Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1668:de1413733c97 db-changes
reconstructing main dicom tags
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 30 Sep 2015 17:18:39 +0200 |
| parents | 09be34b2f30e |
| children | 4aaaecae5803 |
| 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/Images/ImageBuffer.h" |
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91 #include "../Core/Images/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/Images/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)), |
| 1616 | 275 offset_(0), |
| 276 chunkSize_(0) | |
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277 { |
| 1521 | 278 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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279 chunk_.resize(CHUNK_SIZE); |
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280 } |
| 790 | 281 |
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282 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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283 bool /*deflateAllowed*/) |
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284 { |
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285 // No support for compression |
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286 return HttpCompression_None; |
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287 } |
| 790 | 288 |
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289 virtual bool HasContentFilename(std::string& filename) |
| 790 | 290 { |
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291 return false; |
| 790 | 292 } |
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293 |
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294 virtual std::string GetContentType() |
| 790 | 295 { |
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296 return ""; |
| 790 | 297 } |
| 298 | |
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299 virtual uint64_t GetContentLength() |
| 790 | 300 { |
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301 return length_; |
| 790 | 302 } |
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303 |
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304 virtual bool ReadNextChunk() |
| 790 | 305 { |
| 1520 | 306 assert(offset_ <= length_); |
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307 |
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308 if (offset_ == length_) |
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309 { |
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310 return false; |
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311 } |
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312 else |
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313 { |
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314 if (length_ - offset_ < chunk_.size()) |
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315 { |
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316 chunkSize_ = length_ - offset_; |
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317 } |
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318 else |
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319 { |
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320 chunkSize_ = chunk_.size(); |
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321 } |
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322 |
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323 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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324 |
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325 offset_ += chunkSize_; |
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326 |
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327 if (!cond.good()) |
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328 { |
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329 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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330 throw OrthancException(ErrorCode_InternalError); |
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331 } |
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332 |
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333 return true; |
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334 } |
| 790 | 335 } |
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336 |
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337 virtual const char *GetChunkContent() |
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338 { |
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339 return chunk_.c_str(); |
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340 } |
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341 |
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342 virtual size_t GetChunkSize() |
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343 { |
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344 return chunkSize_; |
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345 } |
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346 }; |
| 790 | 347 } |
| 348 | |
| 349 | |
| 350 static bool AnswerPixelData(RestApiOutput& output, | |
| 351 DcmItem& dicom, | |
| 352 E_TransferSyntax transferSyntax, | |
| 353 const std::string* blockUri) | |
| 354 { | |
| 355 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 356 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 357 | |
| 358 DcmElement *element = NULL; | |
| 359 if (!dicom.findAndGetElement(k, element).good() || | |
| 360 element == NULL) | |
| 361 { | |
| 362 return false; | |
| 363 } | |
| 364 | |
| 365 try | |
| 366 { | |
| 367 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 368 if (blockUri == NULL) | |
| 369 { | |
| 370 // The user asks how many blocks are presents in this pixel data | |
| 371 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 372 | |
| 373 Json::Value result(Json::arrayValue); | |
| 374 for (unsigned int i = 0; i < blocks; i++) | |
| 375 { | |
| 376 result.append(boost::lexical_cast<std::string>(i)); | |
| 377 } | |
| 378 | |
| 379 output.AnswerJson(result); | |
| 380 return true; | |
| 381 } | |
| 382 | |
| 383 | |
| 384 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 385 | |
| 386 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 387 { | |
| 388 DcmPixelSequence* pixelSequence = NULL; | |
| 389 if (pixelData.getEncapsulatedRepresentation | |
| 390 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 391 { | |
| 392 // This is the case for JPEG transfer syntaxes | |
| 393 if (block < pixelSequence->card()) | |
| 394 { | |
| 395 DcmPixelItem* pixelItem = NULL; | |
| 396 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 397 { | |
| 398 if (pixelItem->getLength() == 0) | |
| 399 { | |
| 400 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 401 return true; | |
| 402 } | |
| 403 | |
| 404 Uint8* buffer = NULL; | |
| 405 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 406 { | |
| 407 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 408 return true; | |
| 409 } | |
| 410 } | |
| 411 } | |
| 412 } | |
| 413 else | |
| 414 { | |
| 415 // This is the case for raw, uncompressed image buffers | |
| 416 assert(*blockUri == "0"); | |
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417 DicomFieldStream stream(*element, transferSyntax); |
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418 output.AnswerStream(stream); |
| 790 | 419 } |
| 420 } | |
| 421 } | |
| 422 catch (boost::bad_lexical_cast&) | |
| 423 { | |
| 424 // The URI entered by the user is not a number | |
| 425 } | |
| 426 catch (std::bad_cast&) | |
| 427 { | |
| 428 // This should never happen | |
| 429 } | |
| 430 | |
| 431 return false; | |
| 432 } | |
| 433 | |
| 434 | |
| 435 | |
