Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1555:d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 20 Aug 2015 15:18:13 +0200 |
| parents | c388502a066d |
| children | b8dc2f855a83 |
| rev | line source |
|---|---|
| 790 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
|
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
| 790 | 5 * |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 10 * | |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 22 * | |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 | |
| 34 /*========================================================================= | |
| 35 | |
| 36 This file is based on portions of the following project: | |
| 37 | |
| 38 Program: GDCM (Grassroots DICOM). A DICOM library | |
| 39 Module: http://gdcm.sourceforge.net/Copyright.html | |
| 40 | |
| 41 Copyright (c) 2006-2011 Mathieu Malaterre | |
| 42 Copyright (c) 1993-2005 CREATIS | |
| 43 (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) | |
| 44 All rights reserved. | |
| 45 | |
| 46 Redistribution and use in source and binary forms, with or without | |
| 47 modification, are permitted provided that the following conditions are met: | |
| 48 | |
| 49 * Redistributions of source code must retain the above copyright notice, | |
| 50 this list of conditions and the following disclaimer. | |
| 51 | |
| 52 * Redistributions in binary form must reproduce the above copyright notice, | |
| 53 this list of conditions and the following disclaimer in the documentation | |
| 54 and/or other materials provided with the distribution. | |
| 55 | |
| 56 * Neither name of Mathieu Malaterre, or CREATIS, nor the names of any | |
| 57 contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to | |
| 58 endorse or promote products derived from this software without specific | |
| 59 prior written permission. | |
| 60 | |
| 61 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' | |
| 62 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| 63 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 64 ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR | |
| 65 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | |
| 66 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | |
| 67 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | |
| 68 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | |
| 69 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | |
| 70 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 71 | |
| 72 =========================================================================*/ | |
| 73 | |
| 74 | |
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75 #include "PrecompiledHeadersServer.h" |
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76 |
| 790 | 77 #ifndef NOMINMAX |
| 78 #define NOMINMAX | |
| 79 #endif | |
| 80 | |
| 81 #include "ParsedDicomFile.h" | |
| 82 | |
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83 #include "ServerToolbox.h" |
| 790 | 84 #include "FromDcmtkBridge.h" |
| 85 #include "ToDcmtkBridge.h" | |
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86 #include "Internals/DicomImageDecoder.h" |
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87 #include "../Core/Logging.h" |
| 790 | 88 #include "../Core/Toolbox.h" |
| 89 #include "../Core/OrthancException.h" | |
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90 #include "../Core/ImageFormats/ImageBuffer.h" |
| 799 | 91 #include "../Core/ImageFormats/PngWriter.h" |
| 790 | 92 #include "../Core/Uuid.h" |
| 93 #include "../Core/DicomFormat/DicomString.h" | |
| 94 #include "../Core/DicomFormat/DicomNullValue.h" | |
| 95 #include "../Core/DicomFormat/DicomIntegerPixelAccessor.h" | |
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96 #include "../Core/ImageFormats/PngReader.h" |
| 790 | 97 |
| 98 #include <list> | |
| 99 #include <limits> | |
| 100 | |
| 101 #include <boost/lexical_cast.hpp> | |
| 102 | |
| 103 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 104 #include <dcmtk/dcmdata/dcdicent.h> | |
| 105 #include <dcmtk/dcmdata/dcdict.h> | |
| 106 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 107 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 108 #include <dcmtk/dcmdata/dcuid.h> | |
| 109 #include <dcmtk/dcmdata/dcmetinf.h> | |
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110 #include <dcmtk/dcmdata/dcdeftag.h> |
| 790 | 111 |
| 112 #include <dcmtk/dcmdata/dcvrae.h> | |
| 113 #include <dcmtk/dcmdata/dcvras.h> | |
| 114 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 115 #include <dcmtk/dcmdata/dcvrda.h> | |
| 116 #include <dcmtk/dcmdata/dcvrds.h> | |
| 117 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 118 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 119 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 120 #include <dcmtk/dcmdata/dcvris.h> | |
| 121 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 122 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 123 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 124 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 125 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 126 #include <dcmtk/dcmdata/dcvrss.h> | |
| 127 #include <dcmtk/dcmdata/dcvrst.h> | |
| 128 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 129 #include <dcmtk/dcmdata/dcvrui.h> | |
| 130 #include <dcmtk/dcmdata/dcvrul.h> | |
| 131 #include <dcmtk/dcmdata/dcvrus.h> | |
| 132 #include <dcmtk/dcmdata/dcvrut.h> | |
| 133 #include <dcmtk/dcmdata/dcpixel.h> | |
| 134 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 135 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 136 | |
| 137 | |
| 138 #include <boost/math/special_functions/round.hpp> | |
| 139 #include <dcmtk/dcmdata/dcostrmb.h> | |
| 140 | |
| 141 | |
| 142 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 143 | |
| 144 | |
| 145 | |
| 146 namespace Orthanc | |
| 147 { | |
| 794 | 148 struct ParsedDicomFile::PImpl |
| 149 { | |
| 150 std::auto_ptr<DcmFileFormat> file_; | |
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151 Encoding encoding_; |
| 794 | 152 }; |
| 153 | |
| 154 | |
| 155 // This method can only be called from the constructors! | |
| 790 | 156 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 157 { | |
| 158 DcmInputBufferStream is; | |
| 159 if (size > 0) | |
| 160 { | |
| 161 is.setBuffer(buffer, size); | |
| 162 } | |
| 163 is.setEos(); | |
| 164 | |
| 794 | 165 pimpl_->file_.reset(new DcmFileFormat); |
| 166 pimpl_->file_->transferInit(); | |
| 167 if (!pimpl_->file_->read(is).good()) | |
| 790 | 168 { |
| 794 | 169 delete pimpl_; // Avoid a memory leak due to exception |
| 170 // throwing, as we are in the constructor | |
| 171 | |
| 790 | 172 throw OrthancException(ErrorCode_BadFileFormat); |
| 173 } | |
| 794 | 174 pimpl_->file_->loadAllDataIntoMemory(); |
| 175 pimpl_->file_->transferEnd(); | |
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176 |
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177 pimpl_->encoding_ = FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
| 790 | 178 } |
| 179 | |
| 180 | |
| 181 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 182 DcmItem& dicom) | |
| 183 { | |
| 184 Json::Value v = Json::arrayValue; | |
| 185 | |
| 186 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 187 { | |
| 188 DcmElement* element = dicom.getElement(i); | |
| 189 if (element) | |
| 190 { | |
| 191 char buf[16]; | |
| 192 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 193 v.append(buf); | |
| 194 } | |
| 195 } | |
| 196 | |
| 197 output.AnswerJson(v); | |
| 198 } | |
| 199 | |
| 200 static inline uint16_t GetCharValue(char c) | |
| 201 { | |
| 202 if (c >= '0' && c <= '9') | |
| 203 return c - '0'; | |
| 204 else if (c >= 'a' && c <= 'f') | |
| 205 return c - 'a' + 10; | |
| 206 else if (c >= 'A' && c <= 'F') | |
| 207 return c - 'A' + 10; | |
| 208 else | |
| 209 return 0; | |
| 210 } | |
| 211 | |
| 212 static inline uint16_t GetTagValue(const char* c) | |
| 213 { | |
| 214 return ((GetCharValue(c[0]) << 12) + | |
| 215 (GetCharValue(c[1]) << 8) + | |
| 216 (GetCharValue(c[2]) << 4) + | |
| 217 GetCharValue(c[3])); | |
| 218 } | |
| 219 | |
| 220 static void ParseTagAndGroup(DcmTagKey& key, | |
| 221 const std::string& tag) | |
| 222 { | |
| 223 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 224 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 225 } | |
| 226 | |
| 227 | |
| 228 static void SendSequence(RestApiOutput& output, | |
| 229 DcmSequenceOfItems& sequence) | |
| 230 { | |
| 231 // This element is a sequence | |
| 232 Json::Value v = Json::arrayValue; | |
| 233 | |
| 234 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 235 { | |
| 236 v.append(boost::lexical_cast<std::string>(i)); | |
| 237 } | |
| 238 | |
| 239 output.AnswerJson(v); | |
| 240 } | |
| 241 | |
| 242 | |
| 243 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 244 E_TransferSyntax transferSyntax) | |
| 245 { | |
| 246 DcmPixelSequence* pixelSequence = NULL; | |
| 247 if (pixelData.getEncapsulatedRepresentation | |
| 248 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 249 { | |
| 250 return pixelSequence->card(); | |
