Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1941:d7b176f7dd1b
test dicom patterns
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 25 Mar 2016 11:27:38 +0100 |
| parents | e251606c1433 |
| children | 76ff6eecf07f |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
|
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4 * Department, University Hospital of Liege, Belgium |
| 790 | 5 * |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 | |
| 34 /*========================================================================= | |
| 35 | |
| 36 This file is based on portions of the following project: | |
| 37 | |
| 38 Program: GDCM (Grassroots DICOM). A DICOM library | |
| 39 Module: http://gdcm.sourceforge.net/Copyright.html | |
| 40 | |
| 41 Copyright (c) 2006-2011 Mathieu Malaterre | |
| 42 Copyright (c) 1993-2005 CREATIS | |
| 43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
| 44 All rights reserved. | |
| 45 | |
| 46 Redistribution and use in source and binary forms, with or without | |
| 47 modification, are permitted provided that the following conditions are met: | |
| 48 | |
| 49 * Redistributions of source code must retain the above copyright notice, | |
| 50 this list of conditions and the following disclaimer. | |
| 51 | |
| 52 * Redistributions in binary form must reproduce the above copyright notice, | |
| 53 this list of conditions and the following disclaimer in the documentation | |
| 54 and/or other materials provided with the distribution. | |
| 55 | |
| 56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
| 57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
| 58 endorse or promote products derived from this software without specific | |
| 59 prior written permission. | |
| 60 | |
| 61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
| 62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| 63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
| 65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
| 66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
| 67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
| 68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
| 69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| 70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 71 | |
| 72 =========================================================================*/ | |
| 73 | |
| 74 | |
|
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pch for unit tests and server
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75 #include "PrecompiledHeadersServer.h" |
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76 |
| 790 | 77 #ifndef NOMINMAX |
| 78 #define NOMINMAX | |
| 79 #endif | |
| 80 | |
| 81 #include "ParsedDicomFile.h" | |
| 82 | |
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83 #include "OrthancInitialization.h" |
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84 #include "ServerToolbox.h" |
| 790 | 85 #include "FromDcmtkBridge.h" |
| 86 #include "ToDcmtkBridge.h" | |
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87 #include "Internals/DicomFrameIndex.h" |
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88 #include "../Core/Images/JpegReader.h" |
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89 #include "../Core/Images/PngReader.h" |
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90 #include "../Core/Logging.h" |
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91 #include "../Core/OrthancException.h" |
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92 #include "../Core/Toolbox.h" |
| 790 | 93 #include "../Core/Uuid.h" |
| 94 | |
| 95 #include <list> | |
| 96 #include <limits> | |
| 97 | |
| 98 #include <boost/lexical_cast.hpp> | |
| 99 | |
| 100 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 101 #include <dcmtk/dcmdata/dcdicent.h> | |
| 102 #include <dcmtk/dcmdata/dcdict.h> | |
| 103 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 104 #include <dcmtk/dcmdata/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 | |
| 139 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 140 | |
| 141 | |
| 142 | |
| 143 namespace Orthanc | |
| 144 { | |
| 794 | 145 struct ParsedDicomFile::PImpl |
| 146 { | |
| 147 std::auto_ptr<DcmFileFormat> file_; | |
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148 std::auto_ptr<DicomFrameIndex> frameIndex_; |
| 794 | 149 }; |
| 150 | |
| 151 | |
| 790 | 152 static void SendPathValueForDictionary(RestApiOutput& output, |
| 153 DcmItem& dicom) | |
| 154 { | |
| 155 Json::Value v = Json::arrayValue; | |
| 156 | |
| 157 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 158 { | |
| 159 DcmElement* element = dicom.getElement(i); | |
| 160 if (element) | |
| 161 { | |
| 162 char buf[16]; | |
| 163 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 164 v.append(buf); | |
| 165 } | |
| 166 } | |
| 167 | |
| 168 output.AnswerJson(v); | |
| 169 } | |
| 170 | |
| 171 static inline uint16_t GetCharValue(char c) | |
| 172 { | |
| 173 if (c >= '0' && c <= '9') | |
| 174 return c - '0'; | |
| 175 else if (c >= 'a' && c <= 'f') | |
| 176 return c - 'a' + 10; | |
| 177 else if (c >= 'A' && c <= 'F') | |
| 178 return c - 'A' + 10; | |
| 179 else | |
| 180 return 0; | |
| 181 } | |
| 182 | |
| 183 static inline uint16_t GetTagValue(const char* c) | |
| 184 { | |
| 185 return ((GetCharValue(c[0]) << 12) + | |
| 186 (GetCharValue(c[1]) << 8) + | |
| 187 (GetCharValue(c[2]) << 4) + | |
| 188 GetCharValue(c[3])); | |
| 189 } | |
| 190 | |
| 191 static void ParseTagAndGroup(DcmTagKey& key, | |
| 192 const std::string& tag) | |
| 193 { | |
| 194 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 195 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 196 } | |
| 197 | |
| 198 | |
| 199 static void SendSequence(RestApiOutput& output, | |
| 200 DcmSequenceOfItems& sequence) | |
| 201 { | |
| 202 // This element is a sequence | |
| 203 Json::Value v = Json::arrayValue; | |
| 204 | |
| 205 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 206 { | |
| 207 v.append(boost::lexical_cast<std::string>(i)); | |
| 208 } | |
| 209 | |
| 210 output.AnswerJson(v); | |
| 211 } | |
| 212 | |
| 213 | |
| 214 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 215 E_TransferSyntax transferSyntax) | |
| 216 { | |
| 217 DcmPixelSequence* pixelSequence = NULL; | |
| 218 if (pixelData.getEncapsulatedRepresentation | |
| 219 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 220 { | |
| 221 return pixelSequence->card(); | |
| 222 } | |
| 223 else | |
| 224 { | |
| 225 return 1; | |
| 226 } | |
| 227 } | |
| 228 | |
| 229 | |
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230 namespace |
| 790 | 231 { |
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232 class DicomFieldStream : public IHttpStreamAnswer |
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233 { |
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234 private: |
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235 DcmElement& element_; |
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236 uint32_t length_; |
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237 uint32_t offset_; |
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238 std::string chunk_; |
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239 size_t chunkSize_; |
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240 |
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241 public: |
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242 DicomFieldStream(DcmElement& element, |
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243 E_TransferSyntax transferSyntax) : |
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244 element_(element), |
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245 length_(element.getLength(transferSyntax)), |
| 1616 | 246 offset_(0), |
| 247 chunkSize_(0) | |
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248 { |
| 1521 | 249 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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250 chunk_.resize(CHUNK_SIZE); |
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251 } |
| 790 | 252 |
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253 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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254 bool /*deflateAllowed*/) |
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255 { |
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256 // No support for compression |
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257 return HttpCompression_None; |
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258 } |
| 790 | 259 |
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260 virtual bool HasContentFilename(std::string& filename) |
| 790 | 261 { |
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262 return false; |
| 790 | 263 } |
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264 |
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265 virtual std::string GetContentType() |
| 790 | 266 { |
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267 return ""; |
| 790 | 268 } |
| 269 | |
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270 virtual uint64_t GetContentLength() |
| 790 | 271 { |
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272 return length_; |
| 790 | 273 } |
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274 |
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275 virtual bool ReadNextChunk() |