| 436 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 437 const std::string& tag, | |
| 438 DcmItem& dicom, | |
| 439 E_TransferSyntax transferSyntax) | |
| 440 { | |
| 441 DcmTagKey k; | |
| 442 ParseTagAndGroup(k, tag); | |
| 443 | |
| 444 DcmSequenceOfItems* sequence = NULL; | |
| 445 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 446 sequence != NULL && | |
| 447 sequence->getVR() == EVR_SQ) | |
| 448 { | |
| 449 SendSequence(output, *sequence); | |
| 450 return; | |
| 451 } | |
| 452 | |
| 453 DcmElement* element = NULL; | |
| 454 if (dicom.findAndGetElement(k, element).good() && | |
| 455 element != NULL && | |
| 456 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 457 element->getVR() != EVR_SQ) | |
| 458 { | |
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459 DicomFieldStream stream(*element, transferSyntax); |
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460 output.AnswerStream(stream); |
| 790 | 461 } |
| 462 } | |
| 463 | |
| 464 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 465 const UriComponents& uri) | |
| 466 { | |
| 794 | 467 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 468 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 469 |
| 470 // Special case: Accessing the pixel data | |
| 471 if (uri.size() == 1 || | |
| 472 uri.size() == 2) | |
| 473 { | |
| 474 DcmTagKey tag; | |
| 475 ParseTagAndGroup(tag, uri[0]); | |
| 476 | |
| 477 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 478 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 479 { | |
| 480 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 481 return; | |
| 482 } | |
| 483 } | |
| 484 | |
| 485 // Go down in the tag hierarchy according to the URI | |
| 486 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 487 { | |
| 488 size_t index; | |
| 489 try | |
| 490 { | |
| 491 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 492 } | |
| 493 catch (boost::bad_lexical_cast&) | |
| 494 { | |
| 495 return; | |
| 496 } | |
| 497 | |
| 498 DcmTagKey k; | |
| 499 DcmItem *child = NULL; | |
| 500 ParseTagAndGroup(k, uri[2 * pos]); | |
| 501 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 502 child == NULL) | |
| 503 { | |
| 504 return; | |
| 505 } | |
| 506 | |
| 507 dicom = child; | |
| 508 } | |
| 509 | |
| 510 // We have reached the end of the URI | |
| 511 if (uri.size() % 2 == 0) | |
| 512 { | |
| 513 SendPathValueForDictionary(output, *dicom); | |
| 514 } | |
| 515 else | |
| 516 { | |
| 517 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 518 } | |
| 519 } | |
| 520 | |
| 521 | |
| 522 | |
| 523 | |
| 524 | |
| 525 static DcmElement* CreateElementForTag(const DicomTag& tag) | |
| 526 { | |
| 527 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 528 | |
| 529 switch (key.getEVR()) | |
| 530 { | |
| 531 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 532 | |
| 533 /** | |
| 534 * TODO. | |
| 535 **/ | |
| 536 | |
| 537 case EVR_OB: // other byte | |
| 538 case EVR_OF: // other float | |
| 539 case EVR_OW: // other word | |
| 540 case EVR_AT: // attribute tag | |
| 541 throw OrthancException(ErrorCode_NotImplemented); | |
| 542 | |
| 543 case EVR_UN: // unknown value representation | |
| 544 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 545 | |
| 546 | |
| 547 /** | |
| 548 * String types. | |
| 549 * http://support.dcmtk.org/docs/classDcmByteString.html | |
| 550 **/ | |
| 551 | |
| 552 case EVR_AS: // age string | |
| 553 return new DcmAgeString(key); | |
| 554 | |
| 555 case EVR_AE: // application entity title | |
| 556 return new DcmApplicationEntity(key); | |
| 557 | |
| 558 case EVR_CS: // code string | |
| 559 return new DcmCodeString(key); | |
| 560 | |
| 561 case EVR_DA: // date string | |
| 562 return new DcmDate(key); | |
| 563 | |
| 564 case EVR_DT: // date time string | |
| 565 return new DcmDateTime(key); | |
| 566 | |
| 567 case EVR_DS: // decimal string | |
| 568 return new DcmDecimalString(key); | |
| 569 | |
| 570 case EVR_IS: // integer string | |
| 571 return new DcmIntegerString(key); | |
| 572 | |
| 573 case EVR_TM: // time string | |
| 574 return new DcmTime(key); | |
| 575 | |
| 576 case EVR_UI: // unique identifier | |
| 577 return new DcmUniqueIdentifier(key); | |
| 578 | |
| 579 case EVR_ST: // short text | |
| 580 return new DcmShortText(key); | |
| 581 | |
| 582 case EVR_LO: // long string | |
| 583 return new DcmLongString(key); | |
| 584 | |
| 585 case EVR_LT: // long text | |
| 586 return new DcmLongText(key); | |
| 587 | |
| 588 case EVR_UT: // unlimited text | |
| 589 return new DcmUnlimitedText(key); | |
| 590 | |
| 591 case EVR_SH: // short string | |
| 592 return new DcmShortString(key); | |
| 593 | |
| 594 case EVR_PN: // person name | |
| 595 return new DcmPersonName(key); | |
| 596 | |
| 597 | |
| 598 /** | |
| 599 * Numerical types | |
| 600 **/ | |
| 601 | |
| 602 case EVR_SL: // signed long | |
| 603 return new DcmSignedLong(key); | |
| 604 | |
| 605 case EVR_SS: // signed short | |
| 606 return new DcmSignedShort(key); | |
| 607 | |
| 608 case EVR_UL: // unsigned long | |
| 609 return new DcmUnsignedLong(key); | |
| 610 | |
| 611 case EVR_US: // unsigned short | |
| 612 return new DcmUnsignedShort(key); | |
| 613 | |
| 614 case EVR_FL: // float single-precision | |
| 615 return new DcmFloatingPointSingle(key); | |
| 616 | |
| 617 case EVR_FD: // float double-precision | |
| 618 return new DcmFloatingPointDouble(key); | |
| 619 | |
| 620 | |
| 621 /** | |
| 622 * Sequence types, should never occur at this point. | |
| 623 **/ | |
| 624 | |
| 625 case EVR_SQ: // sequence of items | |
| 626 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 627 | |
| 628 | |
| 629 /** | |
| 630 * Internal to DCMTK. | |
| 631 **/ | |
| 632 | |
| 633 case EVR_ox: // OB or OW depending on context | |
| 634 case EVR_xs: // SS or US depending on context | |
| 635 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 636 case EVR_na: // na="not applicable", for data which has no VR | |
| 637 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 638 case EVR_item: // used internally for items | |
| 639 case EVR_metainfo: // used internally for meta info datasets | |
| 640 case EVR_dataset: // used internally for datasets | |
| 641 case EVR_fileFormat: // used internally for DICOM files | |
| 642 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 643 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 644 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 645 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 646 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 647 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 648 case EVR_OverlayData: // used internally for overlay data | |
| 649 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 650 default: | |
| 651 break; | |
| 652 } | |
| 653 | |
| 654 throw OrthancException(ErrorCode_InternalError); | |
| 655 } | |
| 656 | |
| 657 | |
| 658 | |
| 659 static void FillElementWithString(DcmElement& element, | |
| 660 const DicomTag& tag, | |
| 661 const std::string& value) | |
| 662 { | |
| 663 DcmTag key(tag.GetGroup(), tag.GetElement()); | |
| 664 bool ok = false; | |
| 665 | |
| 666 try | |
| 667 { | |
| 668 switch (key.getEVR()) | |
| 669 { | |
| 670 // http://support.dcmtk.org/docs/dcvr_8h-source.html | |
| 671 | |
| 672 /** | |
| 673 * TODO. | |
| 674 **/ | |
| 675 | |
| 676 case EVR_OB: // other byte | |
| 677 case EVR_OF: // other float | |
| 678 case EVR_OW: // other word | |
| 679 case EVR_AT: // attribute tag | |
| 680 throw OrthancException(ErrorCode_NotImplemented); | |
| 681 | |
| 682 case EVR_UN: // unknown value representation | |
| 683 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 684 | |
| 685 | |
| 686 /** | |
| 687 * String types. | |
| 688 **/ | |
| 689 | |
| 690 case EVR_DS: // decimal string | |
| 691 case EVR_IS: // integer string | |