| 251 } | |
| 252 else | |
| 253 { | |
| 254 return 1; | |
| 255 } | |
| 256 } | |
| 257 | |
| 258 | |
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259 namespace |
| 790 | 260 { |
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261 class DicomFieldStream : public IHttpStreamAnswer |
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262 { |
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263 private: |
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264 DcmElement& element_; |
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265 uint32_t length_; |
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266 uint32_t offset_; |
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267 std::string chunk_; |
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268 size_t chunkSize_; |
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269 |
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270 public: |
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271 DicomFieldStream(DcmElement& element, |
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272 E_TransferSyntax transferSyntax) : |
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273 element_(element), |
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274 length_(element.getLength(transferSyntax)), |
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275 offset_(0) |
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276 { |
| 1521 | 277 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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278 chunk_.resize(CHUNK_SIZE); |
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279 } |
| 790 | 280 |
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281 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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282 bool /*deflateAllowed*/) |
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283 { |
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284 // No support for compression |
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285 return HttpCompression_None; |
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286 } |
| 790 | 287 |
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288 virtual bool HasContentFilename(std::string& filename) |
| 790 | 289 { |
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290 return false; |
| 790 | 291 } |
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292 |
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293 virtual std::string GetContentType() |
| 790 | 294 { |
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295 return ""; |
| 790 | 296 } |
| 297 | |
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298 virtual uint64_t GetContentLength() |
| 790 | 299 { |
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300 return length_; |
| 790 | 301 } |
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302 |
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303 virtual bool ReadNextChunk() |
| 790 | 304 { |
| 1520 | 305 assert(offset_ <= length_); |
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306 |
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307 if (offset_ == length_) |
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308 { |
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309 return false; |
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310 } |
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311 else |
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312 { |
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313 if (length_ - offset_ < chunk_.size()) |
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314 { |
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315 chunkSize_ = length_ - offset_; |
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316 } |
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317 else |
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318 { |
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319 chunkSize_ = chunk_.size(); |
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320 } |
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321 |
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322 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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323 |
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324 offset_ += chunkSize_; |
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325 |
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326 if (!cond.good()) |
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327 { |
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328 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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329 throw OrthancException(ErrorCode_InternalError); |
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330 } |
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331 |
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332 return true; |
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333 } |
| 790 | 334 } |
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335 |
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336 virtual const char *GetChunkContent() |
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337 { |
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338 return chunk_.c_str(); |
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339 } |
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340 |
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341 virtual size_t GetChunkSize() |
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342 { |
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343 return chunkSize_; |
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344 } |
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345 }; |
| 790 | 346 } |
| 347 | |
| 348 | |
| 349 static bool AnswerPixelData(RestApiOutput& output, | |
| 350 DcmItem& dicom, | |
| 351 E_TransferSyntax transferSyntax, | |
| 352 const std::string* blockUri) | |
| 353 { | |
| 354 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 355 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 356 | |
| 357 DcmElement *element = NULL; | |
| 358 if (!dicom.findAndGetElement(k, element).good() || | |
| 359 element == NULL) | |
| 360 { | |
| 361 return false; | |
| 362 } | |
| 363 | |
| 364 try | |
| 365 { | |
| 366 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 367 if (blockUri == NULL) | |
| 368 { | |
| 369 // The user asks how many blocks are presents in this pixel data | |
| 370 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 371 | |
| 372 Json::Value result(Json::arrayValue); | |
| 373 for (unsigned int i = 0; i < blocks; i++) | |
| 374 { | |
| 375 result.append(boost::lexical_cast<std::string>(i)); | |
| 376 } | |
| 377 | |
| 378 output.AnswerJson(result); | |
| 379 return true; | |
| 380 } | |
| 381 | |
| 382 | |
| 383 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 384 | |
| 385 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 386 { | |
| 387 DcmPixelSequence* pixelSequence = NULL; | |
| 388 if (pixelData.getEncapsulatedRepresentation | |
| 389 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 390 { | |
| 391 // This is the case for JPEG transfer syntaxes | |
| 392 if (block < pixelSequence->card()) | |
| 393 { | |
| 394 DcmPixelItem* pixelItem = NULL; | |
| 395 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 396 { | |
| 397 if (pixelItem->getLength() == 0) | |
| 398 { | |
| 399 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 400 return true; | |
| 401 } | |
| 402 | |
| 403 Uint8* buffer = NULL; | |
| 404 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 405 { | |
| 406 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 407 return true; | |
| 408 } | |
| 409 } | |
| 410 } | |
| 411 } | |
| 412 else | |
| 413 { | |
| 414 // This is the case for raw, uncompressed image buffers | |
| 415 assert(*blockUri == "0"); | |
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416 DicomFieldStream stream(*element, transferSyntax); |
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417 output.AnswerStream(stream); |
| 790 | 418 } |
| 419 } | |
| 420 } | |
| 421 catch (boost::bad_lexical_cast&) | |
| 422 { | |
| 423 // The URI entered by the user is not a number | |
| 424 } | |
| 425 catch (std::bad_cast&) | |
| 426 { | |
| 427 // This should never happen | |
| 428 } | |
| 429 | |
| 430 return false; | |
| 431 } | |
| 432 | |
| 433 | |
| 434 | |
| 435 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 436 const std::string& tag, | |
| 437 DcmItem& dicom, | |
| 438 E_TransferSyntax transferSyntax) | |
| 439 { | |
| 440 DcmTagKey k; | |
| 441 ParseTagAndGroup(k, tag); | |
| 442 | |
| 443 DcmSequenceOfItems* sequence = NULL; | |
| 444 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 445 sequence != NULL && | |
| 446 sequence->getVR() == EVR_SQ) | |
| 447 { | |
| 448 SendSequence(output, *sequence); | |
| 449 return; | |
| 450 } | |
| 451 | |
| 452 DcmElement* element = NULL; | |
| 453 if (dicom.findAndGetElement(k, element).good() && | |