| 790 | 276 { |
| 1520 | 277 assert(offset_ <= length_); |
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278 |
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279 if (offset_ == length_) |
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280 { |
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281 return false; |
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282 } |
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283 else |
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284 { |
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285 if (length_ - offset_ < chunk_.size()) |
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286 { |
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287 chunkSize_ = length_ - offset_; |
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288 } |
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289 else |
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290 { |
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291 chunkSize_ = chunk_.size(); |
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292 } |
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294 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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295 |
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296 offset_ += chunkSize_; |
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297 |
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298 if (!cond.good()) |
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299 { |
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300 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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301 throw OrthancException(ErrorCode_InternalError); |
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302 } |
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303 |
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304 return true; |
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305 } |
| 790 | 306 } |
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307 |
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308 virtual const char *GetChunkContent() |
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309 { |
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310 return chunk_.c_str(); |
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311 } |
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312 |
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313 virtual size_t GetChunkSize() |
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314 { |
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315 return chunkSize_; |
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316 } |
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317 }; |
| 790 | 318 } |
| 319 | |
| 320 | |
| 321 static bool AnswerPixelData(RestApiOutput& output, | |
| 322 DcmItem& dicom, | |
| 323 E_TransferSyntax transferSyntax, | |
| 324 const std::string* blockUri) | |
| 325 { | |
| 326 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 327 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 328 | |
| 329 DcmElement *element = NULL; | |
| 330 if (!dicom.findAndGetElement(k, element).good() || | |
| 331 element == NULL) | |
| 332 { | |
| 333 return false; | |
| 334 } | |
| 335 | |
| 336 try | |
| 337 { | |
| 338 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 339 if (blockUri == NULL) | |
| 340 { | |
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341 // The user asks how many blocks are present in this pixel data |
| 790 | 342 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); |
| 343 | |
| 344 Json::Value result(Json::arrayValue); | |
| 345 for (unsigned int i = 0; i < blocks; i++) | |
| 346 { | |
| 347 result.append(boost::lexical_cast<std::string>(i)); | |
| 348 } | |
| 349 | |
| 350 output.AnswerJson(result); | |
| 351 return true; | |
| 352 } | |
| 353 | |
| 354 | |
| 355 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 356 | |
| 357 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 358 { | |
| 359 DcmPixelSequence* pixelSequence = NULL; | |
| 360 if (pixelData.getEncapsulatedRepresentation | |
| 361 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 362 { | |
| 363 // This is the case for JPEG transfer syntaxes | |
| 364 if (block < pixelSequence->card()) | |
| 365 { | |
| 366 DcmPixelItem* pixelItem = NULL; | |
| 367 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 368 { | |
| 369 if (pixelItem->getLength() == 0) | |
| 370 { | |
| 371 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 372 return true; | |
| 373 } | |
| 374 | |
| 375 Uint8* buffer = NULL; | |
| 376 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 377 { | |
| 378 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 379 return true; | |
| 380 } | |
| 381 } | |
| 382 } | |
| 383 } | |
| 384 else | |
| 385 { | |
| 386 // This is the case for raw, uncompressed image buffers | |
| 387 assert(*blockUri == "0"); | |
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388 DicomFieldStream stream(*element, transferSyntax); |
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389 output.AnswerStream(stream); |
| 790 | 390 } |
| 391 } | |
| 392 } | |
| 393 catch (boost::bad_lexical_cast&) | |
| 394 { | |
| 395 // The URI entered by the user is not a number | |
| 396 } | |
| 397 catch (std::bad_cast&) | |
| 398 { | |
| 399 // This should never happen | |
| 400 } | |
| 401 | |
| 402 return false; | |
| 403 } | |
| 404 | |
| 405 | |
| 406 | |
| 407 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 408 const std::string& tag, | |
| 409 DcmItem& dicom, | |
| 410 E_TransferSyntax transferSyntax) | |
| 411 { | |
| 412 DcmTagKey k; | |
| 413 ParseTagAndGroup(k, tag); | |
| 414 | |
| 415 DcmSequenceOfItems* sequence = NULL; | |
| 416 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 417 sequence != NULL && | |
| 418 sequence->getVR() == EVR_SQ) | |
| 419 { | |
| 420 SendSequence(output, *sequence); | |
| 421 return; | |
| 422 } | |
| 423 | |
| 424 DcmElement* element = NULL; | |
| 425 if (dicom.findAndGetElement(k, element).good() && | |
| 426 element != NULL && | |
| 427 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 428 element->getVR() != EVR_SQ) | |
| 429 { | |
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430 DicomFieldStream stream(*element, transferSyntax); |
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431 output.AnswerStream(stream); |
| 790 | 432 } |
| 433 } | |
| 434 | |
| 435 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 436 const UriComponents& uri) | |
| 437 { | |
| 794 | 438 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 439 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 440 |
| 441 // Special case: Accessing the pixel data | |
| 442 if (uri.size() == 1 || | |
| 443 uri.size() == 2) | |
| 444 { | |
| 445 DcmTagKey tag; | |
| 446 ParseTagAndGroup(tag, uri[0]); | |
| 447 | |
| 448 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 449 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 450 { | |
| 451 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 452 return; | |
| 453 } | |
| 454 } | |
| 455 | |
| 456 // Go down in the tag hierarchy according to the URI | |
| 457 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 458 { | |
| 459 size_t index; | |
| 460 try | |
| 461 { | |
| 462 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 463 } | |
| 464 catch (boost::bad_lexical_cast&) | |
| 465 { | |
| 466 return; | |
| 467 } | |
| 468 | |
| 469 DcmTagKey k; | |
| 470 DcmItem *child = NULL; | |
| 471 ParseTagAndGroup(k, uri[2 * pos]); | |
| 472 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 473 child == NULL) | |
| 474 { | |
| 475 return; | |
| 476 } | |
| 477 | |
| 478 dicom = child; | |
| 479 } | |
| 480 | |
| 481 // We have reached the end of the URI | |
| 482 if (uri.size() % 2 == 0) | |
| 483 { | |
| 484 SendPathValueForDictionary(output, *dicom); | |
| 485 } | |
| 486 else | |
| 487 { | |
| 488 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 489 } | |
| 490 } | |
| 491 | |
| 492 | |
| 493 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 494 { | |
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495 InvalidateCache(); |
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496 |
| 790 | 497 DcmTagKey key(tag.GetGroup(), tag.GetElement()); |
| 794 | 498 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 499 if (element != NULL) |
| 500 { | |
| 501 delete element; | |
| 502 } | |
| 503 } | |
| 504 | |
| 505 | |
| 506 | |
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507 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 508 { |
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509 InvalidateCache(); |
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510 |
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511 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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512 |
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513 // Loop over the dataset to detect its private tags |
| 790 | 514 typedef std::list<DcmElement*> Tags; |
| 515 Tags privateTags; | |
| 516 | |
| 517 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 518 { | |
| 519 DcmElement* element = dataset.getElement(i); | |
| 520 DcmTag tag(element->getTag()); | |
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521 |
