforge.net/Copyright.html | |
| 41 | |
| 42 Copyright (c) 2006-2011 Mathieu Malaterre | |
| 43 Copyright (c) 1993-2005 CREATIS | |
| 44 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
| 45 All rights reserved. | |
| 46 | |
| 47 Redistribution and use in source and binary forms, with or without | |
| 48 modification, are permitted provided that the following conditions are met: | |
| 49 | |
| 50 * Redistributions of source code must retain the above copyright notice, | |
| 51 this list of conditions and the following disclaimer. | |
| 52 | |
| 53 * Redistributions in binary form must reproduce the above copyright notice, | |
| 54 this list of conditions and the following disclaimer in the documentation | |
| 55 and/or other materials provided with the distribution. | |
| 56 | |
| 57 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
| 58 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
| 59 endorse or promote products derived from this software without specific | |
| 60 prior written permission. | |
| 61 | |
| 62 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
| 63 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| 64 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 65 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
| 66 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
| 67 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
| 68 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
| 69 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
| 70 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| 71 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 72 | |
| 73 =========================================================================*/ | |
| 74 | |
| 75 | |
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76 #include "PrecompiledHeadersServer.h" |
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77 |
| 790 | 78 #ifndef NOMINMAX |
| 79 #define NOMINMAX | |
| 80 #endif | |
| 81 | |
| 82 #include "ParsedDicomFile.h" | |
| 83 | |
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84 #include "OrthancInitialization.h" |
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85 #include "ServerToolbox.h" |
| 790 | 86 #include "FromDcmtkBridge.h" |
| 87 #include "ToDcmtkBridge.h" | |
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88 #include "Internals/DicomFrameIndex.h" |
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89 #include "../Core/Images/JpegReader.h" |
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90 #include "../Core/Images/PngReader.h" |
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91 #include "../Core/Logging.h" |
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92 #include "../Core/OrthancException.h" |
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93 #include "../Core/Toolbox.h" |
| 790 | 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/dcuid.h> | |
| 105 #include <dcmtk/dcmdata/dcmetinf.h> | |
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106 #include <dcmtk/dcmdata/dcdeftag.h> |
| 790 | 107 |
| 108 #include <dcmtk/dcmdata/dcvrae.h> | |
| 109 #include <dcmtk/dcmdata/dcvras.h> | |
| 110 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 111 #include <dcmtk/dcmdata/dcvrda.h> | |
| 112 #include <dcmtk/dcmdata/dcvrds.h> | |
| 113 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 114 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 115 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 116 #include <dcmtk/dcmdata/dcvris.h> | |
| 117 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 118 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 119 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 120 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 121 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 122 #include <dcmtk/dcmdata/dcvrss.h> | |
| 123 #include <dcmtk/dcmdata/dcvrst.h> | |
| 124 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 125 #include <dcmtk/dcmdata/dcvrui.h> | |
| 126 #include <dcmtk/dcmdata/dcvrul.h> | |
| 127 #include <dcmtk/dcmdata/dcvrus.h> | |
| 128 #include <dcmtk/dcmdata/dcvrut.h> | |
| 129 #include <dcmtk/dcmdata/dcpixel.h> | |
| 130 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 131 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 132 | |
| 133 | |
| 134 #include <boost/math/special_functions/round.hpp> | |
| 135 #include <dcmtk/dcmdata/dcostrmb.h> | |
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136 #include <boost/algorithm/string/predicate.hpp> |
| 790 | 137 |
| 138 | |
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139 #if DCMTK_VERSION_NUMBER <= 360 |
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140 # define EXS_JPEGProcess1 EXS_JPEGProcess1TransferSyntax |
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141 #endif |
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142 |
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143 |
| 790 | 144 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; |
| 145 | |
| 146 | |
| 147 | |
| 148 namespace Orthanc | |
| 149 { | |
| 794 | 150 struct ParsedDicomFile::PImpl |
| 151 { | |
| 152 std::auto_ptr<DcmFileFormat> file_; | |
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153 std::auto_ptr<DicomFrameIndex> frameIndex_; |
| 794 | 154 }; |
| 155 | |
| 156 | |
| 790 | 157 static void SendPathValueForDictionary(RestApiOutput& output, |
| 158 DcmItem& dicom) | |
| 159 { | |
| 160 Json::Value v = Json::arrayValue; | |
| 161 | |
| 162 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 163 { | |
| 164 DcmElement* element = dicom.getElement(i); | |
| 165 if (element) | |
| 166 { | |
| 167 char buf[16]; | |
| 168 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 169 v.append(buf); | |
| 170 } | |
| 171 } | |
| 172 | |
| 173 output.AnswerJson(v); | |
| 174 } | |
| 175 | |
| 176 static inline uint16_t GetCharValue(char c) | |
| 177 { | |
| 178 if (c >= '0' && c <= '9') | |
| 179 return c - '0'; | |
| 180 else if (c >= 'a' && c <= 'f') | |
| 181 return c - 'a' + 10; | |
| 182 else if (c >= 'A' && c <= 'F') | |
| 183 return c - 'A' + 10; | |
| 184 else | |
| 185 return 0; | |
| 186 } | |
| 187 | |
| 188 static inline uint16_t GetTagValue(const char* c) | |
| 189 { | |
| 190 return ((GetCharValue(c[0]) << 12) + | |
| 191 (GetCharValue(c[1]) << 8) + | |
| 192 (GetCharValue(c[2]) << 4) + | |
| 193 GetCharValue(c[3])); | |
| 194 } | |
| 195 | |
| 196 static void ParseTagAndGroup(DcmTagKey& key, | |
| 197 const std::string& tag) | |
| 198 { | |
| 199 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 200 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 201 } | |
| 202 | |
| 203 | |
| 204 static void SendSequence(RestApiOutput& output, | |
| 205 DcmSequenceOfItems& sequence) | |
| 206 { | |
| 207 // This element is a sequence | |
| 208 Json::Value v = Json::arrayValue; | |
| 209 | |
| 210 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 211 { | |
| 212 v.append(boost::lexical_cast<std::string>(i)); | |
| 213 } | |
| 214 | |
| 215 output.AnswerJson(v); | |
| 216 } | |
| 217 | |
| 218 | |
| 219 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 220 E_TransferSyntax transferSyntax) | |
| 221 { | |
| 222 DcmPixelSequence* pixelSequence = NULL; | |
| 223 if (pixelData.getEncapsulatedRepresentation | |
| 224 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 225 { | |
| 226 return pixelSequence->card(); | |
| 227 } | |
| 228 else | |
| 229 { | |
| 230 return 1; | |
| 231 } | |
| 232 } | |
| 233 | |
| 234 | |
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235 namespace |
| 790 | 236 { |
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237 class DicomFieldStream : public IHttpStreamAnswer |
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238 { |
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239 private: |
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240 DcmElement& element_; |
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241 uint32_t length_; |
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242 uint32_t offset_; |
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243 std::string chunk_; |
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244 size_t chunkSize_; |
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245 |
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246 public: |
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247 DicomFieldStream(DcmElement& element, |
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248 E_TransferSyntax transferSyntax) : |
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249 element_(element), |
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250 length_(element.getLength(transferSyntax)), |
| 1616 | 251 offset_(0), |
| 252 chunkSize_(0) | |
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253 { |
| 1521 | 254 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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255 chunk_.resize(CHUNK_SIZE); |
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256 } |
| 790 | 257 |
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258 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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259 bool /*deflateAllowed*/) |
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260 { |
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261 // No support for compression |
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262 return HttpCompression_None; |
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263 } |
| 790 | 264 |
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265 virtual bool HasContentFilename(std::string& filename) |
| 790 | 266 { |
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267 return false; |
| 790 | 268 } |
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269 |
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270 virtual std::string GetContentType() |
| 790 | 271 { |
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272 return ""; |
| 790 | 273 } |
| 274 | |
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275 virtual uint64_t GetContentLength() |
| 790 | 276 { |
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277 return length_; |
| 790 | 278 } |
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279 |
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280 virtual bool ReadNextChunk() |
| 790 | 281 { |
| 1520 | 282 assert(offset_ <= length_); |
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283 |
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284 if (offset_ == length_) |
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285 { |
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286 return false; |
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287 } |
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288 else |
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289 { |
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290 if (length_ - offset_ < chunk_.size()) |