| 454 element != NULL && | |
| 455 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 456 element->getVR() != EVR_SQ) | |
| 457 { | |
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458 DicomFieldStream stream(*element, transferSyntax); |
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459 output.AnswerStream(stream); |
| 790 | 460 } |
| 461 } | |
| 462 | |
| 463 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 464 const UriComponents& uri) | |
| 465 { | |
| 794 | 466 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 467 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 468 |
| 469 // Special case: Accessing the pixel data | |
| 470 if (uri.size() == 1 || | |
| 471 uri.size() == 2) | |
| 472 { | |
| 473 DcmTagKey tag; | |
| 474 ParseTagAndGroup(tag, uri[0]); | |
| 475 | |
| 476 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 477 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 478 { | |
| 479 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 480 return; | |
| 481 } | |
| 482 } | |
| 483 | |
| 484 // Go down in the tag hierarchy according to the URI | |
| 485 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 486 { | |
| 487 size_t index; | |
| 488 try | |
| 489 { | |
| 490 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 491 } | |
| 492 catch (boost::bad_lexical_cast&) | |
| 493 { | |
| 494 return; | |
| 495 } | |
| 496 | |
| 497 DcmTagKey k; | |
| 498 DcmItem *child = NULL; | |
| 499 ParseTagAndGroup(k, uri[2 * pos]); | |
| 500 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 501 child == NULL) | |
| 502 { | |
| 503 return; | |
| 504 } | |
| 505 | |
| 506 dicom = child; | |
| 507 } | |
| 508 | |
| 509 // We have reached the end of the URI | |
| 510 if (uri.size() % 2 == 0) | |
| 511 { | |
| 512 SendPathValueForDictionary(output, *dicom); | |
| 513 } | |
| 514 else | |
| 515 { | |
| 516 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 517 } | |
| 518 } | |
| 519 | |
| 520 | |
| 521 | |
| 522 | |
| 523 | |
| 524 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 525 { | |
| 526 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 527 | |
| 528 switch (key.getEVR()) | |
| 529 { | |
| 530 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 531 | |
| 532 /** | |
| 533 * TODO. | |
| 534 **/ | |
| 535 | |
| 536 case EVR_OB: // other byte | |
| 537 case EVR_OF: // other float | |
| 538 case EVR_OW: // other word | |
| 539 case EVR_AT: // attribute tag | |
| 540 throw OrthancException(ErrorCode_NotImplemented); | |
| 541 | |
| 542 case EVR_UN: // unknown value representation | |
| 543 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 544 | |
| 545 | |
| 546 /** | |
| 547 * String types. | |
| 548 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 549 **/ | |
| 550 | |
| 551 case EVR_AS: // age string | |
| 552 return new DcmAgeString(key); | |
| 553 | |
| 554 case EVR_AE: // application entity title | |
| 555 return new DcmApplicationEntity(key); | |
| 556 | |
| 557 case EVR_CS: // code string | |
| 558 return new DcmCodeString(key); | |
| 559 | |
| 560 case EVR_DA: // date string | |
| 561 return new DcmDate(key); | |
| 562 | |
| 563 case EVR_DT: // date time string | |
| 564 return new DcmDateTime(key); | |
| 565 | |
| 566 case EVR_DS: // decimal string | |
| 567 return new DcmDecimalString(key); | |
| 568 | |
| 569 case EVR_IS: // integer string | |
| 570 return new DcmIntegerString(key); | |
| 571 | |
| 572 case EVR_TM: // time string | |
| 573 return new DcmTime(key); | |
| 574 | |
| 575 case EVR_UI: // unique identifier | |
| 576 return new DcmUniqueIdentifier(key); | |
| 577 | |
| 578 case EVR_ST: // short text | |
| 579 return new DcmShortText(key); | |
| 580 | |
| 581 case EVR_LO: // long string | |
| 582 return new DcmLongString(key); | |
| 583 | |
| 584 case EVR_LT: // long text | |
| 585 return new DcmLongText(key); | |
| 586 | |
| 587 case EVR_UT: // unlimited text | |
| 588 return new DcmUnlimitedText(key); | |
| 589 | |
| 590 case EVR_SH: // short string | |
| 591 return new DcmShortString(key); | |
| 592 | |
| 593 case EVR_PN: // person name | |
| 594 return new DcmPersonName(key); | |
| 595 | |
| 596 | |
| 597 /** | |
| 598 * Numerical types | |
| 599 **/ | |
| 600 | |
| 601 case EVR_SL: // signed long | |
| 602 return new DcmSignedLong(key); | |
| 603 | |
| 604 case EVR_SS: // signed short | |
| 605 return new DcmSignedShort(key); | |
| 606 | |
| 607 case EVR_UL: // unsigned long | |
| 608 return new DcmUnsignedLong(key); | |
| 609 | |
| 610 case EVR_US: // unsigned short | |
| 611 return new DcmUnsignedShort(key); | |
| 612 | |
| 613 case EVR_FL: // float single-precision | |
| 614 return new DcmFloatingPointSingle(key); | |
| 615 | |
| 616 case EVR_FD: // float double-precision | |
| 617 return new DcmFloatingPointDouble(key); | |
| 618 | |
| 619 | |
| 620 /** | |
| 621 * Sequence types, should never occur at this point. | |
| 622 **/ | |
| 623 | |
| 624 case EVR_SQ: // sequence of items | |
| 625 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 626 | |
| 627 | |
| 628 /** | |
| 629 * Internal to DCMTK. | |
| 630 **/ | |
| 631 | |
| 632 case EVR_ox: // OB or OW depending on context | |
| 633 case EVR_xs: // SS or US depending on context | |
| 634 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 635 case EVR_na: // na="not applicable", for data which has no VR | |
| 636 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 637 case EVR_item: // used internally for items | |
| 638 case EVR_metainfo: // used internally for meta info datasets | |
| 639 case EVR_dataset: // used internally for datasets | |
| 640 case EVR_fileFormat: // used internally for DICOM files | |
| 641 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 642 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 643 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 644 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 645 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 646 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 647 case EVR_OverlayData: // used internally for overlay data | |
| 648 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 649 default: | |
| 650 break; | |
| 651 } | |
| 652 | |
| 653 throw OrthancException(ErrorCode_InternalError); | |
| 654 } | |
| 655 | |
| 656 | |
| 657 | |
| 658 static void FillElementWithString(DcmElement& element, | |
| 659 const DicomTag& tag, | |
| 660 const std::string& value) | |
| 661 { | |
| 662 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 663 bool ok = false; | |
| 664 | |
| 665 try | |
| 666 { | |
| 667 switch (key.getEVR()) | |
| 668 { | |
| 669 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 670 | |
| 671 /** | |
| 672 * TODO. | |
| 673 **/ | |
| 674 | |
| 675 case EVR_OB: // other byte | |
| 676 case EVR_OF: // other float | |
| 677 case EVR_OW: // other word | |
| 678 case EVR_AT: // attribute tag | |
| 679 throw OrthancException(ErrorCode_NotImplemented); | |
| 680 | |
| 681 case EVR_UN: // unknown value representation | |
| 682 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 683 | |
| 684 | |
| 685 /** | |
| 686 * String types. | |
| 687 **/ | |
| 688 | |
| 689 case EVR_DS: // decimal string | |
| 690 case EVR_IS: // integer string | |
| 691 case EVR_AS: // age string | |
| 692 case EVR_DA: // date string | |
| 693 case EVR_DT: // date time string | |
| 694 case EVR_TM: // time string | |
| 695 case EVR_AE: // application entity title | |
| 696 case EVR_CS: // code string | |
| 697 case EVR_SH: // short string | |
| 698 case EVR_LO: // long string | |
| 699 case EVR_ST: // short text | |
| 700 case EVR_LT: // long text | |
| 701 case EVR_UT: // unlimited text | |
| 702 case EVR_PN: // person name | |
| 703 case EVR_UI: // unique identifier | |
| 704 { | |
| 705 ok = element.putString(value.c_str()).good(); | |
| 706 break; | |
| 707 } | |
| 708 | |
| 709 | |
| 710 /** | |
| 711 * Numerical types | |
| 712 **/ | |
| 713 | |
| 714 case EVR_SL: // signed long | |
| 715 { | |
| 716 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 717 break; | |
| 718 } | |
| 719 | |
| 720 case EVR_SS: // signed short | |
| 721 { | |
| 722 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 723 break; | |
| 724 } | |
| 725 | |
| 726 case EVR_UL: // unsigned long | |
| 727 { | |
| 728 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 729 break; | |
| 730 } | |
| 731 | |
| 732 case EVR_US: // unsigned short | |
| 733 { | |
| 734 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 735 break; | |
| 736 } | |
| 737 | |
| 738 case EVR_FL: // float single-precision | |
| 739 { | |
| 740 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 741 break; | |
| 742 } | |
| 743 | |
| 744 case EVR_FD: // float double-precision | |
| 745 { | |
| 746 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 747 break; | |
| 748 } | |
| 749 | |
| 750 | |
| 751 /** | |
| 752 * Sequence types, should never occur at this point. | |
| 753 **/ | |
| 754 | |
| 755 case EVR_SQ: // sequence of items | |
| 756 { | |
| 757 ok = false; | |
| 758 break; | |
| 759 } | |
| 760 | |
| 761 | |
| 762 /** | |
| 763 * Internal to DCMTK. | |
| 764 **/ | |
