Mercurial > hg > orthanc
annotate OrthancServer/ParsedDicomFile.cpp @ 1737:ec66a16aa398
removal of DicomStringValue and DicomNullValue
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 22 Oct 2015 07:52:24 +0200 |
| parents | b953c6eef28d |
| children | 5ad4e4d92ecb |
| 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/DicomIntegerPixelAccessor.h" | |
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94 #include "../Core/Images/PngReader.h" |
| 790 | 95 |
| 96 #include <list> | |
| 97 #include <limits> | |
| 98 | |
| 99 #include <boost/lexical_cast.hpp> | |
| 100 | |
| 101 #include <dcmtk/dcmdata/dcchrstr.h> | |
| 102 #include <dcmtk/dcmdata/dcdicent.h> | |
| 103 #include <dcmtk/dcmdata/dcdict.h> | |
| 104 #include <dcmtk/dcmdata/dcfilefo.h> | |
| 105 #include <dcmtk/dcmdata/dcistrmb.h> | |
| 106 #include <dcmtk/dcmdata/dcuid.h> | |
| 107 #include <dcmtk/dcmdata/dcmetinf.h> | |
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108 #include <dcmtk/dcmdata/dcdeftag.h> |
| 790 | 109 |
| 110 #include <dcmtk/dcmdata/dcvrae.h> | |
| 111 #include <dcmtk/dcmdata/dcvras.h> | |
| 112 #include <dcmtk/dcmdata/dcvrcs.h> | |
| 113 #include <dcmtk/dcmdata/dcvrda.h> | |
| 114 #include <dcmtk/dcmdata/dcvrds.h> | |
| 115 #include <dcmtk/dcmdata/dcvrdt.h> | |
| 116 #include <dcmtk/dcmdata/dcvrfd.h> | |
| 117 #include <dcmtk/dcmdata/dcvrfl.h> | |
| 118 #include <dcmtk/dcmdata/dcvris.h> | |
| 119 #include <dcmtk/dcmdata/dcvrlo.h> | |
| 120 #include <dcmtk/dcmdata/dcvrlt.h> | |
| 121 #include <dcmtk/dcmdata/dcvrpn.h> | |
| 122 #include <dcmtk/dcmdata/dcvrsh.h> | |
| 123 #include <dcmtk/dcmdata/dcvrsl.h> | |
| 124 #include <dcmtk/dcmdata/dcvrss.h> | |
| 125 #include <dcmtk/dcmdata/dcvrst.h> | |
| 126 #include <dcmtk/dcmdata/dcvrtm.h> | |
| 127 #include <dcmtk/dcmdata/dcvrui.h> | |
| 128 #include <dcmtk/dcmdata/dcvrul.h> | |
| 129 #include <dcmtk/dcmdata/dcvrus.h> | |
| 130 #include <dcmtk/dcmdata/dcvrut.h> | |
| 131 #include <dcmtk/dcmdata/dcpixel.h> | |
| 132 #include <dcmtk/dcmdata/dcpixseq.h> | |
| 133 #include <dcmtk/dcmdata/dcpxitem.h> | |
| 134 | |
| 135 | |
| 136 #include <boost/math/special_functions/round.hpp> | |
| 137 #include <dcmtk/dcmdata/dcostrmb.h> | |
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138 #include <boost/algorithm/string/predicate.hpp> |
| 790 | 139 |
| 140 | |
| 141 static const char* CONTENT_TYPE_OCTET_STREAM = "application/octet-stream"; | |
| 142 | |
| 143 | |
| 144 | |
| 145 namespace Orthanc | |
| 146 { | |
| 794 | 147 struct ParsedDicomFile::PImpl |
| 148 { | |
| 149 std::auto_ptr<DcmFileFormat> file_; | |
| 150 }; | |
| 151 | |
| 152 | |
| 153 // This method can only be called from the constructors! | |
| 790 | 154 void ParsedDicomFile::Setup(const char* buffer, size_t size) |
| 155 { | |
| 156 DcmInputBufferStream is; | |
| 157 if (size > 0) | |
| 158 { | |
| 159 is.setBuffer(buffer, size); | |
| 160 } | |
| 161 is.setEos(); | |
| 162 | |
| 794 | 163 pimpl_->file_.reset(new DcmFileFormat); |
| 164 pimpl_->file_->transferInit(); | |
| 165 if (!pimpl_->file_->read(is).good()) | |
| 790 | 166 { |
| 794 | 167 delete pimpl_; // Avoid a memory leak due to exception |
| 168 // throwing, as we are in the constructor | |
| 169 | |
| 790 | 170 throw OrthancException(ErrorCode_BadFileFormat); |
| 171 } | |
| 794 | 172 pimpl_->file_->loadAllDataIntoMemory(); |
| 173 pimpl_->file_->transferEnd(); | |
| 790 | 174 } |
| 175 | |
| 176 | |
| 177 static void SendPathValueForDictionary(RestApiOutput& output, | |
| 178 DcmItem& dicom) | |
| 179 { | |
| 180 Json::Value v = Json::arrayValue; | |
| 181 | |
| 182 for (unsigned long i = 0; i < dicom.card(); i++) | |
| 183 { | |
| 184 DcmElement* element = dicom.getElement(i); | |
| 185 if (element) | |
| 186 { | |
| 187 char buf[16]; | |
| 188 sprintf(buf, "%04x-%04x", element->getTag().getGTag(), element->getTag().getETag()); | |
| 189 v.append(buf); | |
| 190 } | |
| 191 } | |
| 192 | |
| 193 output.AnswerJson(v); | |
| 194 } | |
| 195 | |
| 196 static inline uint16_t GetCharValue(char c) | |
| 197 { | |
| 198 if (c >= '0' && c <= '9') | |
| 199 return c - '0'; | |
| 200 else if (c >= 'a' && c <= 'f') | |
| 201 return c - 'a' + 10; | |
| 202 else if (c >= 'A' && c <= 'F') | |
| 203 return c - 'A' + 10; | |
| 204 else | |
| 205 return 0; | |
| 206 } | |
| 207 | |
| 208 static inline uint16_t GetTagValue(const char* c) | |
| 209 { | |
| 210 return ((GetCharValue(c[0]) << 12) + | |
| 211 (GetCharValue(c[1]) << 8) + | |
| 212 (GetCharValue(c[2]) << 4) + | |
| 213 GetCharValue(c[3])); | |
| 214 } | |
| 215 | |
| 216 static void ParseTagAndGroup(DcmTagKey& key, | |
| 217 const std::string& tag) | |
| 218 { | |
| 219 DicomTag t = FromDcmtkBridge::ParseTag(tag); | |
| 220 key = DcmTagKey(t.GetGroup(), t.GetElement()); | |
| 221 } | |
| 222 | |
| 223 | |
| 224 static void SendSequence(RestApiOutput& output, | |
| 225 DcmSequenceOfItems& sequence) | |
| 226 { | |
| 227 // This element is a sequence | |
| 228 Json::Value v = Json::arrayValue; | |
| 229 | |
| 230 for (unsigned long i = 0; i < sequence.card(); i++) | |
| 231 { | |
| 232 v.append(boost::lexical_cast<std::string>(i)); | |
| 233 } | |
| 234 | |
| 235 output.AnswerJson(v); | |
| 236 } | |
| 237 | |
| 238 | |
| 239 static unsigned int GetPixelDataBlockCount(DcmPixelData& pixelData, | |
| 240 E_TransferSyntax transferSyntax) | |
| 241 { | |
| 242 DcmPixelSequence* pixelSequence = NULL; | |
| 243 if (pixelData.getEncapsulatedRepresentation | |
| 244 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 245 { | |
| 246 return pixelSequence->card(); | |
| 247 } | |
| 248 else | |
| 249 { | |
| 250 return 1; | |
| 251 } | |
| 252 } | |
| 253 | |
| 254 | |
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255 namespace |
| 790 | 256 { |
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257 class DicomFieldStream : public IHttpStreamAnswer |