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291 { |
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292 chunkSize_ = length_ - offset_; |
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293 } |
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294 else |
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295 { |
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296 chunkSize_ = chunk_.size(); |
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297 } |
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298 |
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299 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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300 |
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301 offset_ += chunkSize_; |
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302 |
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303 if (!cond.good()) |
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304 { |
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305 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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306 throw OrthancException(ErrorCode_InternalError); |
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307 } |
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308 |
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309 return true; |
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310 } |
| 790 | 311 } |
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312 |
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313 virtual const char *GetChunkContent() |
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314 { |
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315 return chunk_.c_str(); |
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316 } |
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317 |
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318 virtual size_t GetChunkSize() |
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319 { |
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320 return chunkSize_; |
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321 } |
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322 }; |
| 790 | 323 } |
| 324 | |
| 325 | |
| 326 static bool AnswerPixelData(RestApiOutput& output, | |
| 327 DcmItem& dicom, | |
| 328 E_TransferSyntax transferSyntax, | |
| 329 const std::string* blockUri) | |
| 330 { | |
| 331 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 332 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 333 | |
| 334 DcmElement *element = NULL; | |
| 335 if (!dicom.findAndGetElement(k, element).good() || | |
| 336 element == NULL) | |
| 337 { | |
| 338 return false; | |
| 339 } | |
| 340 | |
| 341 try | |
| 342 { | |
| 343 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 344 if (blockUri == NULL) | |
| 345 { | |
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346 // The user asks how many blocks are present in this pixel data |
| 790 | 347 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); |
| 348 | |
| 349 Json::Value result(Json::arrayValue); | |
| 350 for (unsigned int i = 0; i < blocks; i++) | |
| 351 { | |
| 352 result.append(boost::lexical_cast<std::string>(i)); | |
| 353 } | |
| 354 | |
| 355 output.AnswerJson(result); | |
| 356 return true; | |
| 357 } | |
| 358 | |
| 359 | |
| 360 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 361 | |
| 362 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 363 { | |
| 364 DcmPixelSequence* pixelSequence = NULL; | |
| 365 if (pixelData.getEncapsulatedRepresentation | |
| 366 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 367 { | |
| 368 // This is the case for JPEG transfer syntaxes | |
| 369 if (block < pixelSequence->card()) | |
| 370 { | |
| 371 DcmPixelItem* pixelItem = NULL; | |
| 372 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 373 { | |
| 374 if (pixelItem->getLength() == 0) | |
| 375 { | |
| 376 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 377 return true; | |
| 378 } | |
| 379 | |
| 380 Uint8* buffer = NULL; | |
| 381 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 382 { | |
| 383 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 384 return true; | |
| 385 } | |
| 386 } | |
| 387 } | |
| 388 } | |
| 389 else | |
| 390 { | |
| 391 // This is the case for raw, uncompressed image buffers | |
| 392 assert(*blockUri == "0"); | |
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393 DicomFieldStream stream(*element, transferSyntax); |
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394 output.AnswerStream(stream); |
| 790 | 395 } |
| 396 } | |
| 397 } | |
| 398 catch (boost::bad_lexical_cast&) | |
| 399 { | |
| 400 // The URI entered by the user is not a number | |
| 401 } | |
| 402 catch (std::bad_cast&) | |
| 403 { | |
| 404 // This should never happen | |
| 405 } | |
| 406 | |
| 407 return false; | |
| 408 } | |
| 409 | |
| 410 | |
| 411 | |
| 412 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 413 const std::string& tag, | |
| 414 DcmItem& dicom, | |
| 415 E_TransferSyntax transferSyntax) | |
| 416 { | |
| 417 DcmTagKey k; | |
| 418 ParseTagAndGroup(k, tag); | |
| 419 | |
| 420 DcmSequenceOfItems* sequence = NULL; | |
| 421 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 422 sequence != NULL && | |
| 423 sequence->getVR() == EVR_SQ) | |
| 424 { | |
| 425 SendSequence(output, *sequence); | |
| 426 return; | |
| 427 } | |
| 428 | |
| 429 DcmElement* element = NULL; | |
| 430 if (dicom.findAndGetElement(k, element).good() && | |
| 431 element != NULL && | |
| 432 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 433 element->getVR() != EVR_SQ) | |
| 434 { | |
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435 DicomFieldStream stream(*element, transferSyntax); |
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436 output.AnswerStream(stream); |
| 790 | 437 } |
| 438 } | |
| 439 | |
| 440 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 441 const UriComponents& uri) | |
| 442 { | |
| 794 | 443 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 444 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 445 |
| 446 // Special case: Accessing the pixel data | |
| 447 if (uri.size() == 1 || | |
| 448 uri.size() == 2) | |
| 449 { | |
| 450 DcmTagKey tag; | |
| 451 ParseTagAndGroup(tag, uri[0]); | |
| 452 | |
| 453 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 454 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 455 { | |
| 456 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 457 return; | |
| 458 } | |
| 459 } | |
| 460 | |
| 461 // Go down in the tag hierarchy according to the URI | |
| 462 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 463 { | |
| 464 size_t index; | |
| 465 try | |
| 466 { | |
| 467 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 468 } | |
| 469 catch (boost::bad_lexical_cast&) | |
| 470 { | |
| 471 return; | |
| 472 } | |
| 473 | |
| 474 DcmTagKey k; | |
| 475 DcmItem *child = NULL; | |
| 476 ParseTagAndGroup(k, uri[2 * pos]); | |
| 477 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 478 child == NULL) | |
| 479 { | |
| 480 return; | |
| 481 } | |
| 482 | |
| 483 dicom = child; | |
| 484 } | |
| 485 | |
| 486 // We have reached the end of the URI | |
| 487 if (uri.size() % 2 == 0) | |
| 488 { | |
| 489 SendPathValueForDictionary(output, *dicom); | |
| 490 } | |
| 491 else | |
| 492 { | |
| 493 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 494 } | |
| 495 } | |
| 496 | |
| 497 | |
| 498 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 499 { | |
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500 InvalidateCache(); |
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501 |
| 790 | 502 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
| 794 | 503 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 504 if (element != NULL) |
| 505 { | |
| 506 delete element; | |
| 507 } | |
| 508 } | |
| 509 | |
| 510 | |
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511 void ParsedDicomFile::Clear(const DicomTag& tag, |
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512 bool onlyIfExists) |
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513 { |
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514 InvalidateCache(); |
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515 |
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516 DcmItem* dicom = pimpl_->file_->getDataset(); |
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517 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
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518 |
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519 if (onlyIfExists && |
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520 !dicom->tagExists(key)) |
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521 { |
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522 // The tag is non-existing, do not clear it |
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523 } |
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524 else |
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525 { |
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526 if (!dicom->insertEmptyElement(key, OFTrue /* replace old value */).good()) |
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527 { |
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528 throw OrthancException(ErrorCode_InternalError); |
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529 } |
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530 } |
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531 } |
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532 |
| 790 | 533 |
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534 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 535 { |
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536 InvalidateCache(); |
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537 |
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538 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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539 |
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540 // Loop over the dataset to detect its private tags |
| 790 | 541 typedef std::list<DcmElement*> Tags; |
| 542 Tags privateTags; | |
| 543 | |
| 544 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 545 { | |
| 546 DcmElement* element = dataset.getElement(i); | |
| 547 DcmTag tag(element->getTag()); | |
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548 |
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549 // Is this a private tag? |
| 1694 | 550 if (tag.isPrivate()) |
| 790 | 551 { |
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552 bool remove = true; |
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553 |
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554 // Check whether this private tag is to be kept |