| 692 case EVR_AS: // age string | |
| 693 case EVR_DA: // date string | |
| 694 case EVR_DT: // date time string | |
| 695 case EVR_TM: // time string | |
| 696 case EVR_AE: // application entity title | |
| 697 case EVR_CS: // code string | |
| 698 case EVR_SH: // short string | |
| 699 case EVR_LO: // long string | |
| 700 case EVR_ST: // short text | |
| 701 case EVR_LT: // long text | |
| 702 case EVR_UT: // unlimited text | |
| 703 case EVR_PN: // person name | |
| 704 case EVR_UI: // unique identifier | |
| 705 { | |
| 706 ok = element.putString(value.c_str()).good(); | |
| 707 break; | |
| 708 } | |
| 709 | |
| 710 | |
| 711 /** | |
| 712 * Numerical types | |
| 713 **/ | |
| 714 | |
| 715 case EVR_SL: // signed long | |
| 716 { | |
| 717 ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good(); | |
| 718 break; | |
| 719 } | |
| 720 | |
| 721 case EVR_SS: // signed short | |
| 722 { | |
| 723 ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good(); | |
| 724 break; | |
| 725 } | |
| 726 | |
| 727 case EVR_UL: // unsigned long | |
| 728 { | |
| 729 ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good(); | |
| 730 break; | |
| 731 } | |
| 732 | |
| 733 case EVR_US: // unsigned short | |
| 734 { | |
| 735 ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good(); | |
| 736 break; | |
| 737 } | |
| 738 | |
| 739 case EVR_FL: // float single-precision | |
| 740 { | |
| 741 ok = element.putFloat32(boost::lexical_cast<float>(value)).good(); | |
| 742 break; | |
| 743 } | |
| 744 | |
| 745 case EVR_FD: // float double-precision | |
| 746 { | |
| 747 ok = element.putFloat64(boost::lexical_cast<double>(value)).good(); | |
| 748 break; | |
| 749 } | |
| 750 | |
| 751 | |
| 752 /** | |
| 753 * Sequence types, should never occur at this point. | |
| 754 **/ | |
| 755 | |
| 756 case EVR_SQ: // sequence of items | |
| 757 { | |
| 758 ok = false; | |
| 759 break; | |
| 760 } | |
| 761 | |
| 762 | |
| 763 /** | |
| 764 * Internal to DCMTK. | |
| 765 **/ | |
| 766 | |
| 767 case EVR_ox: // OB or OW depending on context | |
| 768 case EVR_xs: // SS or US depending on context | |
| 769 case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) | |
| 770 case EVR_na: // na="not applicable", for data which has no VR | |
| 771 case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor | |
| 772 case EVR_item: // used internally for items | |
| 773 case EVR_metainfo: // used internally for meta info datasets | |
| 774 case EVR_dataset: // used internally for datasets | |
| 775 case EVR_fileFormat: // used internally for DICOM files | |
| 776 case EVR_dicomDir: // used internally for DICOMDIR objects | |
| 777 case EVR_dirRecord: // used internally for DICOMDIR records | |
| 778 case EVR_pixelSQ: // used internally for pixel sequences in a compressed image | |
| 779 case EVR_pixelItem: // used internally for pixel items in a compressed image | |
| 780 case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) | |
| 781 case EVR_PixelData: // used internally for uncompressed pixeld data | |
| 782 case EVR_OverlayData: // used internally for overlay data | |
| 783 case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR | |
| 784 default: | |
| 785 break; | |
| 786 } | |
| 787 } | |
| 788 catch (boost::bad_lexical_cast&) | |
| 789 { | |
| 790 ok = false; | |
| 791 } | |
| 792 | |
| 793 if (!ok) | |
| 794 { | |
| 795 throw OrthancException(ErrorCode_InternalError); | |
| 796 } | |
| 797 } | |
| 798 | |
| 799 | |
| 800 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 801 { | |
| 802 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 803 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 804 if (element != NULL) |
| 805 { | |
| 806 delete element; | |
| 807 } | |
| 808 } | |
| 809 | |
| 810 | |
| 811 | |
|
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812 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 813 { |
|
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814 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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815 |
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|
816 // Loop over the dataset to detect its private tags |
| 790 | 817 typedef std::list<DcmElement*> Tags; |
| 818 Tags privateTags; | |
| 819 | |
| 820 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 821 { | |
| 822 DcmElement* element = dataset.getElement(i); | |
| 823 DcmTag tag(element->getTag()); | |
|
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824 |
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825 // Is this a private tag? |
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826 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 827 { |
|
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828 bool remove = true; |
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829 |
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830 // Check whether this private tag is to be kept |
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831 if (toKeep != NULL) |
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832 { |
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833 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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834 if (toKeep->find(tmp) != toKeep->end()) |
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835 { |
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836 remove = false; // Keep it |
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837 } |
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838 } |
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839 |
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840 if (remove) |
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841 { |
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842 privateTags.push_back(element); |
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843 } |
| 790 | 844 } |
| 845 } | |
| 846 | |
|
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847 // Loop over the detected private tags to remove them |
| 790 | 848 for (Tags::iterator it = privateTags.begin(); |
| 849 it != privateTags.end(); ++it) | |
| 850 { | |
| 851 DcmElement* tmp = dataset.remove(*it); | |
| 852 if (tmp != NULL) | |
| 853 { | |
| 854 delete tmp; | |
| 855 } | |
| 856 } | |
| 857 } | |
| 858 | |
| 859 | |
| 860 | |
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861 |
| 790 | 862 void ParsedDicomFile::Insert(const DicomTag& tag, |
| 863 const std::string& value) | |
| 864 { | |
|
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865 OFCondition cond; |
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866 |
|
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867 if (FromDcmtkBridge::IsPrivateTag(tag) || |
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868 FromDcmtkBridge::IsUnknownTag(tag)) |
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869 { |
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870 // This is a private tag |
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871 // http://support.dcmtk.org/redmine/projects/dcmtk/wiki/howto_addprivatedata |
| 790 | 872 |
|
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873 DcmTag key(tag.GetGroup(), tag.GetElement(), EVR_OB); |
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874 cond = pimpl_->file_->getDataset()->putAndInsertUint8Array |
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875 (key, (const Uint8*) value.c_str(), value.size(), false); |
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876 } |
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877 else |
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878 { |
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879 std::auto_ptr<DcmElement> element(CreateElementForTag(tag)); |