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258 { |
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259 private: |
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260 DcmElement& element_; |
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261 uint32_t length_; |
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262 uint32_t offset_; |
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263 std::string chunk_; |
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264 size_t chunkSize_; |
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265 |
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266 public: |
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267 DicomFieldStream(DcmElement& element, |
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268 E_TransferSyntax transferSyntax) : |
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269 element_(element), |
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270 length_(element.getLength(transferSyntax)), |
| 1616 | 271 offset_(0), |
| 272 chunkSize_(0) | |
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273 { |
| 1521 | 274 static const size_t CHUNK_SIZE = 64 * 1024; // Use chunks of max 64KB |
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275 chunk_.resize(CHUNK_SIZE); |
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276 } |
| 790 | 277 |
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278 virtual HttpCompression SetupHttpCompression(bool /*gzipAllowed*/, |
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279 bool /*deflateAllowed*/) |
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280 { |
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281 // No support for compression |
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282 return HttpCompression_None; |
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283 } |
| 790 | 284 |
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285 virtual bool HasContentFilename(std::string& filename) |
| 790 | 286 { |
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287 return false; |
| 790 | 288 } |
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289 |
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290 virtual std::string GetContentType() |
| 790 | 291 { |
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292 return ""; |
| 790 | 293 } |
| 294 | |
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295 virtual uint64_t GetContentLength() |
| 790 | 296 { |
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297 return length_; |
| 790 | 298 } |
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299 |
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300 virtual bool ReadNextChunk() |
| 790 | 301 { |
| 1520 | 302 assert(offset_ <= length_); |
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303 |
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304 if (offset_ == length_) |
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305 { |
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306 return false; |
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307 } |
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308 else |
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309 { |
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310 if (length_ - offset_ < chunk_.size()) |
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311 { |
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312 chunkSize_ = length_ - offset_; |
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313 } |
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314 else |
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315 { |
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316 chunkSize_ = chunk_.size(); |
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317 } |
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318 |
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319 OFCondition cond = element_.getPartialValue(&chunk_[0], offset_, chunkSize_); |
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320 |
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321 offset_ += chunkSize_; |
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322 |
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323 if (!cond.good()) |
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324 { |
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325 LOG(ERROR) << "Error while sending a DICOM field: " << cond.text(); |
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326 throw OrthancException(ErrorCode_InternalError); |
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327 } |
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328 |
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329 return true; |
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330 } |
| 790 | 331 } |
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332 |
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333 virtual const char *GetChunkContent() |
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334 { |
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335 return chunk_.c_str(); |
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336 } |
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337 |
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338 virtual size_t GetChunkSize() |
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339 { |
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340 return chunkSize_; |
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341 } |
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342 }; |
| 790 | 343 } |
| 344 | |
| 345 | |
| 346 static bool AnswerPixelData(RestApiOutput& output, | |
| 347 DcmItem& dicom, | |
| 348 E_TransferSyntax transferSyntax, | |
| 349 const std::string* blockUri) | |
| 350 { | |
| 351 DcmTag k(DICOM_TAG_PIXEL_DATA.GetGroup(), | |