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555 if (toKeep != NULL) |
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556 { |
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557 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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558 if (toKeep->find(tmp) != toKeep->end()) |
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559 { |
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560 remove = false; // Keep it |
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561 } |
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562 } |
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563 |
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564 if (remove) |
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565 { |
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566 privateTags.push_back(element); |
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567 } |
| 790 | 568 } |
| 569 } | |
| 570 | |
|
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571 // Loop over the detected private tags to remove them |
| 790 | 572 for (Tags::iterator it = privateTags.begin(); |
| 573 it != privateTags.end(); ++it) | |
| 574 { | |
| 575 DcmElement* tmp = dataset.remove(*it); | |
| 576 if (tmp != NULL) | |
| 577 { | |
| 578 delete tmp; | |
| 579 } | |
| 580 } | |
| 581 } | |
| 582 | |
| 583 | |
|
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584 static void InsertInternal(DcmDataset& dicom, |
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585 DcmElement* element) |
| 790 | 586 { |
|
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587 OFCondition cond = dicom.insert(element, false, false); |
|
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588 if (!cond.good()) |
| 790 | 589 { |
| 590 // This field already exists | |
|
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591 delete element; |
| 790 | 592 throw OrthancException(ErrorCode_InternalError); |
| 593 } | |
| 594 } | |
| 595 | |
| 596 | |
|
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597 void ParsedDicomFile::Insert(const DicomTag& tag, |
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598 const Json::Value& value, |
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599 bool decodeDataUriScheme) |
| 790 | 600 { |
|
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601 if (pimpl_->file_->getDataset()->tagExists(ToDcmtkBridge::Convert(tag))) |
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602 { |
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603 throw OrthancException(ErrorCode_AlreadyExistingTag); |
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604 } |
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605 |
|
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606 if (decodeDataUriScheme && |
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607 value.type() == Json::stringValue && |
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608 (tag == DICOM_TAG_ENCAPSULATED_DOCUMENT || |
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609 tag == DICOM_TAG_PIXEL_DATA)) |
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610 { |
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611 if (EmbedContentInternal(value.asString())) |
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612 { |
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613 return; |
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614 } |
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615 } |
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616 |
|
1924
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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617 InvalidateCache(); |
|
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618 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
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619 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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620 } |
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621 |
| 790 | 622 |
|
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623 static bool CanReplaceProceed(DcmDataset& dicom, |
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624 const DcmTagKey& tag, |
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625 DicomReplaceMode mode) |
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626 { |
| 1979 | 627 if (dicom.findAndDeleteElement(tag).good()) |
| 790 | 628 { |
| 1979 | 629 // This tag was existing, it has been deleted |
| 630 return true; | |
| 631 } | |
| 632 else | |
| 633 { | |
| 634 // This tag was absent, act wrt. the specified "mode" | |
| 790 | 635 switch (mode) |
| 636 { | |
| 637 case DicomReplaceMode_InsertIfAbsent: | |
| 1979 | 638 return true; |
| 790 | 639 |
| 640 case DicomReplaceMode_ThrowIfAbsent: | |
| 641 throw OrthancException(ErrorCode_InexistentItem); | |
| 642 | |
| 643 case DicomReplaceMode_IgnoreIfAbsent: | |
| 1979 | 644 return false; |
| 645 | |
| 646 default: | |
| 647 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 790 | 648 } |
| 649 } | |
|
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650 } |
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651 |
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652 |
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653 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
| 1695 | 654 const std::string& utf8Value, |
|
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655 bool decodeDataUriScheme) |
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656 { |
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657 if (tag != DICOM_TAG_SOP_CLASS_UID && |
|
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658 tag != DICOM_TAG_SOP_INSTANCE_UID) |
| 790 | 659 { |
|
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|
660 return; |
| 790 | 661 } |
| 662 | |
|
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|
663 std::string binary; |
| 1695 | 664 const std::string* decoded = &utf8Value; |
|
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|
665 |
|
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ParsedDicomFile::CreateFromJson
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|
666 if (decodeDataUriScheme && |
| 1695 | 667 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
|
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|
668 { |
|
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|
669 std::string mime; |
|
1981
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
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parents:
1980
diff
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|
670 if (!Toolbox::DecodeDataUriScheme(mime, binary, utf8Value)) |
|
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
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diff
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|
671 { |
|
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return code in Toolbox::DecodeDataUriScheme
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1980
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|
672 throw OrthancException(ErrorCode_BadFileFormat); |
|
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return code in Toolbox::DecodeDataUriScheme
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parents:
1980
diff
changeset
|
673 } |
|
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return code in Toolbox::DecodeDataUriScheme
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1980
diff
changeset
|
674 |
|
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|
675 decoded = &binary; |
|
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|
676 } |
| 1695 | 677 else |
| 678 { | |
| 679 Encoding encoding = GetEncoding(); | |
| 680 if (GetEncoding() != Encoding_Utf8) | |
| 681 { | |
| 682 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
| 683 decoded = &binary; | |
| 684 } | |
| 685 } | |
| 790 | 686 |
| 687 /** | |
| 688 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 689 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 690 * you make changes to the related tags in the dataset ('SOP Class | |
| 691 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 692 * options. You can disable this behaviour by using the -nmu | |
| 693 * option. | |
| 694 **/ | |
| 695 | |
| 696 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 697 { | |
|
1982
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Modification of instances can now replace PixelData
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|
698 ReplacePlainString(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded); |
| 790 | 699 } |
| 700 | |
| 701 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 702 { | |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
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parents:
1981
diff
changeset
|
703 ReplacePlainString(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded); |
|
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|
704 } |
|
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changeset
|
705 } |
|
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changeset
|
706 |
|
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changeset
|
707 |
|
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changeset
|
708 void ParsedDicomFile::Replace(const DicomTag& tag, |
| 1695 | 709 const std::string& utf8Value, |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
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1981
diff
changeset
|
710 bool decodeDataUriScheme, |
|
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|
711 DicomReplaceMode mode) |
|
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|
712 { |
|
1924
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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1913
diff
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|
713 InvalidateCache(); |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
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diff
changeset
|
714 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
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1981
diff
changeset
|
715 DcmDataset& dicom = *pimpl_->file_->getDataset(); |
|
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1981
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|
716 if (CanReplaceProceed(dicom, ToDcmtkBridge::Convert(tag), mode)) |
|
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1981
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|
717 { |
|
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Modification of instances can now replace PixelData
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1981
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|
718 // Either the tag was previously existing (and now removed), or |
|
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Modification of instances can now replace PixelData
