Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1689:26083d84d237
refactoring
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 07 Oct 2015 16:54:05 +0200 |
| parents | 14a32b2fa63e |
| children | 558b25228a23 |
| 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 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 523 { | |
| 524 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 525 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 526 if (element != NULL) |
| 527 { | |
| 528 delete element; | |
| 529 } | |
| 530 } | |
| 531 | |
| 532 | |
| 533 | |
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534 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 535 { |
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536 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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537 |
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538 // Loop over the dataset to detect its private tags |
| 790 | 539 typedef std::list<DcmElement*> Tags; |
| 540 Tags privateTags; | |
| 541 | |
| 542 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 543 { | |
| 544 DcmElement* element = dataset.getElement(i); | |
| 545 DcmTag tag(element->getTag()); | |
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546 |
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547 // Is this a private tag? |
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548 if (FromDcmtkBridge::IsPrivateTag(tag)) |
| 790 | 549 { |
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550 bool remove = true; |
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551 |
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552 // Check whether this private tag is to be kept |
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553 if (toKeep != NULL) |
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554 { |
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555 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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556 if (toKeep->find(tmp) != toKeep->end()) |
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557 { |
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558 remove = false; // Keep it |
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559 } |
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560 } |
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561 |
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562 if (remove) |
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563 { |
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564 privateTags.push_back(element); |
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565 } |
| 790 | 566 } |
| 567 } | |
| 568 | |
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569 // Loop over the detected private tags to remove them |
| 790 | 570 for (Tags::iterator it = privateTags.begin(); |
| 571 it != privateTags.end(); ++it) | |
| 572 { | |
| 573 DcmElement* tmp = dataset.remove(*it); | |
| 574 if (tmp != NULL) | |
| 575 { | |
| 576 delete tmp; | |
| 577 } | |
| 578 } | |
| 579 } | |
| 580 | |
| 581 | |
| 582 void ParsedDicomFile::Insert(const DicomTag& tag, | |
| 583 const std::string& value) | |
| 584 { | |
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585 OFCondition cond; |
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586 |
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587 if (FromDcmtkBridge::IsPrivateTag(tag) || |
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588 FromDcmtkBridge::IsUnknownTag(tag)) |
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589 { |
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590 // This is a private tag |
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591 // http://support.dcmtk.org/redmine/projects/dcmtk/wiki/howto_addprivatedata |
| 790 | 592 |
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593 DcmTag key(tag.GetGroup(), tag.GetElement(), EVR_OB); |
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594 cond = pimpl_->file_->getDataset()->putAndInsertUint8Array |
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595 (key, (const Uint8*) value.c_str(), value.size(), false); |
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596 } |
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597 else |
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598 { |
| 1689 | 599 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
| 600 FromDcmtkBridge::FillElementWithString(*element, tag, value, false); | |
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601 |
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602 cond = pimpl_->file_->getDataset()->insert(element.release(), false, false); |
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603 } |
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604 |
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605 if (!cond.good()) |
| 790 | 606 { |
| 607 // This field already exists | |
| 608 throw OrthancException(ErrorCode_InternalError); | |
| 609 } | |
| 610 } | |
| 611 | |
| 612 | |
| 613 void ParsedDicomFile::Replace(const DicomTag& tag, | |
| 614 const std::string& value, | |
| 615 DicomReplaceMode mode) | |
| 616 { | |
| 617 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 618 DcmElement* element = NULL; | |
| 619 | |
| 794 | 620 if (!pimpl_->file_->getDataset()->findAndGetElement(key, element).good() || |
| 790 | 621 element == NULL) |
| 622 { | |
| 623 // This field does not exist, act wrt. the specified "mode" | |
| 624 switch (mode) | |
| 625 { | |
| 626 case DicomReplaceMode_InsertIfAbsent: | |
| 627 Insert(tag, value); | |
| 628 break; | |
| 629 | |
| 630 case DicomReplaceMode_ThrowIfAbsent: | |
| 631 throw OrthancException(ErrorCode_InexistentItem); | |
| 632 | |
| 633 case DicomReplaceMode_IgnoreIfAbsent: | |
| 634 return; | |
| 635 } | |
| 636 } | |
| 637 else | |
| 638 { | |
| 1689 | 639 FromDcmtkBridge::FillElementWithString(*element, tag, value, false); |
| 790 | 640 } |
| 641 | |
| 642 | |
| 643 /** | |
| 644 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 645 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 646 * you make changes to the related tags in the dataset ('SOP Class | |
| 647 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 648 * options. You can disable this behaviour by using the -nmu | |
| 649 * option. | |
| 650 **/ | |
| 651 | |
| 652 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 653 { | |
| 654 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 655 } | |
| 656 | |
| 657 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 658 { | |
| 659 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, value, DicomReplaceMode_InsertIfAbsent); | |
| 660 } | |
| 661 } | |
| 662 | |
| 663 | |
| 664 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 665 { | |
| 666 std::string serialized; | |
|
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667 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 668 { |
| 669 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 670 } | |
| 671 } | |
| 672 | |
| 673 | |
| 674 | |
| 675 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 676 const DicomTag& tag) | |
| 677 { | |
| 678 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 679 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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680 |
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681 if (FromDcmtkBridge::IsPrivateTag(tag) || |
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682 FromDcmtkBridge::IsUnknownTag(tag) || |
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683 tag == DICOM_TAG_PIXEL_DATA || |
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684 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 685 { |
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686 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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687 long unsigned int count = 0; |
| 790 | 688 |
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689 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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690 { |