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880 FillElementWithString(*element, tag, value); |
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881 |
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882 cond = pimpl_->file_->getDataset()->insert(element.release(), false, false); |
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883 } |
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884 |
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885 if (!cond.good()) |
| 790 | 886 { |
| 887 // This field already exists | |
| 888 throw OrthancException(ErrorCode_InternalError); | |
| 889 } | |
| 890 } | |
| 891 | |
| 892 | |
| 893 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 894 const std::string& value, | |
| 895 DicomReplaceMode mode) | |
| 896 { | |
| 897 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 898 DcmElement* element = NULL; | |
| 899 | |
| 794 | 900 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 901 element == NULL) |
| 902 { | |
| 903 // This field does not exist, act wrt. the specified "mode" | |
| 904 switch (mode) | |
| 905 { | |
| 906 case DicomReplaceMode_InsertIfAbsent: | |
| 907 Insert(tag, value); | |
| 908 break; | |
| 909 | |
| 910 case DicomReplaceMode_ThrowIfAbsent: | |
| 911 throw OrthancException(ErrorCode_InexistentItem); | |
| 912 | |
| 913 case DicomReplaceMode_IgnoreIfAbsent: | |
| 914 return; | |
| 915 } | |
| 916 } | |
| 917 else | |
| 918 { | |
|
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919 if (FromDcmtkBridge::IsPrivateTag(tag) || |
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920 FromDcmtkBridge::IsUnknownTag(tag)) |
|
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921 { |
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922 if (!element->putUint8Array((const Uint8*) value.c_str(), value.size()).good()) |
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923 { |
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924 throw OrthancException(ErrorCode_InternalError); |
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925 } |
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926 } |
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927 else |
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928 { |
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929 FillElementWithString(*element, tag, value); |
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|
930 } |
| 790 | 931 } |
| 932 | |
| 933 | |
| 934 /** | |
| 935 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 936 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 937 * you make changes to the related tags in the dataset ('SOP Class | |
| 938 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 939 * options. You can disable this behaviour by using the -nmu | |
| 940 * option. | |
| 941 **/ | |
| 942 | |
| 943 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 944 { | |
| 945 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 946 } | |
| 947 | |
| 948 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 949 { | |
| 950 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 951 } | |
| 952 } | |
| 953 | |
| 954 | |
| 955 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 956 { | |
| 957 std::string serialized; | |
|
1004
a226e0959d8b
DicomInstanceToStore
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958 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 959 { |
| 960 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 961 } | |
| 962 } | |
| 963 | |
| 964 | |
| 965 | |
| 966 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 967 const DicomTag& tag) | |
| 968 { | |
| 969 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 970 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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971 |
|
1556
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972 if (FromDcmtkBridge::IsPrivateTag(tag) || |
|
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973 FromDcmtkBridge::IsUnknownTag(tag) || |
|
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974 tag == DICOM_TAG_PIXEL_DATA || |
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975 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 976 { |
|
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977 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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978 long unsigned int count = 0; |
| 790 | 979 |
|
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980 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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981 { |
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982 if (count > 0) |
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983 { |
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984 assert(data != NULL); |
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985 value.assign(reinterpret_cast<const char*>(data), count); |
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986 } |
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987 else |
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988 { |
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989 value.clear(); |
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990 } |
| 790 | 991 |
|
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992 return true; |
|
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993 } |
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994 else |
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995 { |
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996 return false; |
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997 } |
| 790 | 998 } |
| 999 else | |
| 1000 { | |
|
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1001 DcmElement* element = NULL; |
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1002 if (!dataset.findAndGetElement(k, element).good() || |
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1003 element == NULL) |
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1004 { |
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1005 return false; |
|
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1006 } |
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1007 |
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1008 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
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1009 |
|
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1010 if (v.get() == NULL) |
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1011 { |
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1012 value = ""; |
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1013 } |
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1014 else |
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1015 { |
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1016 value = v->AsString(); |
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1017 } |
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1018 |
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1019 return true; |
| 790 | 1020 } |
| 1021 } | |
| 1022 | |
| 1023 | |
| 1024 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 1025 { | |
| 1026 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 1027 | |
| 1028 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 1029 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 1030 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 1031 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 1032 { | |
| 1033 throw OrthancException(ErrorCode_BadFileFormat); | |
| 1034 } | |
| 1035 | |
| 1036 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 1037 } | |
| 1038 | |
| 1039 | |
| 1040 template <typename T> | |