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1981
diff
changeset
|
719 // the replace mode was set to "InsertIfAbsent" |
| 1979 | 720 |
|
1982
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Modification of instances can now replace PixelData
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1981
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|
721 if (decodeDataUriScheme && |
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|
722 (tag == DICOM_TAG_ENCAPSULATED_DOCUMENT || |
|
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|
723 tag == DICOM_TAG_PIXEL_DATA)) |
|
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|
724 { |
|
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Modification of instances can now replace PixelData
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1981
diff
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|
725 if (EmbedContentInternal(utf8Value)) |
|
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Modification of instances can now replace PixelData
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1981
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|
726 { |
|
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Modification of instances can now replace PixelData
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|
727 return; |
|
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Modification of instances can now replace PixelData
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1981
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changeset
|
728 } |
|
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Modification of instances can now replace PixelData
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1981
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|
729 } |
|
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Modification of instances can now replace PixelData
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1981
diff
changeset
|
730 |
|
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Modification of instances can now replace PixelData
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1981
diff
changeset
|
731 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
|
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1981
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|
732 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, decodeDataUriScheme, GetEncoding()); |
|
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1981
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|
733 |
| 1979 | 734 InsertInternal(dicom, element.release()); |
| 735 UpdateStorageUid(tag, utf8Value, false); | |
| 736 } | |
|
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|
737 } |
|
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|
738 |
|
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|
739 |
|
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|
740 void ParsedDicomFile::Replace(const DicomTag& tag, |
|
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|
741 const Json::Value& value, |
|
1818
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ParsedDicomFile::CreateFromJson
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1805
diff
changeset
|
742 bool decodeDataUriScheme, |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
743 DicomReplaceMode mode) |
|
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
744 { |
|
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
|
745 InvalidateCache(); |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
746 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
747 DcmDataset& dicom = *pimpl_->file_->getDataset(); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
748 if (CanReplaceProceed(dicom, ToDcmtkBridge::Convert(tag), mode)) |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
749 { |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
750 // Either the tag was previously existing (and now removed), or |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
751 // the replace mode was set to "InsertIfAbsent" |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
752 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
753 if (decodeDataUriScheme && |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
754 value.type() == Json::stringValue && |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
755 (tag == DICOM_TAG_ENCAPSULATED_DOCUMENT || |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
756 tag == DICOM_TAG_PIXEL_DATA)) |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
757 { |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
758 if (EmbedContentInternal(value.asString())) |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
759 { |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
760 return; |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
761 } |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
762 } |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
763 |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
764 InsertInternal(dicom, FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
| 1979 | 765 |
| 766 if (tag == DICOM_TAG_SOP_CLASS_UID || | |
| 767 tag == DICOM_TAG_SOP_INSTANCE_UID) | |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
768 { |
| 1979 | 769 if (value.type() != Json::stringValue) |
| 770 { | |
| 771 throw OrthancException(ErrorCode_BadParameterType); | |
| 772 } | |
| 773 | |
| 774 UpdateStorageUid(tag, value.asString(), decodeDataUriScheme); | |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
775 } |
| 790 | 776 } |
| 777 } | |
| 778 | |
| 779 | |
| 780 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 781 { | |
| 782 std::string serialized; | |
|
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
991
diff
changeset
|
783 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 784 { |
| 785 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 786 } | |
| 787 } | |
| 788 | |
| 789 | |
| 790 | |
| 791 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 792 const DicomTag& tag) | |
| 793 { | |
| 794 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 795 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
796 |
|
1818
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1805
diff
changeset
|
797 if (tag.IsPrivate() || |
|
1655
e40fd0d925c5
/tools/create-dicom can create tags with unknown VR
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1641
diff
changeset
|
798 FromDcmtkBridge::IsUnknownTag(tag) || |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
799 tag == DICOM_TAG_PIXEL_DATA || |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
800 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 801 { |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
802 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
803 long unsigned int count = 0; |
| 790 | 804 |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
805 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
806 { |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
807 if (count > 0) |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
808 { |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
809 assert(data != NULL); |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
810 value.assign(reinterpret_cast<const char*>(data), count); |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
811 } |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
812 else |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
813 { |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
814 value.clear(); |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
815 } |
| 790 | 816 |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
817 return true; |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
818 } |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
819 else |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
820 { |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
821 return false; |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
822 } |
| 790 | 823 } |
| 824 else | |
| 825 { | |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
826 DcmElement* element = NULL; |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
827 if (!dataset.findAndGetElement(k, element).good() || |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
828 element == NULL) |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
829 { |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
830 return false; |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
831 } |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
832 |
|
1736
b953c6eef28d
ToJson: IncludePrivateTags and IncludeUnknownTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1735
diff
changeset
|
833 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
|
1929
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1928
diff
changeset
|
834 (*element, DicomToJsonFlags_Default, |
|
cda5b0ab4ce5
ORTHANC_MAXIMUM_TAG_LENGTH made explicit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1928
diff
changeset
|
835 ORTHANC_MAXIMUM_TAG_LENGTH, GetEncoding())); |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
836 |
|
1737
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
837 if (v.get() == NULL || |
|
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
838 v->IsNull()) |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
839 { |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
840 value = ""; |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
841 } |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
842 else |
|
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
843 { |
|
1737
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
844 // TODO v->IsBinary() |
|
ec66a16aa398
removal of DicomStringValue and DicomNullValue
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1736
diff
changeset
|
845 value = v->GetContent(); |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
846 } |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
847 |
|
1307
f796207e3df1
Fix replacement and insertion of private DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1288
diff
changeset
|
848 return true; |
| 790 | 849 } |
| 850 } | |
| 851 | |
| 852 | |
| 853 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 854 { | |
| 855 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 856 | |
| 857 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 858 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 859 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 860 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 861 { | |
| 862 throw OrthancException(ErrorCode_BadFileFormat); | |
| 863 } | |
| 864 | |
| 865 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 866 } | |
| 867 | |
| 868 | |
| 869 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 870 { | |
|
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
991
diff
changeset
|