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691 if (count > 0) |
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692 { |
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693 assert(data != NULL); |
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694 value.assign(reinterpret_cast<const char*>(data), count); |
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695 } |
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696 else |
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697 { |
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698 value.clear(); |
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699 } |
| 790 | 700 |
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701 return true; |
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702 } |
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703 else |
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704 { |
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705 return false; |
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706 } |
| 790 | 707 } |
| 708 else | |
| 709 { | |
|
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710 DcmElement* element = NULL; |
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711 if (!dataset.findAndGetElement(k, element).good() || |
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712 element == NULL) |
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713 { |
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714 return false; |
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715 } |
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716 |
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717 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement(*element, pimpl_->encoding_)); |
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718 |
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719 if (v.get() == NULL) |
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720 { |
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721 value = ""; |
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722 } |
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723 else |
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724 { |
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725 value = v->AsString(); |
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726 } |
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727 |
|
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728 return true; |
| 790 | 729 } |
| 730 } | |
| 731 | |
| 732 | |
| 733 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 734 { | |
| 735 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 736 | |
| 737 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 738 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 739 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 740 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 741 { | |
| 742 throw OrthancException(ErrorCode_BadFileFormat); | |
| 743 } | |
| 744 | |
| 745 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 746 } | |
| 747 | |
| 748 | |
| 749 template <typename T> | |
| 750 static void ExtractPngImageTruncate(std::string& result, | |
| 751 DicomIntegerPixelAccessor& accessor, | |
| 752 PixelFormat format) | |
| 753 { | |
|
853
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DicomImageInformation
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|
754 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 755 |
| 756 PngWriter w; | |
| 757 | |
|
853
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DicomImageInformation
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758 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 759 T* pixel = &image[0]; |
|
853
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|
760 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 761 { |
|
853
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DicomImageInformation
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|
762 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 763 { |
| 764 int32_t v = accessor.GetValue(x, y); | |
| 765 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 766 *pixel = std::numeric_limits<T>::min(); | |
| 767 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 768 *pixel = std::numeric_limits<T>::max(); | |
| 769 else | |
| 770 *pixel = static_cast<T>(v); | |
| 771 } | |
| 772 } | |
| 773 | |
|
853
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DicomImageInformation
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|
774 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
|
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changeset
|
775 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 776 } |
| 777 | |
| 778 | |
| 779 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 780 { | |
|
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DicomInstanceToStore
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|
781 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 782 } |
| 783 | |
| 784 | |
| 785 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 786 { | |
| 787 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 788 std::string content; | |
| 789 SaveToMemoryBuffer(content); | |
| 790 Toolbox::WriteFile(content, path); | |
| 791 } | |
| 792 | |
| 793 | |
| 794 | 794 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 795 { |
| 794 | 796 pimpl_->file_.reset(new DcmFileFormat); |
|
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797 pimpl_->encoding_ = Encoding_Ascii; |
| 790 | 798 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 799 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 800 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 801 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 802 } | |
| 803 | |
| 791 | 804 |
| 794 | 805 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 806 { |
| 807 Setup(content, size); | |
| 808 } | |
| 809 | |
| 794 | 810 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 811 { |
| 812 if (content.size() == 0) | |
| 813 { | |
| 814 Setup(NULL, 0); | |
| 815 } | |
| 816 else | |
| 817 { | |
| 818 Setup(&content[0], content.size()); | |
| 819 } | |
| 820 } | |
| 792 | 821 |
| 822 | |
| 794 | 823 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 824 pimpl_(new PImpl) | |
| 792 | 825 { |
| 794 | 826 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
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827 pimpl_->encoding_ = other.pimpl_->encoding_; |
|
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828 |
|
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829 // Create a new instance-level identifier |
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830 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 831 } |
| 832 | |
| 833 | |
| 834 ParsedDicomFile::~ParsedDicomFile() | |
| 835 { | |
| 794 | 836 delete pimpl_; |
| 792 | 837 } |
| 838 | |
| 793 | 839 |
| 840 void* ParsedDicomFile::GetDcmtkObject() | |
| 841 { | |
| 794 | 842 return pimpl_->file_.get(); |
| 793 | 843 } |
| 844 | |
| 845 | |
| 846 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 847 { | |
| 794 | 848 return new ParsedDicomFile(*this); |
| 793 | 849 } |
|
800
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850 |
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851 |
| 1562 | 852 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
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853 { |
|
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854 std::string mime, content; |
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855 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
| 1562 | 856 Toolbox::ToLowerCase(mime); |
|
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857 |
| 1562 | 858 if (mime == "image/png") |
| 859 { | |
| 860 EmbedImage(mime, content); | |
| 861 } | |
| 862 else if (mime == "application/pdf") | |
| 863 { | |
| 864 EmbedPdf(content); | |
| 865 } | |
| 866 else | |
| 867 { | |