| 352 DICOM_TAG_PIXEL_DATA.GetElement()); | |
| 353 | |
| 354 DcmElement *element = NULL; | |
| 355 if (!dicom.findAndGetElement(k, element).good() || | |
| 356 element == NULL) | |
| 357 { | |
| 358 return false; | |
| 359 } | |
| 360 | |
| 361 try | |
| 362 { | |
| 363 DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); | |
| 364 if (blockUri == NULL) | |
| 365 { | |
| 366 // The user asks how many blocks are presents in this pixel data | |
| 367 unsigned int blocks = GetPixelDataBlockCount(pixelData, transferSyntax); | |
| 368 | |
| 369 Json::Value result(Json::arrayValue); | |
| 370 for (unsigned int i = 0; i < blocks; i++) | |
| 371 { | |
| 372 result.append(boost::lexical_cast<std::string>(i)); | |
| 373 } | |
| 374 | |
| 375 output.AnswerJson(result); | |
| 376 return true; | |
| 377 } | |
| 378 | |
| 379 | |
| 380 unsigned int block = boost::lexical_cast<unsigned int>(*blockUri); | |
| 381 | |
| 382 if (block < GetPixelDataBlockCount(pixelData, transferSyntax)) | |
| 383 { | |
| 384 DcmPixelSequence* pixelSequence = NULL; | |
| 385 if (pixelData.getEncapsulatedRepresentation | |
| 386 (transferSyntax, NULL, pixelSequence).good() && pixelSequence) | |
| 387 { | |
| 388 // This is the case for JPEG transfer syntaxes | |
| 389 if (block < pixelSequence->card()) | |
| 390 { | |
| 391 DcmPixelItem* pixelItem = NULL; | |
| 392 if (pixelSequence->getItem(pixelItem, block).good() && pixelItem) | |
| 393 { | |
| 394 if (pixelItem->getLength() == 0) | |
| 395 { | |
| 396 output.AnswerBuffer(NULL, 0, CONTENT_TYPE_OCTET_STREAM); | |
| 397 return true; | |
| 398 } | |
| 399 | |
| 400 Uint8* buffer = NULL; | |
| 401 if (pixelItem->getUint8Array(buffer).good() && buffer) | |
| 402 { | |
| 403 output.AnswerBuffer(buffer, pixelItem->getLength(), CONTENT_TYPE_OCTET_STREAM); | |
| 404 return true; | |
| 405 } | |
| 406 } | |
| 407 } | |
| 408 } | |
| 409 else | |
| 410 { | |
| 411 // This is the case for raw, uncompressed image buffers | |
| 412 assert(*blockUri == "0"); | |
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413 DicomFieldStream stream(*element, transferSyntax); |
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414 output.AnswerStream(stream); |
| 790 | 415 } |
| 416 } | |
| 417 } | |
| 418 catch (boost::bad_lexical_cast&) | |
| 419 { | |
| 420 // The URI entered by the user is not a number | |
| 421 } | |
| 422 catch (std::bad_cast&) | |
| 423 { | |
| 424 // This should never happen | |
| 425 } | |
| 426 | |
| 427 return false; | |
| 428 } | |
| 429 | |
| 430 | |
| 431 | |
| 432 static void SendPathValueForLeaf(RestApiOutput& output, | |
| 433 const std::string& tag, | |
| 434 DcmItem& dicom, | |
| 435 E_TransferSyntax transferSyntax) | |
| 436 { | |
| 437 DcmTagKey k; | |
| 438 ParseTagAndGroup(k, tag); | |
| 439 | |
| 440 DcmSequenceOfItems* sequence = NULL; | |
| 441 if (dicom.findAndGetSequence(k, sequence).good() && | |
| 442 sequence != NULL && | |
| 443 sequence->getVR() == EVR_SQ) | |
| 444 { | |
| 445 SendSequence(output, *sequence); | |
| 446 return; | |
| 447 } | |
| 448 | |
| 449 DcmElement* element = NULL; | |
| 450 if (dicom.findAndGetElement(k, element).good() && | |
| 451 element != NULL && | |
| 452 //element->getVR() != EVR_UNKNOWN && // This would forbid private tags | |
| 453 element->getVR() != EVR_SQ) | |
| 454 { | |
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455 DicomFieldStream stream(*element, transferSyntax); |
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456 output.AnswerStream(stream); |
| 790 | 457 } |
| 458 } | |
| 459 | |
| 460 void ParsedDicomFile::SendPathValue(RestApiOutput& output, | |
| 461 const UriComponents& uri) | |
| 462 { | |
| 794 | 463 DcmItem* dicom = pimpl_->file_->getDataset(); |
| 464 E_TransferSyntax transferSyntax = pimpl_->file_->getDataset()->getOriginalXfer(); | |
| 790 | 465 |
| 466 // Special case: Accessing the pixel data | |
| 467 if (uri.size() == 1 || | |
| 468 uri.size() == 2) | |
| 469 { | |
| 470 DcmTagKey tag; | |
| 471 ParseTagAndGroup(tag, uri[0]); | |
| 472 | |
| 473 if (tag.getGroup() == DICOM_TAG_PIXEL_DATA.GetGroup() && | |
| 474 tag.getElement() == DICOM_TAG_PIXEL_DATA.GetElement()) | |
| 475 { | |
| 476 AnswerPixelData(output, *dicom, transferSyntax, uri.size() == 1 ? NULL : &uri[1]); | |
| 477 return; | |
| 478 } | |
| 479 } | |
| 480 | |
| 481 // Go down in the tag hierarchy according to the URI | |
| 482 for (size_t pos = 0; pos < uri.size() / 2; pos++) | |
| 483 { | |
| 484 size_t index; | |
| 485 try | |
| 486 { | |
| 487 index = boost::lexical_cast<size_t>(uri[2 * pos + 1]); | |
| 488 } | |
| 489 catch (boost::bad_lexical_cast&) | |
| 490 { | |
| 491 return; | |
| 492 } | |
| 493 | |
| 494 DcmTagKey k; | |
| 495 DcmItem *child = NULL; | |
| 496 ParseTagAndGroup(k, uri[2 * pos]); | |
| 497 if (!dicom->findAndGetSequenceItem(k, child, index).good() || | |
| 498 child == NULL) | |
| 499 { | |
| 500 return; | |
| 501 } | |
| 502 | |
| 503 dicom = child; | |
| 504 } | |
| 505 | |
| 506 // We have reached the end of the URI | |
| 507 if (uri.size() % 2 == 0) | |
| 508 { | |
| 509 SendPathValueForDictionary(output, *dicom); | |
| 510 } | |
| 511 else | |
| 512 { | |
| 513 SendPathValueForLeaf(output, uri.back(), *dicom, transferSyntax); | |
| 514 } | |
| 515 } | |
| 516 | |
| 517 | |
| 518 void ParsedDicomFile::Remove(const DicomTag& tag) | |
| 519 { | |
| 520 DcmTagKey key(tag.GetGroup(), tag.GetElement()); | |
| 794 | 521 DcmElement* element = pimpl_->file_->getDataset()->remove(key); |
| 790 | 522 if (element != NULL) |
| 523 { | |
| 524 delete element; | |
| 525 } | |
| 526 } | |
| 527 | |
| 528 | |
| 529 | |
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530 void ParsedDicomFile::RemovePrivateTagsInternal(const std::set<DicomTag>* toKeep) |
| 790 | 531 { |
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532 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