871 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 872 } |
| 873 | |
| 874 | |
| 875 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 876 { | |
| 877 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 878 std::string content; | |
| 879 SaveToMemoryBuffer(content); | |
| 2140 | 880 SystemToolbox::WriteFile(content, path); |
| 790 | 881 } |
| 882 | |
| 883 | |
|
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
884 ParsedDicomFile::ParsedDicomFile(bool createIdentifiers) : pimpl_(new PImpl) |
| 790 | 885 { |
| 794 | 886 pimpl_->file_.reset(new DcmFileFormat); |
|
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
887 |
|
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
888 if (createIdentifiers) |
|
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
889 { |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
890 ReplacePlainString(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
891 ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
892 ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
893 ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
|
1805
f08978b1f45b
c-find scu for modality worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1800
diff
changeset
|
894 } |
| 790 | 895 } |
| 896 | |
| 791 | 897 |
|
2202
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
898 void ParsedDicomFile::CreateFromDicomMap(const DicomMap& source, |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
899 Encoding defaultEncoding) |
|
1786
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
900 { |
|
2202
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
901 pimpl_->file_.reset(new DcmFileFormat); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
902 |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
903 const DicomValue* tmp = source.TestAndGetValue(DICOM_TAG_SPECIFIC_CHARACTER_SET); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
904 if (tmp != NULL) |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
905 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
906 Encoding encoding; |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
907 if (tmp->IsNull() || |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
908 tmp->IsBinary() || |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
909 !GetDicomEncoding(encoding, tmp->GetContent().c_str())) |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
910 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
911 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
912 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
913 else |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
914 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
915 SetEncoding(encoding); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
916 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
917 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
918 else |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
919 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
920 SetEncoding(defaultEncoding); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
921 } |
|
1787
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
922 |
|
2202
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
923 for (DicomMap::Map::const_iterator |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
924 it = source.map_.begin(); it != source.map_.end(); ++it) |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
925 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
926 if (it->first != DICOM_TAG_SPECIFIC_CHARACTER_SET && |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
927 !it->second->IsNull()) |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
928 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
929 ReplacePlainString(it->first, it->second->GetContent()); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
930 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
931 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
932 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
933 |
|
1787
1b1d5470233f
refactoring of DicomFindAnswers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1786
diff
changeset
|
934 |
|
2202
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
935 ParsedDicomFile::ParsedDicomFile(const DicomMap& map, |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
936 Encoding defaultEncoding) : |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
937 pimpl_(new PImpl) |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
938 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
939 CreateFromDicomMap(map, defaultEncoding); |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
940 } |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
941 |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
942 |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
943 ParsedDicomFile::ParsedDicomFile(const DicomMap& map) : |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
944 pimpl_(new PImpl) |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
945 { |
|
9b373b7d6713
Fix handling of encodings in C-FIND requests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2142
diff
changeset
|
946 CreateFromDicomMap(map, Configuration::GetDefaultEncoding()); |
|
1786
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
947 } |
|
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
948 |
|
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
949 |
|
1800
30e97a1f4093
callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1788
diff
changeset
|
950 ParsedDicomFile::ParsedDicomFile(const void* content, |
|
30e97a1f4093
callback for handling worklists with plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1788
diff
changeset
|
951 size_t size) : pimpl_(new PImpl) |
| 791 | 952 { |
|
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
953 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(content, size)); |
| 791 | 954 } |
| 955 | |
| 794 | 956 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 957 { |
| 958 if (content.size() == 0) | |
| 959 { | |
|
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
960 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(NULL, 0)); |
| 791 | 961 } |
| 962 else | |
| 963 { | |
|
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
964 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(&content[0], content.size())); |
| 791 | 965 } |
| 966 } | |
| 792 | 967 |
| 968 | |
| 794 | 969 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 970 pimpl_(new PImpl) | |
| 792 | 971 { |
| 794 | 972 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
|
973 |
|
1564
1b7def486e62
creation of DICOM series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1562
diff
changeset
|
974 // Create a new instance-level identifier |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
975 ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 976 } |
| 977 | |
| 978 | |
|
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
979 ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl) |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
980 { |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
981 pimpl_->file_.reset(new DcmFileFormat(&dicom)); |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
982 } |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
983 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
984 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
985 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl) |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
986 { |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
987 pimpl_->file_.reset(new DcmFileFormat(dicom)); |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
988 } |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
989 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
990 |
| 792 | 991 ParsedDicomFile::~ParsedDicomFile() |
| 992 { | |
| 794 | 993 delete pimpl_; |
| 792 | 994 } |
| 995 | |
| 793 | 996 |
|
1824
b530c3dfe2a6
refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1818
diff
changeset
|
997 DcmFileFormat& ParsedDicomFile::GetDcmtkObject() const |
| 793 | 998 { |
|
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
999 return *pimpl_->file_.get(); |
| 793 | 1000 } |
| 1001 | |
| 1002 | |
| 1003 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1004 { | |
| 794 | 1005 return new ParsedDicomFile(*this); |
| 793 | 1006 } |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1007 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1008 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1009 bool ParsedDicomFile::EmbedContentInternal(const std::string& dataUriScheme) |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1010 { |
|
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1616
diff
changeset
|
1011 std::string mime, content; |
|
1981
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
1012 if (!Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme)) |
|
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
1013 { |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1014 return false; |
|
1981
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
1015 } |
|
4b545a8b1f95
return code in Toolbox::DecodeDataUriScheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1980
diff
changeset
|
1016 |
| 1562 | 1017 Toolbox::ToLowerCase(mime); |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1018 |
|
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1019 if (mime == "image/png" || |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1020 mime == "image/jpeg") |
| 1562 | 1021 { |
| 1022 EmbedImage(mime, content); | |
| 1023 } | |
| 1024 else if (mime == "application/pdf") | |
| 1025 { | |
| 1026 EmbedPdf(content); | |
| 1027 } | |
| 1028 else | |
| 1029 { | |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
1030 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
| 1562 | 1031 throw OrthancException(ErrorCode_NotImplemented); |
| 1032 } | |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1033 |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1034 return true; |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1035 } |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1036 |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1037 |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1038 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1039 { |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1040 if (!EmbedContentInternal(dataUriScheme)) |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1041 { |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1042 throw OrthancException(ErrorCode_BadFileFormat); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1043 } |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1044 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1045 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1046 |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1047 void ParsedDicomFile::EmbedImage(const std::string& mime, |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1048 const std::string& content) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1049 { |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1050 if (mime == "image/png") |