| 1041 static void ExtractPngImageTruncate(std::string& result, | |
| 1042 DicomIntegerPixelAccessor& accessor, | |
| 1043 PixelFormat format) | |
| 1044 { | |
|
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1045 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 1046 |
| 1047 PngWriter w; | |
| 1048 | |
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1049 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 1050 T* pixel = &image[0]; |
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1051 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 1052 { |
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1053 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 1054 { |
| 1055 int32_t v = accessor.GetValue(x, y); | |
| 1056 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 1057 *pixel = std::numeric_limits<T>::min(); | |
| 1058 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 1059 *pixel = std::numeric_limits<T>::max(); | |
| 1060 else | |
| 1061 *pixel = static_cast<T>(v); | |
| 1062 } | |
| 1063 } | |
| 1064 | |
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1065 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
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1066 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 1067 } |
| 1068 | |
| 1069 | |
| 1070 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 1071 { | |
|
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1072 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 1073 } |
| 1074 | |
| 1075 | |
| 1076 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 1077 { | |
| 1078 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 1079 std::string content; | |
| 1080 SaveToMemoryBuffer(content); | |
| 1081 Toolbox::WriteFile(content, path); | |
| 1082 } | |
| 1083 | |
| 1084 | |
| 794 | 1085 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 1086 { |
| 794 | 1087 pimpl_->file_.reset(new DcmFileFormat); |
|
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1088 pimpl_->encoding_ = Encoding_Ascii; |
| 790 | 1089 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 1090 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 1091 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 1092 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 1093 } | |
| 1094 | |
| 791 | 1095 |
| 794 | 1096 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 1097 { |
| 1098 Setup(content, size); | |
| 1099 } | |
| 1100 | |
| 794 | 1101 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 1102 { |
| 1103 if (content.size() == 0) | |
| 1104 { | |
| 1105 Setup(NULL, 0); | |
| 1106 } | |
| 1107 else | |
| 1108 { | |
| 1109 Setup(&content[0], content.size()); | |
| 1110 } | |
| 1111 } | |
| 792 | 1112 |
| 1113 | |
| 794 | 1114 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 1115 pimpl_(new PImpl) | |
| 792 | 1116 { |
| 794 | 1117 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
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1118 pimpl_->encoding_ = other.pimpl_->encoding_; |
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1119 |
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1120 // Create a new instance-level identifier |
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1121 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 1122 } |
| 1123 | |
| 1124 | |
| 1125 ParsedDicomFile::~ParsedDicomFile() | |
| 1126 { | |
| 794 | 1127 delete pimpl_; |
| 792 | 1128 } |
| 1129 | |
| 793 | 1130 |
| 1131 void* ParsedDicomFile::GetDcmtkObject() | |
| 1132 { | |
| 794 | 1133 return pimpl_->file_.get(); |
| 793 | 1134 } |
| 1135 | |
| 1136 | |
| 1137 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 1138 { | |
| 794 | 1139 return new ParsedDicomFile(*this); |
| 793 | 1140 } |
|
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1141 |
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1142 |
| 1562 | 1143 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
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1144 { |
|
1641
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1145 std::string mime, content; |
|
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1146 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
| 1562 | 1147 Toolbox::ToLowerCase(mime); |
|
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1148 |
| 1562 | 1149 if (mime == "image/png") |
| 1150 { | |
| 1151 EmbedImage(mime, content); | |
| 1152 } | |
| 1153 else if (mime == "application/pdf") | |
| 1154 { | |
| 1155 EmbedPdf(content); | |
| 1156 } | |
| 1157 else | |
| 1158 { | |
| 1159 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file"; | |
| 1160 throw OrthancException(ErrorCode_NotImplemented); | |
| 1161 } | |
|
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1162 } |
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1163 |
|
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1164 |
|
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1165 void ParsedDicomFile::EmbedImage(const std::string& mime, |
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1166 const std::string& content) |
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1167 { |
|
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1168 if (mime == "image/png") |
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1169 { |
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1170 PngReader reader; |
|
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1171 reader.ReadFromMemory(content); |
|
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1172 EmbedImage(reader); |
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1173 } |
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1174 else |
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1175 { |
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1176 throw OrthancException(ErrorCode_NotImplemented); |
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1177 } |
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1178 } |
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1179 |
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1180 |
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1181 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
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1182 { |
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1183 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
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1184 accessor.GetFormat() != PixelFormat_Grayscale16 && |
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1185 accessor.GetFormat() != PixelFormat_RGB24 && |
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1186 accessor.GetFormat() != PixelFormat_RGBA32) |
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1187 { |
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1188 throw OrthancException(ErrorCode_NotImplemented); |
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1189 } |
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1190 |
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1191 if (accessor.GetFormat() == PixelFormat_RGBA32) |
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1192 { |
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1193 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
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1194 } |
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1195 |
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1196 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
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1197 |
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1198 Remove(DICOM_TAG_PIXEL_DATA); |
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1199 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