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533 |
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534 // Loop over the dataset to detect its private tags |
| 790 | 535 typedef std::list<DcmElement*> Tags; |
| 536 Tags privateTags; | |
| 537 | |
| 538 for (unsigned long i = 0; i < dataset.card(); i++) | |
| 539 { | |
| 540 DcmElement* element = dataset.getElement(i); | |
| 541 DcmTag tag(element->getTag()); | |
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542 |
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543 // Is this a private tag? |
| 1694 | 544 if (tag.isPrivate()) |
| 790 | 545 { |
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546 bool remove = true; |
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547 |
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548 // Check whether this private tag is to be kept |
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549 if (toKeep != NULL) |
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550 { |
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551 DicomTag tmp = FromDcmtkBridge::Convert(tag); |
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552 if (toKeep->find(tmp) != toKeep->end()) |
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553 { |
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554 remove = false; // Keep it |
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555 } |
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556 } |
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557 |
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558 if (remove) |
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559 { |
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560 privateTags.push_back(element); |
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561 } |
| 790 | 562 } |
| 563 } | |
| 564 | |
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565 // Loop over the detected private tags to remove them |
| 790 | 566 for (Tags::iterator it = privateTags.begin(); |
| 567 it != privateTags.end(); ++it) | |
| 568 { | |
| 569 DcmElement* tmp = dataset.remove(*it); | |
| 570 if (tmp != NULL) | |
| 571 { | |
| 572 delete tmp; | |
| 573 } | |
| 574 } | |
| 575 } | |
| 576 | |
| 577 | |
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578 static void InsertInternal(DcmDataset& dicom, |
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579 DcmElement* element) |
| 790 | 580 { |
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581 OFCondition cond = dicom.insert(element, false, false); |
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582 if (!cond.good()) |
| 790 | 583 { |
| 584 // This field already exists | |
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585 delete element; |
| 790 | 586 throw OrthancException(ErrorCode_InternalError); |
| 587 } | |
| 588 } | |
| 589 | |
| 590 | |
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591 void ParsedDicomFile::Insert(const DicomTag& tag, |
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592 const Json::Value& value, |
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593 bool decodeBinaryTags) |
| 790 | 594 { |
| 1695 | 595 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeBinaryTags, GetEncoding())); |
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596 InsertInternal(*pimpl_->file_->getDataset(), element.release()); |
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597 } |
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598 |
| 790 | 599 |
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600 static void ReplaceInternal(DcmDataset& dicom, |
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601 std::auto_ptr<DcmElement>& element, |
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602 DicomReplaceMode mode) |
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603 { |
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604 const DcmTagKey& tag = element->getTag(); |
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605 |
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606 if (!dicom.findAndDeleteElement(tag).good()) |
| 790 | 607 { |
| 608 // This field does not exist, act wrt. the specified "mode" | |
| 609 switch (mode) | |
| 610 { | |
| 611 case DicomReplaceMode_InsertIfAbsent: | |
| 612 break; | |
| 613 | |
| 614 case DicomReplaceMode_ThrowIfAbsent: | |
| 615 throw OrthancException(ErrorCode_InexistentItem); | |
| 616 | |
| 617 case DicomReplaceMode_IgnoreIfAbsent: | |
| 618 return; | |
| 619 } | |
| 620 } | |
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621 |
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622 // Either the tag was not existing, or the replace mode was set to |
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623 // "InsertIfAbsent" |
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624 InsertInternal(dicom, element.release()); |
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625 } |
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626 |
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627 |
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628 void ParsedDicomFile::UpdateStorageUid(const DicomTag& tag, |
| 1695 | 629 const std::string& utf8Value, |
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630 bool decodeBinaryTags) |
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631 { |
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632 if (tag != DICOM_TAG_SOP_CLASS_UID && |
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633 tag != DICOM_TAG_SOP_INSTANCE_UID) |
| 790 | 634 { |
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635 return; |
| 790 | 636 } |
| 637 | |
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638 std::string binary; |
| 1695 | 639 const std::string* decoded = &utf8Value; |