|
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
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1052 PngReader reader; |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1053 reader.ReadFromMemory(content); |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1054 EmbedImage(reader); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1055 } |
|
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1056 else if (mime == "image/jpeg") |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1057 { |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1058 JpegReader reader; |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1059 reader.ReadFromMemory(content); |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1060 EmbedImage(reader); |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
1061 } |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1062 else |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1063 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1064 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1065 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1066 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1067 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1068 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1069 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1070 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1071 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1072 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1073 accessor.GetFormat() != PixelFormat_SignedGrayscale16 && |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1074 accessor.GetFormat() != PixelFormat_RGB24 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1075 accessor.GetFormat() != PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1076 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1077 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1078 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1079 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1080 InvalidateCache(); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1081 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1082 if (accessor.GetFormat() == PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1083 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1084 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1085 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1086 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1087 // 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:
799
diff
changeset
|
1088 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1089 Remove(DICOM_TAG_PIXEL_DATA); |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1090 ReplacePlainString(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1091 ReplacePlainString(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1092 ReplacePlainString(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1093 ReplacePlainString(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1094 |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1095 if (accessor.GetFormat() == PixelFormat_SignedGrayscale16) |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1096 { |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1097 ReplacePlainString(DICOM_TAG_PIXEL_REPRESENTATION, "1"); |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1098 } |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1099 else |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1100 { |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1101 ReplacePlainString(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1102 } |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1103 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1104 ReplacePlainString(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1105 ReplacePlainString(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1106 |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1107 unsigned int bytesPerPixel = 0; |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1108 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1109 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1110 { |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1111 case PixelFormat_Grayscale8: |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1112 ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1113 ReplacePlainString(DICOM_TAG_BITS_STORED, "8"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1114 ReplacePlainString(DICOM_TAG_HIGH_BIT, "7"); |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1115 bytesPerPixel = 1; |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1116 break; |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1117 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1118 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1119 case PixelFormat_RGBA32: |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1120 ReplacePlainString(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1121 ReplacePlainString(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1122 ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1123 ReplacePlainString(DICOM_TAG_BITS_STORED, "8"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1124 ReplacePlainString(DICOM_TAG_HIGH_BIT, "7"); |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1125 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1126 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1127 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1128 case PixelFormat_Grayscale16: |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1129 case PixelFormat_SignedGrayscale16: |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1130 ReplacePlainString(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1131 ReplacePlainString(DICOM_TAG_BITS_STORED, "16"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1132 ReplacePlainString(DICOM_TAG_HIGH_BIT, "15"); |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1133 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1134 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1135 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1136 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1137 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1138 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1139 |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1140 assert(bytesPerPixel != 0); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1141 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1142 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1143 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1144 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1145 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1146 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1147 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1148 Uint8* target = NULL; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1149 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1150 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1151 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
|
1152 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1153 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1154 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1155 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1156 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1157 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1158 case PixelFormat_SignedGrayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1159 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1160 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
|
1161 target += pitch; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1162 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1163 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1164 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1165 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1166 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1167 // 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
|
1168 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
|
1169 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:
799
diff
changeset
|
1170 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1171 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1172 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1173 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1174 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1175 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1176 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1177 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1178 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1179 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1180 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1181 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1182 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1183 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1184 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
|
1185 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1186 throw OrthancException(ErrorCode_InternalError); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1187 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1188 } |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1189 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1190 |
|
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1191 Encoding ParsedDicomFile::GetEncoding() const |
|
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1192 { |
|
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1193 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset(), |
|
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1924
diff
changeset
|
1194 Configuration::GetDefaultEncoding()); |
|
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1195 } |
|
1090
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1196 |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1197 |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1198 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1199 { |
|
1558
124de28b32ed
fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1556
diff
changeset
|
1200 if (encoding == Encoding_Windows1251) |
|
1090
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1201 { |
|
1558
124de28b32ed
fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1556
diff
changeset
|
1202 // This Cyrillic codepage is not officially supported by the |
|
124de28b32ed
fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1556
diff
changeset
|