| 868 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file"; | |
| 869 throw OrthancException(ErrorCode_NotImplemented); | |
| 870 } | |
|
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871 } |
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872 |
|
800
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873 |
|
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874 void ParsedDicomFile::EmbedImage(const std::string& mime, |
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875 const std::string& content) |
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876 { |
|
800
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877 if (mime == "image/png") |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
878 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
879 PngReader reader; |
|
1555
d6a93e12b1c1
Creation of DICOM files with encapsulated PDF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1523
diff
changeset
|
880 reader.ReadFromMemory(content); |
|
800
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
881 EmbedImage(reader); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
882 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
883 else |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
884 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
885 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
886 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
887 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
888 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
889 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
890 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
891 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
892 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
893 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
894 accessor.GetFormat() != PixelFormat_RGB24 && |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
895 accessor.GetFormat() != PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
896 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
897 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
898 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
899 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
900 if (accessor.GetFormat() == PixelFormat_RGBA32) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
901 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
902 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
903 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
904 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
905 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
906 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
907 Remove(DICOM_TAG_PIXEL_DATA); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
908 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
909 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
910 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
911 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
912 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
913 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
914 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
915 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
916 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
917 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
918 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
919 unsigned int bytesPerPixel = 1; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
920 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
921 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
922 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
923 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
924 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
925 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
926 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
|
927 bytesPerPixel = 3; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
928 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
929 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
930 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
931 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
932 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
933 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
934 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
935 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
936 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
937 bytesPerPixel = 2; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
938 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
939 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
940 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
941 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
942 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
943 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
944 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
|
945 DICOM_TAG_PIXEL_DATA.GetElement()); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
946 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
947 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
|
948 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
949 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
950 Uint8* target = NULL; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
951 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
952 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
953 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
|
954 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
955 switch (accessor.GetFormat()) |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
956 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
957 case PixelFormat_RGB24: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
958 case PixelFormat_Grayscale8: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
959 case PixelFormat_Grayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
960 case PixelFormat_SignedGrayscale16: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
961 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
962 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
|
963 target += pitch; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
964 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
965 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
966 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
967 case PixelFormat_RGBA32: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
968 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
969 // 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
|
970 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
|
971 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
|
972 { |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
973 target[0] = source[0]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
974 target[1] = source[1]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
975 target[2] = source[2]; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
976 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
977 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
978 break; |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
979 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
980 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
981 default: |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
982 throw OrthancException(ErrorCode_NotImplemented); |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
983 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
984 } |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
985 |
|
ecedd89055db
generation of DICOM images from PNG files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
799
diff
changeset
|
986 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
|
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987 { |
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988 throw OrthancException(ErrorCode_InternalError); |
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989 } |