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522 // Is this a private tag? |
| 1694 | 523 if (tag.isPrivate()) |
| 790 | 524 { |
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525 bool remove = true; |
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526 |
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527 // Check whether this private tag is to be kept |
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528 if (toKeep != NULL) |
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529 { |
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530 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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531 if (toKeep->find(tmp) != toKeep->end()) |
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532 { |
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533 remove = false; // Keep it |
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534 } |
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535 } |
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536 |
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537 if (remove) |
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538 { |
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539 privateTags.push_back(element); |
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540 } |
| 790 | 541 } |
| 542 } | |
| 543 | |
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544 // Loop over the detected private tags to remove them |
| 790 | 545 for (Tags::iterator it = privateTags.begin(); |
| 546 it != privateTags.end(); ++it) | |
| 547 { | |
| 548 DcmElement* tmp = dataset.remove(*it); | |
| 549 if (tmp != NULL) | |
| 550 { | |
| 551 delete tmp; | |
| 552 } | |
| 553 } | |
| 554 } | |
| 555 | |
| 556 | |
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557 static void InsertInternal(DcmDataset& dicom, |
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558 DcmElement* element) |
| 790 | 559 { |
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560 OFCondition cond = dicom.insert(element, false, false); |
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561 if (!cond.good()) |
| 790 | 562 { |
| 563 // This field already exists | |
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564 delete element; |
| 790 | 565 throw OrthancException(ErrorCode_InternalError); |
| 566 } | |
| 567 } | |
| 568 | |
| 569 | |
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570 void ParsedDicomFile::Insert(const DicomTag& tag, |
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571 const Json::Value& value, |
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572 bool decodeDataUriScheme) |
| 790 | 573 { |
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574 InvalidateCache(); |
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575 |
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576 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
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577 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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578 } |
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579 |
| 790 | 580 |
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581 static void ReplaceInternal(DcmDataset& dicom, |
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582 std::auto_ptr<DcmElement>& element, |
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583 DicomReplaceMode mode) |
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584 { |
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585 const DcmTagKey& tag = element->getTag(); |
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586 |
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587 if (!dicom.findAndDeleteElement(tag).good()) |
| 790 | 588 { |
| 589 // This field does not exist, act wrt. the specified "mode" | |
| 590 switch (mode) | |
| 591 { | |
| 592 case DicomReplaceMode_InsertIfAbsent: | |
| 593 break; | |
| 594 | |
| 595 case DicomReplaceMode_ThrowIfAbsent: | |
| 596 throw OrthancException(ErrorCode_InexistentItem); | |
| 597 | |
| 598 case DicomReplaceMode_IgnoreIfAbsent: | |
| 599 return; | |
| 600 } | |
| 601 } | |
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602 |
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603 // Either the tag was not existing, or the replace mode was set to |
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604 // "InsertIfAbsent" |
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605 InsertInternal(dicom, element.release()); |
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606 } |
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607 |
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608 |
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609 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
| 1695 | 610 const std::string& utf8Value, |
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611 bool decodeDataUriScheme) |
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612 { |
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613 if (tag != DICOM_TAG_SOP_CLASS_UID && |
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614 tag != DICOM_TAG_SOP_INSTANCE_UID) |
| 790 | 615 { |
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616 return; |
| 790 | 617 } |
| 618 | |
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619 std::string binary; |
| 1695 | 620 const std::string* decoded = &utf8Value; |
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621 |
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622 if (decodeDataUriScheme && |
| 1695 | 623 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
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624 { |
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625 std::string mime; |
| 1695 | 626 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value); |
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627 decoded = &binary; |
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628 } |
| 1695 | 629 else |
| 630 { | |
| 631 Encoding encoding = GetEncoding(); | |
| 632 if (GetEncoding() != Encoding_Utf8) | |
| 633 { | |
| 634 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
| 635 decoded = &binary; | |
| 636 } | |
| 637 } | |
| 790 | 638 |
| 639 /** | |
| 640 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 641 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 642 * you make changes to the related tags in the dataset ('SOP Class | |
| 643 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 644 * options. You can disable this behaviour by using the -nmu | |
| 645 * option. | |
| 646 **/ | |
| 647 | |
| 648 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 649 { | |
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650 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
| 790 | 651 } |
| 652 | |
| 653 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 654 { | |
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655 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
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656 } |
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657 } |
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658 |
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659 |
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660 void ParsedDicomFile::Replace(const DicomTag& tag, |
| 1695 | 661 const std::string& utf8Value, |
|
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662 DicomReplaceMode mode) |
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663 { |
|
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664 InvalidateCache(); |
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665 |
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666 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
| 1695 | 667 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, false, GetEncoding()); |
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668 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
| 1695 | 669 UpdateStorageUid(tag, utf8Value, false); |
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670 } |
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671 |
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672 |
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673 void ParsedDicomFile::Replace(const DicomTag& tag, |
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674 const Json::Value& value, |
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675 bool decodeDataUriScheme, |
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676 DicomReplaceMode mode) |
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677 { |
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678 InvalidateCache(); |
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679 |
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680 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, GetEncoding())); |
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681 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
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682 |
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683 if (tag == DICOM_TAG_SOP_CLASS_UID || |
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684 tag == DICOM_TAG_SOP_INSTANCE_UID) |
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685 { |
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686 if (value.type() != Json::stringValue) |