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640 |
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641 if (decodeBinaryTags && |
| 1695 | 642 boost::starts_with(utf8Value, "data:application/octet-stream;base64,")) |
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643 { |
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644 std::string mime; |
| 1695 | 645 Toolbox::DecodeDataUriScheme(mime, binary, utf8Value); |
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646 decoded = &binary; |
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647 } |
| 1695 | 648 else |
| 649 { | |
| 650 Encoding encoding = GetEncoding(); | |
| 651 if (GetEncoding() != Encoding_Utf8) | |
| 652 { | |
| 653 binary = Toolbox::ConvertFromUtf8(utf8Value, encoding); | |
| 654 decoded = &binary; | |
| 655 } | |
| 656 } | |
| 790 | 657 |
| 658 /** | |
| 659 * dcmodify will automatically correct 'Media Storage SOP Class | |
| 660 * UID' and 'Media Storage SOP Instance UID' in the metaheader, if | |
| 661 * you make changes to the related tags in the dataset ('SOP Class | |
| 662 * UID' and 'SOP Instance UID') via insert or modify mode | |
| 663 * options. You can disable this behaviour by using the -nmu | |
| 664 * option. | |
| 665 **/ | |
| 666 | |
| 667 if (tag == DICOM_TAG_SOP_CLASS_UID) | |
| 668 { | |
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669 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
| 790 | 670 } |
| 671 | |
| 672 if (tag == DICOM_TAG_SOP_INSTANCE_UID) | |
| 673 { | |
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674 Replace(DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID, *decoded, DicomReplaceMode_InsertIfAbsent); |
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675 } |
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676 } |
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677 |
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678 |
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679 void ParsedDicomFile::Replace(const DicomTag& tag, |
| 1695 | 680 const std::string& utf8Value, |
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681 DicomReplaceMode mode) |
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682 { |
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683 std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag)); |
| 1695 | 684 FromDcmtkBridge::FillElementWithString(*element, tag, utf8Value, false, GetEncoding()); |
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685 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
| 1695 | 686 UpdateStorageUid(tag, utf8Value, false); |
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687 } |
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688 |
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689 |
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690 void ParsedDicomFile::Replace(const DicomTag& tag, |
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691 const Json::Value& value, |
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692 bool decodeBinaryTags, |
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693 DicomReplaceMode mode) |
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694 { |
| 1695 | 695 std::auto_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeBinaryTags, GetEncoding())); |
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696 ReplaceInternal(*pimpl_->file_->getDataset(), element, mode); |
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697 |
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698 if (tag == DICOM_TAG_SOP_CLASS_UID || |
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699 tag == DICOM_TAG_SOP_INSTANCE_UID) |
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700 { |
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701 if (value.type() != Json::stringValue) |
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702 { |
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703 throw OrthancException(ErrorCode_BadParameterType); |
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704 } |
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705 |
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706 UpdateStorageUid(tag, value.asString(), decodeBinaryTags); |
| 790 | 707 } |
| 708 } | |
| 709 | |
| 710 | |
| 711 void ParsedDicomFile::Answer(RestApiOutput& output) | |
| 712 { | |
| 713 std::string serialized; | |
|
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|
714 if (FromDcmtkBridge::SaveToMemoryBuffer(serialized, *pimpl_->file_->getDataset())) |
| 790 | 715 { |
| 716 output.AnswerBuffer(serialized, CONTENT_TYPE_OCTET_STREAM); | |
| 717 } | |
| 718 } | |
| 719 | |
| 720 | |
| 721 | |
| 722 bool ParsedDicomFile::GetTagValue(std::string& value, | |
| 723 const DicomTag& tag) | |
| 724 { | |
| 725 DcmTagKey k(tag.GetGroup(), tag.GetElement()); | |
| 794 | 726 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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727 |
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728 if (FromDcmtkBridge::IsPrivateTag(tag) || |
|
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729 FromDcmtkBridge::IsUnknownTag(tag) || |
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730 tag == DICOM_TAG_PIXEL_DATA || |
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731 tag == DICOM_TAG_ENCAPSULATED_DOCUMENT) |
| 790 | 732 { |
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733 const Uint8* data = NULL; // This is freed in the destructor of the dataset |
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734 long unsigned int count = 0; |
| 790 | 735 |
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736 if (dataset.findAndGetUint8Array(k, data, &count).good()) |
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737 { |
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738 if (count > 0) |