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1200 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
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1201 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
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1202 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
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1203 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
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1204 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
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1205 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
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1206 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
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1207 Replace(DICOM_TAG_BITS_STORED, "8"); |
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1208 Replace(DICOM_TAG_HIGH_BIT, "7"); |
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1209 |
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1210 unsigned int bytesPerPixel = 1; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1211 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1212 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1213 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1214 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1215 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1216 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1217 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
|
1218 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1219 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1220 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1221 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1222 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1223 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1224 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1225 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1226 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1227 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1228 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1229 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1230 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1231 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1232 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1233 } |
|
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 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1236 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1237 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1238 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1239 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1240 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1241 Uint8* target = NULL; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1242 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1243 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1244 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
|
1245 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1246 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1247 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1248 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1249 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1250 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1251 case PixelFormat_SignedGrayscale16: |
|
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 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
|
1254 target += pitch; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1255 break; |
|
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 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1259 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1260 // 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
|
1261 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
|
1262 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
|
1263 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1264 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1265 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1266 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1267 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1268 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1269 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1270 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1271 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1272 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1273 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1274 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1275 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1276 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1277 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
|
1278 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1279 throw OrthancException(ErrorCode_InternalError); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1280 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
1281 } |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1282 |
|
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 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1285 unsigned int frame) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1286 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1287 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1288 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1289 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1290 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1291 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1292 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1293 } |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1294 |
|
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 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1297 unsigned int frame, |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1298 ImageExtractionMode mode) |
|
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 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1301 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1302 bool ok = false; |
|
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 switch (mode) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1305 { |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1306 case ImageExtractionMode_UInt8: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1307 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1308 break; |
|
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 case ImageExtractionMode_UInt16: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1311 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1312 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1313 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1314 case ImageExtractionMode_Int16: |
|
1015
f009f7c75069
fix integration tests
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
changeset
|
1315 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1316 break; |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1317 |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1318 case ImageExtractionMode_Preview: |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1319 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1320 break; |
|
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 default: |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1323 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
87791ebc1f50
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|
1324 } |
|
87791ebc1f50
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|