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687 { |
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688 throw OrthancException(ErrorCode_BadParameterType); |
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689 } |
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690 |
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691 UpdateStorageUid(tag, value.asString(), decodeDataUriScheme); |
| 790 | 692 } |
| 693 } | |
| 694 | |
| 695 | |
| 696 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 697 { | |
| 698 std::string serialized; | |
|
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699 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 700 { |
| 701 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 702 } | |
| 703 } | |
| 704 | |
| 705 | |
| 706 | |
| 707 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 708 const DicomTag& tag) | |
| 709 { | |
| 710 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 711 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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712 |
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713 if (tag.IsPrivate() || |
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714 FromDcmtkBridge::IsUnknownTag(tag) || |
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715 tag == DICOM_TAG_PIXEL_DATA || |
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716 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 717 { |
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718 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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|
719 long unsigned int count = 0; |
| 790 | 720 |
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721 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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722 { |
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723 if (count > 0) |
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724 { |
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725 assert(data != NULL); |
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726 value.assign(reinterpret_cast<const char*>(data), count); |
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727 } |
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728 else |
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729 { |
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730 value.clear(); |
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731 } |
| 790 | 732 |
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733 return true; |
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734 } |
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735 else |
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736 { |
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737 return false; |
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738 } |
| 790 | 739 } |
| 740 else | |
| 741 { | |
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742 DcmElement* element = NULL; |
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743 if (!dataset.findAndGetElement(k, element).good() || |
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744 element == NULL) |
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745 { |
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746 return false; |
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747 } |
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748 |
|
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749 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
|
1929
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750 (*element, DicomToJsonFlags_Default, |
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751 ORTHANC_MAXIMUM_TAG_LENGTH, GetEncoding())); |
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752 |
|
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753 if (v.get() == NULL || |
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754 v->IsNull()) |
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|
755 { |
|
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Fix replacement and insertion of private DICOM tags
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changeset
|
756 value = ""; |
|
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Fix replacement and insertion of private DICOM tags
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parents:
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changeset
|
757 } |
|
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Fix replacement and insertion of private DICOM tags
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changeset
|
758 else |
|
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Fix replacement and insertion of private DICOM tags
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diff
changeset
|
759 { |
|
1737
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removal of DicomStringValue and DicomNullValue
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diff
changeset
|
760 // TODO v->IsBinary() |
|
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|
761 value = v->GetContent(); |
|
1307
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|
762 } |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
763 |
|
1307
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Fix replacement and insertion of private DICOM tags
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diff
changeset
|
764 return true; |
| 790 | 765 } |
| 766 } | |
| 767 | |
| 768 | |
| 769 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 770 { | |
| 771 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 772 | |
| 773 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 774 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 775 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 776 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 777 { | |
| 778 throw OrthancException(ErrorCode_BadFileFormat); | |
| 779 } | |
| 780 | |
| 781 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 782 } | |
| 783 | |
| 784 | |
| 785 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 786 { | |
|
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
787 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 788 } |
| 789 | |
| 790 | |
| 791 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 792 { | |
| 793 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 794 std::string content; | |
| 795 SaveToMemoryBuffer(content); | |
| 796 Toolbox::WriteFile(content, path); | |
| 797 } | |
| 798 | |
| 799 | |
|
1805
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diff
changeset
|
800 ParsedDicomFile::ParsedDicomFile(bool createIdentifiers) : pimpl_(new PImpl) |
| 790 | 801 { |
| 794 | 802 pimpl_->file_.reset(new DcmFileFormat); |
|
1805
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diff
changeset
|
803 |
|
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diff
changeset
|
804 if (createIdentifiers) |
|
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c-find scu for modality worklists
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diff
changeset
|
805 { |
|
f08978b1f45b
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diff
changeset
|
806 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
|
f08978b1f45b
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diff
changeset
|
807 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); |
|
f08978b1f45b
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parents:
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diff
changeset
|
808 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); |
|
f08978b1f45b
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diff
changeset
|
809 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
|
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diff
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|
810 } |
| 790 | 811 } |
| 812 | |
| 791 | 813 |
|
1787
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parents:
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diff
changeset
|
814 ParsedDicomFile::ParsedDicomFile(const DicomMap& map) : pimpl_(new PImpl) |
|
1786
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primitives to handle dicom worklists
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parents:
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diff
changeset
|
815 { |
|
1787
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refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
816 std::auto_ptr<DcmDataset> dataset(ToDcmtkBridge::Convert(map)); |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
817 |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
818 // NOTE: This implies an unnecessary memory copy of the dataset, but no way to get around |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
819 // http://support.dcmtk.org/redmine/issues/544 |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
820 std::auto_ptr<DcmFileFormat> fileFormat(new DcmFileFormat(dataset.get())); |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
821 |
|
1b1d5470233f
refactoring of DicomFindAnswers
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parents:
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diff
changeset
|
822 pimpl_->file_.reset(fileFormat.release()); |
|
1786
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primitives to handle dicom worklists