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739 { |
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740 assert(data != NULL); |
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741 value.assign(reinterpret_cast<const char*>(data), count); |
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742 } |
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743 else |
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744 { |
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745 value.clear(); |
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746 } |
| 790 | 747 |
|
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748 return true; |
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749 } |
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750 else |
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751 { |
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752 return false; |
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753 } |
| 790 | 754 } |
| 755 else | |
| 756 { | |
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757 DcmElement* element = NULL; |
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758 if (!dataset.findAndGetElement(k, element).good() || |
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759 element == NULL) |
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760 { |
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761 return false; |
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762 } |
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763 |
|
1736
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diff
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|
764 std::auto_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement |
|
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765 (*element, DicomToJsonFlags_Default, GetEncoding())); |
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766 |
|
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767 if (v.get() == NULL || |
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768 v->IsNull()) |
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769 { |
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770 value = ""; |
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771 } |
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772 else |
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773 { |
|
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774 // TODO v->IsBinary() |
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775 value = v->GetContent(); |
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776 } |
|
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777 |
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778 return true; |
| 790 | 779 } |
| 780 } | |
| 781 | |
| 782 | |
| 783 DicomInstanceHasher ParsedDicomFile::GetHasher() | |
| 784 { | |
| 785 std::string patientId, studyUid, seriesUid, instanceUid; | |
| 786 | |
| 787 if (!GetTagValue(patientId, DICOM_TAG_PATIENT_ID) || | |
| 788 !GetTagValue(studyUid, DICOM_TAG_STUDY_INSTANCE_UID) || | |
| 789 !GetTagValue(seriesUid, DICOM_TAG_SERIES_INSTANCE_UID) || | |
| 790 !GetTagValue(instanceUid, DICOM_TAG_SOP_INSTANCE_UID)) | |
| 791 { | |
| 792 throw OrthancException(ErrorCode_BadFileFormat); | |
| 793 } | |
| 794 | |
| 795 return DicomInstanceHasher(patientId, studyUid, seriesUid, instanceUid); | |
| 796 } | |
| 797 | |
| 798 | |
| 799 template <typename T> | |
| 800 static void ExtractPngImageTruncate(std::string& result, | |
| 801 DicomIntegerPixelAccessor& accessor, | |
| 802 PixelFormat format) | |
| 803 { | |
|
853
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804 assert(accessor.GetInformation().GetChannelCount() == 1); |
| 790 | 805 |
| 806 PngWriter w; | |
| 807 | |
|
853
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808 std::vector<T> image(accessor.GetInformation().GetWidth() * accessor.GetInformation().GetHeight(), 0); |
| 790 | 809 T* pixel = &image[0]; |
|
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810 for (unsigned int y = 0; y < accessor.GetInformation().GetHeight(); y++) |
| 790 | 811 { |
|
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812 for (unsigned int x = 0; x < accessor.GetInformation().GetWidth(); x++, pixel++) |
| 790 | 813 { |
| 814 int32_t v = accessor.GetValue(x, y); | |
| 815 if (v < static_cast<int32_t>(std::numeric_limits<T>::min())) | |
| 816 *pixel = std::numeric_limits<T>::min(); | |
| 817 else if (v > static_cast<int32_t>(std::numeric_limits<T>::max())) | |
| 818 *pixel = std::numeric_limits<T>::max(); | |
| 819 else | |
| 820 *pixel = static_cast<T>(v); | |
| 821 } | |
| 822 } | |
| 823 | |
|
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824 w.WriteToMemory(result, accessor.GetInformation().GetWidth(), accessor.GetInformation().GetHeight(), |
|
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825 accessor.GetInformation().GetWidth() * sizeof(T), format, &image[0]); |
| 790 | 826 } |
| 827 | |
| 828 | |
| 829 void ParsedDicomFile::SaveToMemoryBuffer(std::string& buffer) | |
| 830 { | |
|
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831 FromDcmtkBridge::SaveToMemoryBuffer(buffer, *pimpl_->file_->getDataset()); |
| 790 | 832 } |
| 833 | |
| 834 | |
| 835 void ParsedDicomFile::SaveToFile(const std::string& path) | |
| 836 { | |
| 837 // TODO Avoid using a temporary memory buffer, write directly on disk | |
| 838 std::string content; | |
| 839 SaveToMemoryBuffer(content); | |
| 840 Toolbox::WriteFile(content, path); | |
| 841 } | |
| 842 | |
| 843 | |
| 794 | 844 ParsedDicomFile::ParsedDicomFile() : pimpl_(new PImpl) |
| 790 | 845 { |
| 794 | 846 pimpl_->file_.reset(new DcmFileFormat); |
| 790 | 847 Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient)); |
| 848 Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)); | |