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990 } |
|
874
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|
991 |
|
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992 |
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993 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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994 unsigned int frame) |
|
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995 { |
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996 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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997 |
|
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998 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
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999 { |
|
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1000 throw OrthancException(ErrorCode_BadFileFormat); |
|
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1001 } |
|
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1002 } |
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1003 |
|
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1004 |
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1005 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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1006 unsigned int frame, |
|
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1007 ImageExtractionMode mode) |
|
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1008 { |
|
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1009 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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|
1010 |
|
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|
1011 bool ok = false; |
|
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|
1012 |
|
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|
1013 switch (mode) |
|
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|
1014 { |
|
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|
1015 case ImageExtractionMode_UInt8: |
|
1015
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1016 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
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1017 break; |
|
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|
1018 |
|
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|
1019 case ImageExtractionMode_UInt16: |
|
1015
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|
1020 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
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|
1021 break; |
|
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diff
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|
1022 |
|
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parents:
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diff
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|
1023 case ImageExtractionMode_Int16: |
|
1015
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|
1024 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
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diff
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|
1025 break; |
|
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|
1026 |
|
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|
1027 case ImageExtractionMode_Preview: |
|
87791ebc1f50
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|
1028 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
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diff
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|
1029 break; |
|
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|
1030 |
|
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|
1031 default: |
|
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|
1032 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
87791ebc1f50
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|
1033 } |
|
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|
1034 |
|
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|
1035 if (!ok) |
|
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|
1036 { |
|
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|
1037 throw OrthancException(ErrorCode_BadFileFormat); |
|
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parents:
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|
1038 } |
|
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|
1039 } |
|
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|
1040 |
|
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|
1041 |
|
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|
1042 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
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|
1043 unsigned int frame, |
|
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|
1044 ImageExtractionMode mode) |
|
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diff
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|
1045 { |
|
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|
1046 ImageBuffer buffer; |
|
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|
1047 ExtractImage(buffer, frame, mode); |
|
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|
1048 |
|
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|
1049 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
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|
1050 PngWriter writer; |
|
87791ebc1f50
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|
1051 writer.WriteToMemory(result, accessor); |
|
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diff
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|
1052 } |
|
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|
1053 |
|
956
2fd5a163776d
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|
1054 |
|
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|
1055 Encoding ParsedDicomFile::GetEncoding() const |
|
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1056 { |
|
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|
1057 return pimpl_->encoding_; |
|
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|
1058 } |
|
1090
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|
1059 |
|
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|
1060 |
|
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|
1061 void ParsedDicomFile::SetEncoding(Encoding encoding) |
|
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|
1062 { |
|
1558
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fix encodings of newly created dicom files
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|
1063 if (encoding == Encoding_Windows1251) |
|
1090
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|
1064 { |
|
1558
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|
1065 // This Cyrillic codepage is not officially supported by the |
|
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|
1066 // DICOM standard. Do not set the SpecificCharacterSet tag. |
|
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|
1067 return; |
|
1090
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|
1068 } |
|
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|
1069 |
|
1565
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|
1070 pimpl_->encoding_ = encoding; |
|
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|
1071 |
|
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|
1072 std::string s = GetDicomSpecificCharacterSet(encoding); |
| 1091 | 1073 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
|
1090
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|
1074 } |
|
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|
1075 |
| 1686 | 1076 void ParsedDicomFile::ToJson(Json::Value& target, |
| 1077 DicomToJsonFormat format, | |
| 1078 unsigned int maxStringLength) | |
|
1160
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|
1079 { |
| 1686 | 1080 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), format, maxStringLength); |
|
1160
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|
1081 } |
|
1555
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1082 |