| 765 | |
| 766 case EVR_ox: // OB or OW depending on context | |
| 767 case EVR_xs: // SS or US depending on context | |
| 768 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 769 case EVR_na: // na="not applicable", for data which has no VR | |
| 770 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 771 case EVR_item: // used internally for items | |
| 772 case EVR_metainfo: // used internally for meta info datasets | |
| 773 case EVR_dataset: // used internally for datasets | |
| 774 case EVR_fileFormat: // used internally for DICOM files | |
| 775 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 776 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 777 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 778 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 779 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 780 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 781 case EVR_OverlayData: // used internally for overlay data | |
| 782 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 783 default: | |
| 784 break; | |
| 785 } | |
| 786 } | |
| 787 catch (boost::bad_lexical_cast&) | |
| 788 { | |
| 789 ok = false; | |
| 790 } | |
| 791 | |
| 792 if (!ok) | |
| 793 { | |
| 794 throw OrthancException(ErrorCode_InternalError); | |
| 795 } | |
| 796 } | |
| 797 | |
| 798 | |
| 799 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 800 { | |
| 801 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 802 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 803 if (element != NULL) |
| 804 { | |
| 805 delete element; | |
| 806 } | |
| 807 } | |
| 808 | |
| 809 | |
| 810 | |
|
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811 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 812 { |
|
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813 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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814 |
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815 // Loop over the dataset to detect its private tags |
| 790 | 816 typedef std::list<DcmElement*> Tags; |
| 817 Tags privateTags; | |
| 818 | |
| 819 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 820 { | |
| 821 DcmElement* element = dataset.getElement(i); | |
| 822 DcmTag tag(element->getTag()); | |
|
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823 |
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824 // Is this a private tag? |
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825 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 826 { |
|
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827 bool remove = true; |
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828 |
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829 // Check whether this private tag is to be kept |
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830 if (toKeep != NULL) |
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831 { |
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832 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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833 if (toKeep->find(tmp) != toKeep->end()) |
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834 { |
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835 remove = false; // Keep it |
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836 } |
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837 } |
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838 |
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839 if (remove) |
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840 { |
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841 privateTags.push_back(element); |
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842 } |
| 790 | 843 } |
| 844 } | |
| 845 | |
|
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846 // Loop over the detected private tags to remove them |
| 790 | 847 for (Tags::iterator it = privateTags.begin(); |
| 848 it != privateTags.end(); ++it) | |
| 849 { | |
| 850 DcmElement* tmp = dataset.remove(*it); | |
| 851 if (tmp != NULL) | |
| 852 { | |
| 853 delete tmp; | |
| 854 } | |
| 855 } | |
| 856 } | |
| 857 | |
| 858 | |
| 859 | |
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860 |
| 790 | 861 void ParsedDicomFile::Insert(const DicomTag& tag, |
| 862 const std::string& value) | |
| 863 { | |
|
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864 OFCondition cond; |
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865 |
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866 if (FromDcmtkBridge::IsPrivateTag(tag)) |
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867 { |
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868 // This is a private tag |
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869 // http://support.dcmtk.org/redmine/projects/dcmtk/wiki/howto_addprivatedata |
| 790 | 870 |
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871 DcmTag key(tag.GetGroup(), tag.GetElement(), EVR_OB); |
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872 cond = pimpl_->file_->getDataset()->putAndInsertUint8Array |
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873 (key, (const Uint8*) value.c_str(), value.size(), false); |
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874 } |
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875 else |
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876 { |
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877 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); |
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878 FillElementWithString(*element, tag, value); |
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879 |
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880 cond = pimpl_->file_->getDataset()->insert(element.release(), false, false); |
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881 } |
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882 |
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|
883 if (!cond.good()) |
| 790 | 884 { |
| 885 // This field already exists | |
| 886 throw OrthancException(ErrorCode_InternalError); | |
| 887 } | |
| 888 } | |
| 889 | |
| 890 | |
| 891 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 892 const std::string& value, | |
| 893 DicomReplaceMode mode) | |
| 894 { | |
| 895 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 896 DcmElement* element = NULL; | |
| 897 | |
| 794 | 898 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 899 element == NULL) |
| 900 { | |
| 901 // This field does not exist, act wrt. the specified "mode" | |
| 902 switch (mode) | |
| 903 { | |
| 904 case DicomReplaceMode_InsertIfAbsent: | |
| 905 Insert(tag, value); | |
| 906 break; | |
| 907 | |
| 908 case DicomReplaceMode_ThrowIfAbsent: | |
| 909 throw OrthancException(ErrorCode_InexistentItem); | |
| 910 | |
| 911 case DicomReplaceMode_IgnoreIfAbsent: | |
| 912 return; | |
| 913 } | |
| 914 } | |
| 915 else | |
| 916 { | |
|
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917 if (FromDcmtkBridge::IsPrivateTag(tag)) |
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918 { |
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919 if (!element->putUint8Array((const Uint8*) value.c_str(), value.size()).good()) |
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920 { |
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921 throw OrthancException(ErrorCode_InternalError); |
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922 } |
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923 } |
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924 else |
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925 { |
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926 FillElementWithString(*element, tag, value); |
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|
927 } |
| 790 | 928 } |
| 929 | |
| 930 | |
| 931 /** | |
| 932 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 933 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 934 * you make changes to the related tags in the dataset ('SOP Class | |
| 935 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 936 * options. You can disable this behaviour by using the -nmu | |
| 937 * option. | |
| 938 **/ | |
| 939 | |
| 940 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 941 { | |
| 942 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 943 } | |
| 944 | |
| 945 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 946 { | |
| 947 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 948 } | |
| 949 } | |
| 950 | |
| 951 | |
| 952 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 953 { | |
| 954 std::string serialized; | |
|
1004
a226e0959d8b
DicomInstanceToStore
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|
955 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 956 { |
| 957 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 958 } | |
| 959 } | |
| 960 | |
| 961 | |
| 962 | |
| 963 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 964 const DicomTag& tag) | |
| 965 { | |