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parents:
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diff
changeset
|
823 } |
|
164d78911382
primitives to handle dicom worklists
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parents:
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diff
changeset
|
824 |
|
164d78911382
primitives to handle dicom worklists
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1781
diff
changeset
|
825 |
|
1800
30e97a1f4093
callback for handling worklists with plugins
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parents:
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diff
changeset
|
826 ParsedDicomFile::ParsedDicomFile(const void* content, |
|
30e97a1f4093
callback for handling worklists with plugins
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parents:
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diff
changeset
|
827 size_t size) : pimpl_(new PImpl) |
| 791 | 828 { |
|
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
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parents:
1934
diff
changeset
|
829 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(content, size)); |
| 791 | 830 } |
| 831 | |
| 794 | 832 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 833 { |
| 834 if (content.size() == 0) | |
| 835 { | |
|
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
836 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(NULL, 0)); |
| 791 | 837 } |
| 838 else | |
| 839 { | |
|
1935
e251606c1433
FromDcmtkBridge::LoadFromMemoryBuffer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1934
diff
changeset
|
840 pimpl_->file_.reset(FromDcmtkBridge::LoadFromMemoryBuffer(&content[0], content.size())); |
| 791 | 841 } |
| 842 } | |
| 792 | 843 |
| 844 | |
| 794 | 845 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 846 pimpl_(new PImpl) | |
| 792 | 847 { |
| 794 | 848 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
|
849 |
|
1564
1b7def486e62
creation of DICOM series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
850 // Create a new instance-level identifier |
|
1b7def486e62
creation of DICOM series
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parents:
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diff
changeset
|
851 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 852 } |
| 853 | |
| 854 | |
|
1788
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
855 ParsedDicomFile::ParsedDicomFile(DcmDataset& dicom) : pimpl_(new PImpl) |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
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diff
changeset
|
856 { |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
857 pimpl_->file_.reset(new DcmFileFormat(&dicom)); |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
858 } |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
859 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
860 |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
861 ParsedDicomFile::ParsedDicomFile(DcmFileFormat& dicom) : pimpl_(new PImpl) |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
862 { |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
863 pimpl_->file_.reset(new DcmFileFormat(dicom)); |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
864 } |
|
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
865 |
|
6a2d507ef064
getting rid of opaque data structures
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parents:
1787
diff
changeset
|
866 |
| 792 | 867 ParsedDicomFile::~ParsedDicomFile() |
| 868 { | |
| 794 | 869 delete pimpl_; |
| 792 | 870 } |
| 871 | |
| 793 | 872 |
|
1824
b530c3dfe2a6
refactoring image decoding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1818
diff
changeset
|
873 DcmFileFormat& ParsedDicomFile::GetDcmtkObject() const |
| 793 | 874 { |
|
1788
6a2d507ef064
getting rid of opaque data structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1787
diff
changeset
|
875 return *pimpl_->file_.get(); |
| 793 | 876 } |
| 877 | |
| 878 | |
| 879 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 880 { | |
| 794 | 881 return new ParsedDicomFile(*this); |
| 793 | 882 } |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
883 |
|
ecedd89055db
generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
884 |
| 1562 | 885 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
886 { |
|
1641
4e56b5a206b7
Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1616
diff
changeset
|
887 std::string mime, content; |
|
4e56b5a206b7
Support of binary tags encoded using data URI scheme
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1616
diff
changeset
|
888 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
| 1562 | 889 Toolbox::ToLowerCase(mime); |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
890 |
|
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
891 if (mime == "image/png" || |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
892 mime == "image/jpeg") |
| 1562 | 893 { |
| 894 EmbedImage(mime, content); | |
| 895 } | |
| 896 else if (mime == "application/pdf") | |
| 897 { | |
| 898 EmbedPdf(content); | |
| 899 } | |
| 900 else | |
| 901 { | |
|
1693
558b25228a23
creation of tag hierarchy from json
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1689
diff
changeset
|
902 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
| 1562 | 903 throw OrthancException(ErrorCode_NotImplemented); |
| 904 } | |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
905 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
906 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
907 |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
908 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
|
909 const std::string& content) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
910 { |
|
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
|
911 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
|
912 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
913 if (mime == "image/png") |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
914 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
915 PngReader reader; |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
916 reader.ReadFromMemory(content); |
|
800
ecedd89055db
generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
917 EmbedImage(reader); |
|
ecedd89055db
generation of DICOM images from PNG files
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parents:
799
diff
changeset
|
918 } |
|
1781
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
919 else if (mime == "image/jpeg") |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
920 { |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
921 JpegReader reader; |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
922 reader.ReadFromMemory(content); |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
923 EmbedImage(reader); |
|
5ad4e4d92ecb
AcceptMediaDispatcher bootstrap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1737
diff
changeset
|
924 } |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
925 else |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
926 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
927 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
928 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
929 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
930 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
931 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
932 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
933 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
934 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
935 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
936 accessor.GetFormat() != PixelFormat_SignedGrayscale16 && |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
937 accessor.GetFormat() != PixelFormat_RGB24 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
938 accessor.GetFormat() != PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
939 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
940 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
941 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
942 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
943 if (accessor.GetFormat() == PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
944 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
945 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
|
946 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
947 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
948 // 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
|
949 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
950 Remove(DICOM_TAG_PIXEL_DATA); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
951 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
952 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
953 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
954 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
955 |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
956 if (accessor.GetFormat() == PixelFormat_SignedGrayscale16) |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
957 { |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
958 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "1"); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
959 } |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
960 else |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