1325 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1326 if (!ok) |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1327 { |
|
87791ebc1f50
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diff
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|
1328 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1329 } |
|
87791ebc1f50
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parents:
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diff
changeset
|
1330 } |
|
87791ebc1f50
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parents:
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diff
changeset
|
1331 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1332 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1333 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1334 unsigned int frame, |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1335 ImageExtractionMode mode) |
|
87791ebc1f50
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parents:
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diff
changeset
|
1336 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1337 ImageBuffer buffer; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1338 ExtractImage(buffer, frame, mode); |
|
87791ebc1f50
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parents:
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diff
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|
1339 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1340 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
87791ebc1f50
download matlab images
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1341 PngWriter writer; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1342 writer.WriteToMemory(result, accessor); |
|
87791ebc1f50
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parents:
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diff
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|
1343 } |
|
87791ebc1f50
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parents:
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diff
changeset
|
1344 |
|
956
2fd5a163776d
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|
1345 |
|
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|
1346 Encoding ParsedDicomFile::GetEncoding() const |
|
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|
1347 { |
|
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|
1348 return pimpl_->encoding_; |
|
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|
1349 } |
|
1090
e494ceb8d763
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|
1350 |
|
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changeset
|
1351 |
|
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|
1352 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
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|
1353 { |
|
1558
124de28b32ed
fix encodings of newly created dicom files
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|
1354 if (encoding == Encoding_Windows1251) |
|
1090
e494ceb8d763
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|
1355 { |
|
1558
124de28b32ed
fix encodings of newly created dicom files
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|
1356 // This Cyrillic codepage is not officially supported by the |
|
124de28b32ed
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|
1357 // DICOM standard. Do not set the SpecificCharacterSet tag. |
|
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|
1358 return; |
|
1090
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|
1359 } |
|
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diff
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|
1360 |
|
1565
4b23310eb7e8
add tags per instances in a series
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|
1361 pimpl_->encoding_ = encoding; |
|
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|
1362 |
|
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|
1363 std::string s = GetDicomSpecificCharacterSet(encoding); |
| 1091 | 1364 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
1090
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|
1365 } |
|
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|
1366 |
|
1160
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|
1367 void ParsedDicomFile::ToJson(Json::Value& target, bool simplify) |
|
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1368 { |
|
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|
1369 if (simplify) |
|
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|
1370 { |
|
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|
1371 Json::Value tmp; |
|
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|
1372 FromDcmtkBridge::ToJson(tmp, *pimpl_->file_->getDataset()); |
|
1668
de1413733c97
reconstructing main dicom tags
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|
1373 Toolbox::SimplifyTags(target, tmp); |
|
1160
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|
1374 } |
|
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|
1375 else |
|
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|
1376 { |
|
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generalization of create-dicom
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|
1377 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset()); |
|
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|
1378 } |
|
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diff
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|
1379 } |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1380 |
|
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Creation of DICOM files with encapsulated PDF
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|
1381 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1382 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
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Creation of DICOM files with encapsulated PDF
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|
1383 { |
|
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Creation of DICOM files with encapsulated PDF
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|
1384 DcmTag key(tag.GetGroup(), tag.GetElement()); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1385 return pimpl_->file_->getDataset()->tagExists(key); |
|
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Creation of DICOM files with encapsulated PDF
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|
1386 } |
|
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Creation of DICOM files with encapsulated PDF
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diff
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|
1387 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1388 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1389 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
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Creation of DICOM files with encapsulated PDF
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|
1390 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1391 if (pdf.size() < 5 || // (*) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1392 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1393 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1394 LOG(ERROR) << "Not a PDF file"; |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1395 throw OrthancException(ErrorCode_BadFileFormat); |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1396 } |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1397 |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1398 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1399 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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changeset
|