| 966 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 967 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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968 |
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969 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 970 { |
|
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971 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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972 long unsigned int count = 0; |
| 790 | 973 |
|
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974 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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975 { |
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976 if (count > 0) |
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977 { |
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978 assert(data != NULL); |
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979 value.assign(reinterpret_cast<const char*>(data), count); |
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980 } |
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981 else |
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982 { |
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|
983 value.clear(); |
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984 } |
| 790 | 985 |
|
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986 return true; |
|
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987 } |
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988 else |
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989 { |
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990 return false; |
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991 } |
| 790 | 992 } |
| 993 else | |
| 994 { | |
|
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995 DcmElement* element = NULL; |
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996 if (!dataset.findAndGetElement(k, element).good() || |
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|
997 element == NULL) |
|
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998 { |
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999 return false; |
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1000 } |
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1001 |
|
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|
1002 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
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1003 |
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|
1004 if (v.get() == NULL) |
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1005 { |
|
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1006 value = ""; |
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1007 } |
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1008 else |
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1009 { |
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1010 value = v->AsString(); |
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1011 } |
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1012 |
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1013 return true; |
| 790 | 1014 } |
| 1015 } | |
| 1016 | |
| 1017 | |
| 1018 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 1019 { | |
| 1020 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 1021 | |
| 1022 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 1023 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 1024 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 1025 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 1026 { | |
| 1027 throw OrthancException(ErrorCode_BadFileFormat); | |
| 1028 } | |
| 1029 | |
| 1030 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 1031 } | |
| 1032 | |
| 1033 | |
| 1034 template <typename T> | |
| 1035 static void ExtractPngImageTruncate(std::string& result, | |
| 1036 DicomIntegerPixelAccessor& accessor, | |
| 1037 PixelFormat format) | |
| 1038 { | |
|
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1039 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 1040 |
| 1041 PngWriter w; | |
| 1042 | |
|
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1043 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 1044 T* pixel = &image[0]; |
|
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1045 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 1046 { |
|
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1047 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 1048 { |
| 1049 int32_t v = accessor.GetValue(x, y); | |
| 1050 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 1051 *pixel = std::numeric_limits<T>::min(); | |
| 1052 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 1053 *pixel = std::numeric_limits<T>::max(); | |
| 1054 else | |
| 1055 *pixel = static_cast<T>(v); | |
| 1056 } | |
| 1057 } | |
| 1058 | |
|
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1059 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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1060 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 1061 } |
| 1062 | |
| 1063 | |
| 1064 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 1065 { | |
|
1004
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1066 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 1067 } |
| 1068 | |
| 1069 | |
| 1070 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 1071 { | |
| 1072 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 1073 std::string content; | |
| 1074 SaveToMemoryBuffer(content); | |
| 1075 Toolbox::WriteFile(content, path); | |
| 1076 } | |
| 1077 | |
| 1078 | |
| 794 | 1079 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 1080 { |
| 794 | 1081 pimpl_->file_.reset(new DcmFileFormat); |
|
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1082 pimpl_->encoding_ = Encoding_Ascii; |
| 790 | 1083 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 1084 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 1085 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 1086 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 1087 } | |
| 1088 | |
| 791 | 1089 |
| 794 | 1090 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 1091 { |
| 1092 Setup(content, size); | |
| 1093 } | |
| 1094 | |
| 794 | 1095 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 1096 { |
| 1097 if (content.size() == 0) | |
| 1098 { | |
| 1099 Setup(NULL, 0); | |
| 1100 } | |
| 1101 else | |
| 1102 { | |
| 1103 Setup(&content[0], content.size()); | |
| 1104 } | |
| 1105 } | |
| 792 | 1106 |
| 1107 | |
| 794 | 1108 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1109 pimpl_(new PImpl) | |
| 792 | 1110 { |
| 794 | 1111 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
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1112 |
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1113 pimpl_->encoding_ = other.pimpl_->encoding_; |
| 792 | 1114 } |
| 1115 | |
| 1116 | |
| 1117 ParsedDicomFile::~ParsedDicomFile() | |
| 1118 { | |
| 794 | 1119 delete pimpl_; |
| 792 | 1120 } |
| 1121 | |
| 793 | 1122 |
| 1123 void* ParsedDicomFile::GetDcmtkObject() | |
| 1124 { | |
| 794 | 1125 return pimpl_->file_.get(); |
| 793 | 1126 } |
| 1127 | |
| 1128 | |
| 1129 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1130 { | |
| 794 | 1131 return new ParsedDicomFile(*this); |
| 793 | 1132 } |
|
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1133 |
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1134 |
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1135 void ParsedDicomFile::EmbedImage(const std::string& dataUriScheme) |
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1136 { |
|
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1137 std::string mime, base64; |
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1138 Toolbox::DecodeDataUriScheme(mime, base64, dataUriScheme); |
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1139 |
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1140 std::string content; |
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1141 Toolbox::DecodeBase64(content, base64); |
|
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1142 |
|
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1143 EmbedImage(mime, content); |
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1144 } |
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1145 |
|
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1146 |
|
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1147 void ParsedDicomFile::EmbedImage(const std::string& mime, |
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1148 const std::string& content) |
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1149 { |
|
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1150 if (mime == "image/png") |
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1151 { |
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1152 PngReader reader; |
|
1555
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1153 reader.ReadFromMemory(content); |
|
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1154 EmbedImage(reader); |