961 { |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
962 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
963 } |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
964 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
965 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
966 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
967 |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
968 unsigned int bytesPerPixel = 0; |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
969 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
970 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
971 { |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
972 case PixelFormat_Grayscale8: |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
973 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
974 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
975 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
976 bytesPerPixel = 1; |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
977 break; |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
978 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
979 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
980 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
981 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
982 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
983 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
984 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
985 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
986 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
987 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
988 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
989 case PixelFormat_Grayscale16: |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
990 case PixelFormat_SignedGrayscale16: |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
991 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
992 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
993 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
994 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
995 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
996 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
997 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
998 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
999 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1000 |
|
1941
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1001 assert(bytesPerPixel != 0); |
|
d7b176f7dd1b
test dicom patterns
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1935
diff
changeset
|
1002 |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1003 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
|
1004 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1005 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1006 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
|
1007 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1008 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1009 Uint8* target = NULL; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1010 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1011 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1012 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
|
1013 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1014 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1015 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1016 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1017 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1018 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1019 case PixelFormat_SignedGrayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1020 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1021 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
|
1022 target += pitch; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1023 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1024 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1025 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1026 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1027 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1028 // 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
|
1029 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
|
1030 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
|
1031 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1032 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1033 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1034 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1035 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1036 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1037 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1038 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1039 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1040 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1041 throw OrthancException(ErrorCode_NotImplemented); |
|
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1042 } |
|
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|
1043 } |
|
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|
1044 |
|
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diff
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|
1045 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
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generation of DICOM images from PNG files
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|
1046 { |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1047 throw OrthancException(ErrorCode_InternalError); |
|
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|
1048 } |
|
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generation of DICOM images from PNG files
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|
1049 } |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1050 |
|
87791ebc1f50
download matlab images
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diff
changeset
|
1051 |
|
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1052 Encoding ParsedDicomFile::GetEncoding() const |
|
2fd5a163776d
primitives for proper encoding handling
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diff
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|
1053 { |
|
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
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diff
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|
1054 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset(), |
|
84c7eaeb5244
Configuration::GetDefaultEncoding
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parents:
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diff
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|
1055 Configuration::GetDefaultEncoding()); |
|
956
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parents:
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diff
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|
1056 } |
|
1090
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1057 |
|
e494ceb8d763
support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1058 |
|
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support more encodings
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1059 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
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|
1060 { |
|
1558
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fix encodings of newly created dicom files
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|
1061 if (encoding == Encoding_Windows1251) |
|
1090
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1062 { |
|
1558
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|
1063 // This Cyrillic codepage is not officially supported by the |
|
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|
1064 // DICOM standard. Do not set the SpecificCharacterSet tag. |
|
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|
1065 return; |
|
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|
1066 } |
|
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diff
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|
1067 |
|
1565
4b23310eb7e8
add tags per instances in a series
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diff
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|
1068 std::string s = GetDicomSpecificCharacterSet(encoding); |
| 1091 | 1069 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
1090
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1070 } |
|
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|
1071 |
| 1686 | 1072 void ParsedDicomFile::ToJson(Json::Value& target, |
| 1073 DicomToJsonFormat format, | |
|
1735
a001f6226c7c
primitives for flags in dicom-to-json conversions
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diff
changeset
|
1074 DicomToJsonFlags flags, |
| 1686 | 1075 unsigned int maxStringLength) |
|
1160
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1076 { |
|
1928
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Configuration::GetDefaultEncoding
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diff
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|
1077 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), |
|
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Configuration::GetDefaultEncoding