| 849 Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series)); | |
| 850 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); | |
| 851 } | |
| 852 | |
| 791 | 853 |
| 794 | 854 ParsedDicomFile::ParsedDicomFile(const char* content, size_t size) : pimpl_(new PImpl) |
| 791 | 855 { |
| 856 Setup(content, size); | |
| 857 } | |
| 858 | |
| 794 | 859 ParsedDicomFile::ParsedDicomFile(const std::string& content) : pimpl_(new PImpl) |
| 791 | 860 { |
| 861 if (content.size() == 0) | |
| 862 { | |
| 863 Setup(NULL, 0); | |
| 864 } | |
| 865 else | |
| 866 { | |
| 867 Setup(&content[0], content.size()); | |
| 868 } | |
| 869 } | |
| 792 | 870 |
| 871 | |
| 794 | 872 ParsedDicomFile::ParsedDicomFile(ParsedDicomFile& other) : |
| 873 pimpl_(new PImpl) | |
| 792 | 874 { |
| 794 | 875 pimpl_->file_.reset(dynamic_cast<DcmFileFormat*>(other.pimpl_->file_->clone())); |
|
956
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876 |
|
1564
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877 // Create a new instance-level identifier |
|
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878 Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
| 792 | 879 } |
| 880 | |
| 881 | |
| 882 ParsedDicomFile::~ParsedDicomFile() | |
| 883 { | |
| 794 | 884 delete pimpl_; |
| 792 | 885 } |
| 886 | |
| 793 | 887 |
| 888 void* ParsedDicomFile::GetDcmtkObject() | |
| 889 { | |
| 794 | 890 return pimpl_->file_.get(); |
| 793 | 891 } |
| 892 | |
| 893 | |
| 894 ParsedDicomFile* ParsedDicomFile::Clone() | |
| 895 { | |
| 794 | 896 return new ParsedDicomFile(*this); |
| 793 | 897 } |
|
800
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898 |
|
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899 |
| 1562 | 900 void ParsedDicomFile::EmbedContent(const std::string& dataUriScheme) |
|
800
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901 { |
|
1641
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|
902 std::string mime, content; |
|
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|
903 Toolbox::DecodeDataUriScheme(mime, content, dataUriScheme); |
| 1562 | 904 Toolbox::ToLowerCase(mime); |
|
1555
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Creation of DICOM files with encapsulated PDF
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|
905 |
| 1562 | 906 if (mime == "image/png") |
| 907 { | |
| 908 EmbedImage(mime, content); | |
| 909 } | |
| 910 else if (mime == "application/pdf") | |
| 911 { | |
| 912 EmbedPdf(content); | |
| 913 } | |
| 914 else | |
| 915 { | |
|
1693
558b25228a23
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|
916 LOG(ERROR) << "Unsupported MIME type for the content of a new DICOM file: " << mime; |
| 1562 | 917 throw OrthancException(ErrorCode_NotImplemented); |
| 918 } | |
|
1555
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|
919 } |
|
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|
920 |
|
800
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|
921 |
|
1555
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|
922 void ParsedDicomFile::EmbedImage(const std::string& mime, |
|
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|
923 const std::string& content) |
|
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|
924 { |
|
800
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diff
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|
925 if (mime == "image/png") |
|
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|
926 { |
|
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|
927 PngReader reader; |
|
1555
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diff
changeset
|
928 reader.ReadFromMemory(content); |
|
800
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|
929 EmbedImage(reader); |
|
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|
930 } |
|
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|
931 else |
|
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|
932 { |
|
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diff
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|
933 throw OrthancException(ErrorCode_NotImplemented); |
|
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|
934 } |
|
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|
935 } |
|
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diff
changeset
|
936 |
|
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diff
changeset
|
937 |
|
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diff
changeset
|
938 void ParsedDicomFile::EmbedImage(const ImageAccessor& accessor) |
|
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|
939 { |
|
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diff
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|
940 if (accessor.GetFormat() != PixelFormat_Grayscale8 && |
|
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diff
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|
941 accessor.GetFormat() != PixelFormat_Grayscale16 && |
|
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|
942 accessor.GetFormat() != PixelFormat_RGB24 && |
|
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diff
changeset
|
943 accessor.GetFormat() != PixelFormat_RGBA32) |
|
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|
944 { |
|
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diff
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|
945 throw OrthancException(ErrorCode_NotImplemented); |
|
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|
946 } |
|
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changeset
|
947 |
|
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generation of DICOM images from PNG files
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diff
changeset
|
948 if (accessor.GetFormat() == PixelFormat_RGBA32) |
|
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|
949 { |
|
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diff