1400 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1401 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
| 1566 | 1402 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
|
1555
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1403 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1404 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1405 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1406 size_t s = pdf.size(); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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parents:
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changeset
|
1407 if (s & 1) |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1408 { |
|
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Creation of DICOM files with encapsulated PDF
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diff
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|
1409 // 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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changeset
|
1410 s += 1; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1411 } |
|
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Creation of DICOM files with encapsulated PDF
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|
1412 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1413 Uint8* bytes = NULL; |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1414 OFCondition result = element->createUint8Array(s, bytes); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1415 if (!result.good() || bytes == NULL) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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changeset
|
1416 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1417 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1418 } |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1419 |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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|
1420 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1421 bytes[s - 1] = 0; |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1422 |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1423 memcpy(bytes, pdf.c_str(), pdf.size()); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
1424 |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1425 DcmPolymorphOBOW* obj = element.release(); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1426 result = pimpl_->file_->getDataset()->insert(obj); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1427 |
|
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Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1428 if (!result.good()) |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1429 { |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1430 delete obj; |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1431 throw OrthancException(ErrorCode_NotEnoughMemory); |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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diff
changeset
|
1432 } |
|
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Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1433 } |
|
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
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1434 |
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1556
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1435 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1436 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1437 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1438 std::string sop, mime; |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1439 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
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1440 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1441 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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parents:
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1442 sop != UID_EncapsulatedPDFStorage || |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1443 mime != "application/pdf") |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1444 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1445 return false; |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1446 } |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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parents:
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1447 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
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1448 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1449 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1450 return false; |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1451 } |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1452 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1453 // Strip the possible pad byte at the end of file, because the |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1454 // encapsulated documents must always have an even length. The PDF |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1455 // format expects files to end with %%EOF followed by CR/LF. If |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1456 // the last character of the file is not a CR or LF, we assume it |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1457 // is a pad byte and remove it. |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1458 if (pdf.size() > 0) |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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parents:
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1459 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1460 char last = *pdf.rbegin(); |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
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1461 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1462 if (last != 10 && last != 13) |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
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1463 { |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1464 pdf.resize(pdf.size() - 1); |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1465 } |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1466 } |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
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1467 |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
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1468 return true; |
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Preview of PDF files encapsulated in DICOM from Orthanc Explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1469 } |
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1662
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ParsedDicomFile::Convert()
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1470 |
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ParsedDicomFile::Convert()
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1471 |
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ParsedDicomFile::Convert()
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1472 void ParsedDicomFile::Convert(DicomMap& tags) |
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ParsedDicomFile::Convert()
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parents:
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1473 { |
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ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
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1474 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset()); |
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ParsedDicomFile::Convert()
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1475 } |
| 790 | 1476 } |