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changeset
|
1078 format, flags, maxStringLength, |
|
84c7eaeb5244
Configuration::GetDefaultEncoding
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1079 Configuration::GetDefaultEncoding()); |
|
1160
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|
1080 } |
|
1555
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diff
changeset
|
1081 |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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changeset
|
1082 |
|
1831
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1083 void ParsedDicomFile::HeaderToJson(Json::Value& target, |
|
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"/instances/.../header" to get the meta information (header) of the DICOM instance
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diff
changeset
|
1084 DicomToJsonFormat format) |
|
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"/instances/.../header" to get the meta information (header) of the DICOM instance
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diff
changeset
|
1085 { |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1086 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getMetaInfo(), format, DicomToJsonFlags_None, 0); |
|
3ae2ff249675
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1087 } |
|
3ae2ff249675
"/instances/.../header" to get the meta information (header) of the DICOM instance
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1088 |
|
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"/instances/.../header" to get the meta information (header) of the DICOM instance
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diff
changeset
|
1089 |
|
1555
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1090 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1091 { |
|
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Creation of DICOM files with encapsulated PDF
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diff
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|
1092 DcmTag key(tag.GetGroup(), tag.GetElement()); |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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changeset
|
1093 return pimpl_->file_->getDataset()->tagExists(key); |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1094 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1095 |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1096 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1097 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1098 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1099 if (pdf.size() < 5 || // (*) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1100 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1101 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1102 LOG(ERROR) << "Not a PDF file"; |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1103 throw OrthancException(ErrorCode_BadFileFormat); |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1104 } |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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changeset
|
1105 |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1106 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1107 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1108 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
1523
diff
changeset
|
1109 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
| 1566 | 1110 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
|
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1111 |
|
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Creation of DICOM files with encapsulated PDF
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1523
diff
changeset
|
1112 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1113 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1114 size_t s = pdf.size(); |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1115 if (s & 1) |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1116 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1117 // The size of the buffer must be even |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1118 s += 1; |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1119 } |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1120 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1121 Uint8* bytes = NULL; |
|
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Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1122 OFCondition result = element->createUint8Array(s, bytes); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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diff
changeset
|
1123 if (!result.good() || bytes == NULL) |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1124 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1125 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1126 } |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1127 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1128 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1129 bytes[s - 1] = 0; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1130 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1131 memcpy(bytes, pdf.c_str(), pdf.size()); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1132 |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1133 DcmPolymorphOBOW* obj = element.release(); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1134 result = pimpl_->file_->getDataset()->insert(obj); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1135 |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1136 if (!result.good()) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1137 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1138 delete obj; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1139 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1140 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1141 } |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1142 |
|
1556
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1143 |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1144 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1145 { |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1146 std::string sop, mime; |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1147 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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changeset
|
1148 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
|
b8dc2f855a83
Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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diff
changeset
|
1149 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
|
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|
1150 sop != UID_EncapsulatedPDFStorage || |
|
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|
1151 mime != "application/pdf") |
|
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|
1152 { |
|
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|
1153 return false; |
|
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changeset
|
1154 } |
|
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changeset
|
1155 |
|
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|
1156 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
|
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changeset
|
1157 { |
|
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|
1158 return false; |
|
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changeset
|
1159 } |
|
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changeset
|
1160 |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1161 // Strip the possible pad byte at the end of file, because the |
|
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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|
1162 // 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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|
1163 // 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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|
1164 // 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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changeset
|
1165 // 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
|
1166 if (pdf.size() > 0) |
|
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changeset
|
1167 { |
|
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|
1168 char last = *pdf.rbegin(); |
|
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changeset
|
1169 |
|
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|
1170 if (last != 10 && last != 13) |
|
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|
1171 { |
|
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|
1172 pdf.resize(pdf.size() - 1); |
|
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|
1173 } |
|
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|
1174 } |
|
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|
1175 |
|
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|
1176 return true; |
|
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|
1177 } |
|
1662
09be34b2f30e
ParsedDicomFile::Convert()
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|
1178 |
|
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ParsedDicomFile::Convert()
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|
1179 |
|
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ParsedDicomFile::Convert()