1203 // DICOM standard. Do not set the SpecificCharacterSet tag. |
|
124de28b32ed
fix encodings of newly created dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1556
diff
changeset
|
1204 return; |
|
1090
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1205 } |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1206 |
|
1565
4b23310eb7e8
add tags per instances in a series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1564
diff
changeset
|
1207 std::string s = GetDicomSpecificCharacterSet(encoding); |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1208 ReplacePlainString(DICOM_TAG_SPECIFIC_CHARACTER_SET, s); |
|
1090
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1209 } |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1210 |
|
2128
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1211 void ParsedDicomFile::DatasetToJson(Json::Value& target, |
|
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1212 DicomToJsonFormat format, |
|
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1213 DicomToJsonFlags flags, |
|
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1214 unsigned int maxStringLength) |
|
1160
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1215 { |
| 2126 | 1216 FromDcmtkBridge::ExtractDicomAsJson(target, *pimpl_->file_->getDataset(), |
| 2131 | 1217 format, flags, maxStringLength, Configuration::GetDefaultEncoding()); |
|
1160
80671157d051
generalization of create-dicom
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1113
diff
changeset
|
1218 } |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1219 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1220 |
|
2128
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1221 void ParsedDicomFile::DatasetToJson(Json::Value& target) |
|
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1222 { |
| 2131 | 1223 Configuration::ExtractDicomAsJson(target, *pimpl_->file_->getDataset()); |
|
2128
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1224 } |
|
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1225 |
|
9329ba17a069
Possibility to DELETE "dicom-as-json" attachments to reconstruct them
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2126
diff
changeset
|
1226 |
|
1831
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1227 void ParsedDicomFile::HeaderToJson(Json::Value& target, |
|
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1228 DicomToJsonFormat format) |
|
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1229 { |
| 2126 | 1230 FromDcmtkBridge::ExtractHeaderAsJson(target, *pimpl_->file_->getMetaInfo(), format, DicomToJsonFlags_None, 0); |
|
1831
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1231 } |
|
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1232 |
|
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1827
diff
changeset
|
1233 |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1234 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1235 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1236 DcmTag key(tag.GetGroup(), tag.GetElement()); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1237 return pimpl_->file_->getDataset()->tagExists(key); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1238 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1239 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1240 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1241 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1242 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1243 if (pdf.size() < 5 || // (*) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1244 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1245 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1246 LOG(ERROR) << "Not a PDF file"; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1247 throw OrthancException(ErrorCode_BadFileFormat); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1248 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1249 |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1250 InvalidateCache(); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1251 |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1252 ReplacePlainString(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1253 ReplacePlainString(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1254 ReplacePlainString(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1255 ReplacePlainString(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
|
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1256 //ReplacePlainString(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1257 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1258 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1259 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1260 size_t s = pdf.size(); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1261 if (s & 1) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1262 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1263 // The size of the buffer must be even |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1264 s += 1; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1265 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1266 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1267 Uint8* bytes = NULL; |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1268 OFCondition result = element->createUint8Array(s, bytes); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
|
1269 if (!result.good() || bytes == NULL) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1270 { |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1271 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1272 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1273 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1274 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1275 bytes[s - 1] = 0; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1276 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1277 memcpy(bytes, pdf.c_str(), pdf.size()); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1278 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1279 DcmPolymorphOBOW* obj = element.release(); |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1280 result = pimpl_->file_->getDataset()->insert(obj); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1281 |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1282 if (!result.good()) |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1283 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1284 delete obj; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
1285 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1286 } |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1287 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1288 |
|
1556
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1289 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1290 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1291 { |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1292 std::string sop, mime; |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1293 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1294 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1295 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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parents:
1555
diff
changeset
|
1296 sop != UID_EncapsulatedPDFStorage || |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1297 mime != "application/pdf") |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1298 { |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1299 return false; |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1300 } |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1301 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1302 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1303 { |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1304 return false; |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1305 } |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1306 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1307 // Strip the possible pad byte at the end of file, because the |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1308 // encapsulated documents must always have an even length. The PDF |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1309 // format expects files to end with %%EOF followed by CR/LF. If |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1310 // the last character of the file is not a CR or LF, we assume it |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1311 // is a pad byte and remove it. |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1312 if (pdf.size() > 0) |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1313 { |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1314 char last = *pdf.rbegin(); |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1315 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1316 if (last != 10 && last != 13) |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1317 { |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1318 pdf.resize(pdf.size() - 1); |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1319 } |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1320 } |
|
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changeset
|
1321 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1322 return true; |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1323 } |
|
1662
09be34b2f30e
ParsedDicomFile::Convert()
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changeset
|
1324 |
|
09be34b2f30e
ParsedDicomFile::Convert()
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changeset
|
1325 |
|
1818
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ParsedDicomFile::CreateFromJson
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changeset
|
1326 ParsedDicomFile* ParsedDicomFile::CreateFromJson(const Json::Value& json, |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1327 DicomFromJsonFlags flags) |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1328 { |
| 2028 | 1329 const bool generateIdentifiers = (flags & DicomFromJsonFlags_GenerateIdentifiers) ? true : false; |
| 1330 const bool decodeDataUriScheme = (flags & DicomFromJsonFlags_DecodeDataUriScheme) ? true : false; | |
|
1818
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ParsedDicomFile::CreateFromJson
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|
1331 |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1332 std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(generateIdentifiers)); |
|
1934
72a2fd7fed8b
FromDcmtkBridge::FromJson
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1333 result->SetEncoding(FromDcmtkBridge::ExtractEncoding(json, Configuration::GetDefaultEncoding())); |
|
1818
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1334 |
|
1934
72a2fd7fed8b
FromDcmtkBridge::FromJson
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1929