|
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1083 |
|
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|
1084 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
|
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|
1085 { |
|
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|
1086 DcmTag key(tag.GetGroup(), tag.GetElement()); |
|
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|
1087 return pimpl_->file_->getDataset()->tagExists(key); |
|
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|
1088 } |
|
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|
1089 |
|
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|
1090 |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1091 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
|
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Creation of DICOM files with encapsulated PDF
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|
1092 { |
|
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changeset
|
1093 if (pdf.size() < 5 || // (*) |
|
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|
1094 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
|
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changeset
|
1095 { |
|
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Creation of DICOM files with encapsulated PDF
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changeset
|
1096 LOG(ERROR) << "Not a PDF file"; |
|
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|
1097 throw OrthancException(ErrorCode_BadFileFormat); |
|
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|
1098 } |
|
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changeset
|
1099 |
|
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|
1100 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
|
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|
1101 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
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|
1102 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
|
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1103 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
| 1566 | 1104 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
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1105 |
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1106 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
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1107 |
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1108 size_t s = pdf.size(); |
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1109 if (s & 1) |
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1110 { |
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1111 // The size of the buffer must be even |
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1112 s += 1; |
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1113 } |
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1114 |
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1115 Uint8* bytes = NULL; |
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1116 OFCondition result = element->createUint8Array(s, bytes); |
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1117 if (!result.good() || bytes == NULL) |
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1118 { |
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1119 throw OrthancException(ErrorCode_NotEnoughMemory); |
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1120 } |
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1121 |
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1122 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
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1123 bytes[s - 1] = 0; |
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1124 |
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1125 memcpy(bytes, pdf.c_str(), pdf.size()); |
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1126 |
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1127 DcmPolymorphOBOW* obj = element.release(); |
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1128 result = pimpl_->file_->getDataset()->insert(obj); |
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1129 |
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1130 if (!result.good()) |
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1131 { |
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1132 delete obj; |
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1133 throw OrthancException(ErrorCode_NotEnoughMemory); |
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1134 } |
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1135 } |
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1136 |
|
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1137 |
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1138 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
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1139 { |
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1140 std::string sop, mime; |
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1141 |
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1142 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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1143 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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1144 sop != UID_EncapsulatedPDFStorage || |
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1145 mime != "application/pdf") |
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1146 { |
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1147 return false; |
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1148 } |
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1149 |
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1150 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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1151 { |
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1152 return false; |
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1153 } |
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1154 |
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1155 // Strip the possible pad byte at the end of file, because the |
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1156 // encapsulated documents must always have an even length. The PDF |
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1157 // format expects files to end with %%EOF followed by CR/LF. If |
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1158 // the last character of the file is not a CR or LF, we assume it |
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1159 // is a pad byte and remove it. |
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1160 if (pdf.size() > 0) |
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1161 { |
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1162 char last = *pdf.rbegin(); |
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1163 |
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1164 if (last != 10 && last != 13) |
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1165 { |
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1166 pdf.resize(pdf.size() - 1); |
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1167 } |
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1168 } |
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1169 |
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1170 return true; |
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1171 } |
|
1662
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1172 |
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1173 |
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1174 void ParsedDicomFile::Convert(DicomMap& tags) |
|
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1175 { |
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1176 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset()); |
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1177 } |
| 790 | 1178 } |