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|
1180 void ParsedDicomFile::Convert(DicomMap& tags) |
|
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ParsedDicomFile::Convert()
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|
1181 { |
|
1929
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ORTHANC_MAXIMUM_TAG_LENGTH made explicit
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|
1182 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset(), |
|
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ORTHANC_MAXIMUM_TAG_LENGTH made explicit
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|
1183 ORTHANC_MAXIMUM_TAG_LENGTH, |
|
1928
84c7eaeb5244
Configuration::GetDefaultEncoding
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changeset
|
1184 Configuration::GetDefaultEncoding()); |
|
1662
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ParsedDicomFile::Convert()
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|
1185 } |
|
1818
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ParsedDicomFile::CreateFromJson
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|
1186 |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1187 |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1188 ParsedDicomFile* ParsedDicomFile::CreateFromJson(const Json::Value& json, |
|
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ParsedDicomFile::CreateFromJson
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|
1189 DicomFromJsonFlags flags) |
|
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ParsedDicomFile::CreateFromJson
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|
1190 { |
|
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ParsedDicomFile::CreateFromJson
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|
1191 const bool generateIdentifiers = (flags & DicomFromJsonFlags_GenerateIdentifiers); |
|
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ParsedDicomFile::CreateFromJson
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|
1192 const bool decodeDataUriScheme = (flags & DicomFromJsonFlags_DecodeDataUriScheme); |
|
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ParsedDicomFile::CreateFromJson
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|
1193 |
|
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ParsedDicomFile::CreateFromJson
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|
1194 std::auto_ptr<ParsedDicomFile> result(new ParsedDicomFile(generateIdentifiers)); |
|
1934
72a2fd7fed8b
FromDcmtkBridge::FromJson
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changeset
|
1195 result->SetEncoding(FromDcmtkBridge::ExtractEncoding(json, Configuration::GetDefaultEncoding())); |
|
1818
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1196 |
|
1934
72a2fd7fed8b
FromDcmtkBridge::FromJson
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diff
changeset
|
1197 const Json::Value::Members tags = json.getMemberNames(); |
|
72a2fd7fed8b
FromDcmtkBridge::FromJson
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changeset
|
1198 |
|
1818
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ParsedDicomFile::CreateFromJson
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|
1199 for (size_t i = 0; i < tags.size(); i++) |
|
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ParsedDicomFile::CreateFromJson
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|
1200 { |
|
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ParsedDicomFile::CreateFromJson
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|
1201 DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); |
|
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ParsedDicomFile::CreateFromJson
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|
1202 const Json::Value& value = json[tags[i]]; |
|
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ParsedDicomFile::CreateFromJson
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|
1203 |
|
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ParsedDicomFile::CreateFromJson
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|
1204 if (tag == DICOM_TAG_PIXEL_DATA || |
|
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ParsedDicomFile::CreateFromJson
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|
1205 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
|
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ParsedDicomFile::CreateFromJson
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|
1206 { |
|
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ParsedDicomFile::CreateFromJson
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|
1207 if (value.type() != Json::stringValue) |
|
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ParsedDicomFile::CreateFromJson
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|
1208 { |
|
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ParsedDicomFile::CreateFromJson
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|
1209 throw OrthancException(ErrorCode_BadRequest); |
|
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ParsedDicomFile::CreateFromJson
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|
1210 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1211 else |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1212 { |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1213 result->EmbedContent(value.asString()); |
|
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ParsedDicomFile::CreateFromJson
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|
1214 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1215 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1216 else if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1217 { |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1218 result->Replace(tag, value, decodeDataUriScheme); |
|
1065401501fb
ParsedDicomFile::CreateFromJson
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|
1219 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1220 } |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1221 |
|
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ParsedDicomFile::CreateFromJson
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changeset
|
1222 return result.release(); |
|
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ParsedDicomFile::CreateFromJson
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|
1223 } |
|
1924
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1224 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1225 |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1226 void ParsedDicomFile::GetRawFrame(std::string& target, |
|
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changeset
|
1227 std::string& mime, |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1228 unsigned int frameId) |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1229 { |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1230 if (pimpl_->frameIndex_.get() == NULL) |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1231 { |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1232 pimpl_->frameIndex_.reset(new DicomFrameIndex(*pimpl_->file_->getDataset())); |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1233 } |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1234 |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1235 pimpl_->frameIndex_->GetRawFrame(target, frameId); |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1236 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1237 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1238 switch (transferSyntax) |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1239 { |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1240 case EXS_JPEGProcess1TransferSyntax: |
|
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New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1241 mime = "image/jpeg"; |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1242 break; |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1243 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1244 case EXS_JPEG2000LosslessOnly: |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1245 case EXS_JPEG2000: |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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changeset
|
1246 mime = "image/jp2"; |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1247 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1248 default: |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
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diff
changeset
|
1249 mime = "application/octet-stream"; |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1250 break; |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1251 } |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1252 } |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1253 |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1254 |
|
6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1255 void ParsedDicomFile::InvalidateCache() |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1256 { |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1257 pimpl_->frameIndex_.reset(NULL); |
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6c73df12ca51
New URI: "/instances/.../frames/.../raw" to access the raw frames (bypass image decoding)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1913
diff
changeset
|
1258 } |
| 790 | 1259 } |