diff
changeset
|
1335 const Json::Value::Members tags = json.getMemberNames(); |
|
72a2fd7fed8b
FromDcmtkBridge::FromJson
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1336 |
|
1818
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1337 for (size_t i = 0; i < tags.size(); i++) |
|
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1338 { |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1339 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1340 const Json::Value& value = json[tags[i]]; |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1341 |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1342 if (tag == DICOM_TAG_PIXEL_DATA || |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1343 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1344 { |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1345 if (value.type() != Json::stringValue) |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1346 { |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1347 throw OrthancException(ErrorCode_BadRequest); |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1348 } |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1349 else |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1350 { |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1351 result->EmbedContent(value.asString()); |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1352 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1353 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1354 else if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1355 { |
|
1982
b5d4f9c156ad
Modification of instances can now replace PixelData
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1981
diff
changeset
|
1356 result->Replace(tag, value, decodeDataUriScheme, DicomReplaceMode_InsertIfAbsent); |
|
1818
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1357 } |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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changeset
|
1358 } |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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diff
changeset
|
1359 |
|
1065401501fb
ParsedDicomFile::CreateFromJson
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1360 return result.release(); |
|
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ParsedDicomFile::CreateFromJson
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diff
changeset
|
1361 } |
|
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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1913
diff
changeset
|
1362 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1363 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1364 void ParsedDicomFile::GetRawFrame(std::string& target, |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1365 std::string& mime, |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
1913
diff
changeset
|
1366 unsigned int frameId) |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1367 { |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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parents:
1913
diff
changeset
|
1368 if (pimpl_->frameIndex_.get() == NULL) |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1369 { |
| 1956 | 1370 pimpl_->frameIndex_.reset(new DicomFrameIndex(*pimpl_->file_)); |
|
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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1371 } |
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1372 |
|
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|
1373 pimpl_->frameIndex_->GetRawFrame(target, frameId); |
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1374 |
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1375 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); |
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1376 switch (transferSyntax) |
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1377 { |
|
1946
40b7a0176305
fix compilation against DCMTK 3.6.1
Sebastien Jodogne <s.jodogne@gmail.com>
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1945
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1378 case EXS_JPEGProcess1: |
|
1924
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1379 mime = "image/jpeg"; |
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1380 break; |
|
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1381 |
|
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1382 case EXS_JPEG2000LosslessOnly: |
|
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1383 case EXS_JPEG2000: |
|
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1384 mime = "image/jp2"; |
| 2016 | 1385 break; |
|
1924
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1386 |
|
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diff
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|
1387 default: |
|
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1388 mime = "application/octet-stream"; |
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1389 break; |
|
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|
1390 } |
|
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1391 } |
|
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1392 |
|
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1393 |
|
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1394 void ParsedDicomFile::InvalidateCache() |
|
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1395 { |
|
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|
1396 pimpl_->frameIndex_.reset(NULL); |
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1397 } |
|
1950
533ff46e944b
return a single raw frame from DICOM videos
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1946
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1398 |
|
533ff46e944b
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1399 |
|
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1400 unsigned int ParsedDicomFile::GetFramesCount() const |
|
533ff46e944b
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1401 { |
| 1956 | 1402 return DicomFrameIndex::GetFramesCount(*pimpl_->file_); |
|
1950
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1403 } |
|
2207
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1404 |
|
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1405 |
|
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1406 void ParsedDicomFile::ChangeEncoding(Encoding target) |
|
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1407 { |
|
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|
1408 Encoding source = GetEncoding(); |
|
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|
1409 |
|
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|
1410 if (source != target) // Avoid unnecessary conversion |
|
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|
1411 { |
|
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1412 ReplacePlainString(DICOM_TAG_SPECIFIC_CHARACTER_SET, GetDicomSpecificCharacterSet(target)); |
|
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diff
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|
1413 FromDcmtkBridge::ChangeStringEncoding(*pimpl_->file_->getDataset(), source, target); |
|
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1414 } |
|
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1415 } |
|
2209
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diff
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1416 |
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1417 |
|
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|
1418 void ParsedDicomFile::ExtractDicomSummary(DicomMap& target) const |
|
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1419 { |
|
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|
1420 Configuration::ExtractDicomSummary(target, *pimpl_->file_->getDataset()); |
|
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1421 } |
|
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1422 |
|
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1423 |
|
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|
1424 void ParsedDicomFile::ExtractDicomAsJson(Json::Value& target) const |
|
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1425 { |
|
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|
1426 Configuration::ExtractDicomAsJson(target, *pimpl_->file_->getDataset()); |
|
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1427 } |
|
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|
1428 |
|
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|
1429 |
|
e3fd5bc429a2
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diff
changeset
|
1430 bool ParsedDicomFile::LookupTransferSyntax(std::string& result) |
|
e3fd5bc429a2
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|
1431 { |
|
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changeset
|
1432 return FromDcmtkBridge::LookupTransferSyntax(result, *pimpl_->file_); |
|
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|
1433 } |
|
2281
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|
1434 |
|
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|
1435 |
|
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Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1436 bool ParsedDicomFile::LookupPhotometricInterpretation(PhotometricInterpretation& result) const |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1437 { |
|
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Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1438 DcmTagKey k(DICOM_TAG_PHOTOMETRIC_INTERPRETATION.GetGroup(), |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1439 DICOM_TAG_PHOTOMETRIC_INTERPRETATION.GetElement()); |
|
e002430baa41
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|
1440 |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1441 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1442 |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1443 const char *c = NULL; |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1444 if (dataset.findAndGetString(k, c).good() && |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1445 c != NULL) |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1446 { |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1447 result = StringToPhotometricInterpretation(c); |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1448 return true; |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1449 } |
|
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Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1450 else |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1451 { |
|
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Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1452 return false; |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1453 } |
|
e002430baa41
Fix issue #44 (Bad interpretation of photometric interpretation MONOCHROME1)
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|
1454 } |
| 790 | 1455 } |