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1155 } |
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1156 else |
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1157 { |
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1158 throw OrthancException(ErrorCode_NotImplemented); |
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1159 } |
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1160 } |
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1161 |
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1162 |
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1163 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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1164 { |
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1165 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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1166 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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1167 accessor.GetFormat() != PixelFormat_RGB24 && |
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1168 accessor.GetFormat() != PixelFormat_RGBA32) |
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1169 { |
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1170 throw OrthancException(ErrorCode_NotImplemented); |
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1171 } |
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1172 |
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1173 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1174 { |
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1175 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1176 } |
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1177 |
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1178 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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1179 |
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1180 Remove(DICOM_TAG_PIXEL_DATA); |
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1181 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
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1182 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
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1183 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
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1184 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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1185 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
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1186 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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1187 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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1188 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
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1189 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1190 Replace(DICOM_TAG_HIGH_BIT, "7"); |
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1191 |
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1192 unsigned int bytesPerPixel = 1; |
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1193 |
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1194 switch (accessor.GetFormat()) |
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1195 { |
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1196 case PixelFormat_RGB24: |
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1197 case PixelFormat_RGBA32: |
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1198 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
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changeset
|
1199 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1200 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1201 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1202 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1203 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1204 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1205 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1206 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1207 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1208 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1209 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1210 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1211 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1212 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1213 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1214 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1215 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1216 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1217 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1218 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1219 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1220 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
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generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1221 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1222 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1223 Uint8* target = NULL; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1224 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1225 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1226 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
|
1227 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1228 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1229 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1230 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1231 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1232 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1233 case PixelFormat_SignedGrayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1234 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1235 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
|
1236 target += pitch; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1237 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1238 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1239 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1240 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1241 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1242 // 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
|
1243 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
|
1244 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
|
1245 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1246 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1247 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1248 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1249 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1250 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1251 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1252 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1253 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1254 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1255 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1256 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1257 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1258 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1259 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1260 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1261 throw OrthancException(ErrorCode_InternalError); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1262 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1263 } |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1264 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1265 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1266 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1267 unsigned int frame) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1268 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1269 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1270 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1271 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1272 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1273 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1274 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1275 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1276 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1277 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1278 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1279 unsigned int frame, |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1280 ImageExtractionMode mode) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1281 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1282 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1283 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1284 bool ok = false; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1285 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1286 switch (mode) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1287 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1288 case ImageExtractionMode_UInt8: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1289 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1290 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1291 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1292 case ImageExtractionMode_UInt16: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1293 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1294 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1295 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1296 case ImageExtractionMode_Int16: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1297 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1298 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1299 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1300 case ImageExtractionMode_Preview: |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1301 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1302 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1303 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1304 default: |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1305 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1306 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1307 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1308 if (!ok) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1309 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1310 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1311 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1312 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1313 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1314 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1315 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1316 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1317 ImageExtractionMode mode) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1318 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1319 ImageBuffer buffer; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1320 ExtractImage(buffer, frame, mode); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1321 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1322 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1323 PngWriter writer; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1324 writer.WriteToMemory(result, accessor); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1325 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1326 |
|
956
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
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|
1327 |
|
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1328 Encoding ParsedDicomFile::GetEncoding() const |
|
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1329 { |
|
2fd5a163776d
primitives for proper encoding handling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
874
diff
changeset
|
1330 return pimpl_->encoding_; |
|
2fd5a163776d
primitives for proper encoding handling
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parents:
874
diff
changeset
|
1331 } |
|
1090
e494ceb8d763
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|
1332 |
|
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|
1333 |
|
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|
1334 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
e494ceb8d763
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parents:
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|
1335 { |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1336 std::string s; |
|
e494ceb8d763
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|
1337 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1338 // http://www.dabsoft.ch/dicom/3/C.12.1.1.2/ |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1339 switch (encoding) |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1340 { |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
1341 case Encoding_Utf8: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1342 case Encoding_Ascii: |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
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|
1343 s = "ISO_IR 192"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
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|
1344 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1345 |
| 1347 | 1346 case Encoding_Windows1251: |
| 1347 // This Cyrillic codepage is not officially supported by the | |
| 1348 // DICOM standard. Do not set the SpecificCharacterSet tag. | |
| 1349 return; | |
| 1350 | |
|
1090
e494ceb8d763
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parents:
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|
1351 case Encoding_Latin1: |
|
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parents:
1018
diff
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|
1352 s = "ISO_IR 100"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1353 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1354 |
|
e494ceb8d763
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parents:
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diff
changeset
|
1355 case Encoding_Latin2: |
|
e494ceb8d763
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parents:
1018
diff
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|
1356 s = "ISO_IR 101"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1357 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1358 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1359 case Encoding_Latin3: |
|
e494ceb8d763
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parents:
1018
diff
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|
1360 s = "ISO_IR 109"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1361 break; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1362 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1363 case Encoding_Latin4: |
|
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parents:
1018
diff
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|
1364 s = "ISO_IR 110"; |
|
e494ceb8d763
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parents:
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diff
changeset
|
1365 break; |
|
e494ceb8d763
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parents:
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diff
changeset
|
1366 |
|
e494ceb8d763
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parents:
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diff
changeset
|
1367 case Encoding_Latin5: |
|
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parents:
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|
1368 s = "ISO_IR 148"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1369 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1370 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1371 case Encoding_Cyrillic: |
|
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parents:
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|
1372 s = "ISO_IR 144"; |
|
e494ceb8d763
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parents:
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diff
changeset
|
1373 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1374 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1375 case Encoding_Arabic: |
|
e494ceb8d763
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parents:
1018
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|
1376 s = "ISO_IR 127"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1018
diff
changeset
|
1377 break; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1378 |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1379 case Encoding_Greek: |
|
e494ceb8d763
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parents:
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|
1380 s = "ISO_IR 126"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1381 break; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1382 |
|
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parents:
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diff
changeset
|
1383 case Encoding_Hebrew: |
|
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parents:
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|
1384 s = "ISO_IR 138"; |
|
e494ceb8d763
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1385 break; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1386 |
| 1091 | 1387 case Encoding_Japanese: |
| 1388 s = "ISO_IR 13"; | |
| 1389 break; | |
| 1390 | |
| 1391 case Encoding_Chinese: | |
| 1392 s = "GB18030"; | |
| 1393 break; | |
|
1090
e494ceb8d763
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parents:
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diff
changeset
|
1394 |
|
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parents:
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diff
changeset
|
1395 case Encoding_Thai: |
|
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parents:
1018
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changeset
|
1396 s = "ISO_IR 166"; |
|
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parents:
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diff
changeset
|
1397 break; |
|
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parents:
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diff
changeset
|
1398 |
|
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parents:
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diff
changeset
|
1399 default: |
|
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parents:
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diff
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|
1400 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
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|
1401 } |
|
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parents:
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changeset
|
1402 |
| 1091 | 1403 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
1090
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|
1404 } |
|
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|
1405 |
|
1160
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parents:
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diff
changeset
|
1406 void ParsedDicomFile::ToJson(Json::Value& target, bool simplify) |
|
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parents:
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diff
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|
1407 { |
|
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|
1408 if (simplify) |
|
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|
1409 { |
|
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generalization of create-dicom
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|
1410 Json::Value tmp; |
|
80671157d051
generalization of create-dicom
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changeset
|
1411 FromDcmtkBridge::ToJson(tmp, *pimpl_->file_->getDataset()); |
|
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|
1412 SimplifyTags(target, tmp); |
|
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|
1413 } |
|
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parents:
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|
1414 else |
|
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|
1415 { |
|
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parents:
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changeset
|
1416 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset()); |
|
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|
1417 } |
|
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|
1418 } |
|
1555
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Creation of DICOM files with encapsulated PDF
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parents:
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|
1419 |
|
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Creation of DICOM files with encapsulated PDF
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|
1420 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1421 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
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|
1422 { |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1423 DcmTag key(tag.GetGroup(), tag.GetElement()); |
|
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|
1424 return pimpl_->file_->getDataset()->tagExists(key); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1425 } |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1426 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1427 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1428 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1429 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1430 if (pdf.size() < 5 || // (*) |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1431 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1432 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1433 LOG(ERROR) << "Not a PDF file"; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1434 throw OrthancException(ErrorCode_BadFileFormat); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1435 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1436 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1437 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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1523
diff
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1438 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
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1439 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
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Creation of DICOM files with encapsulated PDF
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1440 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
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1441 Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
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Creation of DICOM files with encapsulated PDF
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1442 |
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Creation of DICOM files with encapsulated PDF
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1443 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
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1444 |
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Creation of DICOM files with encapsulated PDF
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1445 size_t s = pdf.size(); |
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Creation of DICOM files with encapsulated PDF
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1446 if (s & 1) |
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Creation of DICOM files with encapsulated PDF
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1447 { |
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Creation of DICOM files with encapsulated PDF
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1448 // The size of the buffer must be even |
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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1449 s += 1; |
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Creation of DICOM files with encapsulated PDF
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1450 } |
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Creation of DICOM files with encapsulated PDF
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1451 |
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Creation of DICOM files with encapsulated PDF
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1452 Uint8* bytes = NULL; |
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Creation of DICOM files with encapsulated PDF
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1453 OFCondition result = element->createUint8Array(s, bytes); |
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Creation of DICOM files with encapsulated PDF
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1454 if (!result.good() || bytes == NULL) |
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Creation of DICOM files with encapsulated PDF
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1455 { |
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Creation of DICOM files with encapsulated PDF
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1456 throw OrthancException(ErrorCode_NotEnoughMemory); |
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1457 } |
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1458 |
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1459 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
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Creation of DICOM files with encapsulated PDF
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1460 bytes[s - 1] = 0; |
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1461 |
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1462 memcpy(bytes, pdf.c_str(), pdf.size()); |
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1463 |
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1464 DcmPolymorphOBOW* obj = element.release(); |
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1465 result = pimpl_->file_->getDataset()->insert(obj); |
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1466 |
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1467 if (!result.good()) |
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1468 { |
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Creation of DICOM files with encapsulated PDF
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1469 delete obj; |
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Creation of DICOM files with encapsulated PDF
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1470 throw OrthancException(ErrorCode_NotEnoughMemory); |
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1471 } |
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1472 } |
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1473 |
| 790 | 1474 } |