changeset
|
950 LOG(WARNING) << "Getting rid of the alpha channel when embedding a RGBA image inside DICOM"; |
|
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|
951 } |
|
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generation of DICOM images from PNG files
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diff
changeset
|
952 |
|
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generation of DICOM images from PNG files
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diff
changeset
|
953 // http://dicomiseasy.blogspot.be/2012/08/chapter-12-pixel-data.html |
|
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changeset
|
954 |
|
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generation of DICOM images from PNG files
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diff
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|
955 Remove(DICOM_TAG_PIXEL_DATA); |
|
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diff
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|
956 Replace(DICOM_TAG_COLUMNS, boost::lexical_cast<std::string>(accessor.GetWidth())); |
|
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|
957 Replace(DICOM_TAG_ROWS, boost::lexical_cast<std::string>(accessor.GetHeight())); |
|
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|
958 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "1"); |
|
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|
959 Replace(DICOM_TAG_NUMBER_OF_FRAMES, "1"); |
|
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|
960 Replace(DICOM_TAG_PIXEL_REPRESENTATION, "0"); // Unsigned pixels |
|
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|
961 Replace(DICOM_TAG_PLANAR_CONFIGURATION, "0"); // Color channels are interleaved |
|
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|
962 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "MONOCHROME2"); |
|
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|
963 Replace(DICOM_TAG_BITS_ALLOCATED, "8"); |
|
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|
964 Replace(DICOM_TAG_BITS_STORED, "8"); |
|
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changeset
|
965 Replace(DICOM_TAG_HIGH_BIT, "7"); |
|
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|
966 |
|
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|
967 unsigned int bytesPerPixel = 1; |
|
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|
968 |
|
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|
969 switch (accessor.GetFormat()) |
|
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|
970 { |
|
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|
971 case PixelFormat_RGB24: |
|
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|
972 case PixelFormat_RGBA32: |
|
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|
973 Replace(DICOM_TAG_PHOTOMETRIC_INTERPRETATION, "RGB"); |
|
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|
974 Replace(DICOM_TAG_SAMPLES_PER_PIXEL, "3"); |
|
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|
975 bytesPerPixel = 3; |
|
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|
976 break; |
|
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changeset
|
977 |
|
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|
978 case PixelFormat_Grayscale8: |
|
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|
979 break; |
|
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changeset
|
980 |
|
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changeset
|
981 case PixelFormat_Grayscale16: |
|
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|
982 Replace(DICOM_TAG_BITS_ALLOCATED, "16"); |
|
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changeset
|
983 Replace(DICOM_TAG_BITS_STORED, "16"); |
|
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changeset
|
984 Replace(DICOM_TAG_HIGH_BIT, "15"); |
|
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|
985 bytesPerPixel = 2; |
|
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|
986 break; |
|
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changeset
|
987 |
|
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changeset
|
988 default: |
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|
989 throw OrthancException(ErrorCode_NotImplemented); |
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990 } |
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|
991 |
|
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992 DcmTag key(DICOM_TAG_PIXEL_DATA.GetGroup(), |
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993 DICOM_TAG_PIXEL_DATA.GetElement()); |
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|
994 |
|
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995 std::auto_ptr<DcmPixelData> pixels(new DcmPixelData(key)); |
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996 |
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997 unsigned int pitch = accessor.GetWidth() * bytesPerPixel; |
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998 Uint8* target = NULL; |
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999 pixels->createUint8Array(accessor.GetHeight() * pitch, target); |
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1000 |
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1001 for (unsigned int y = 0; y < accessor.GetHeight(); y++) |
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1002 { |
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1003 switch (accessor.GetFormat()) |
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1004 { |
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1005 case PixelFormat_RGB24: |
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1006 case PixelFormat_Grayscale8: |
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1007 case PixelFormat_Grayscale16: |
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1008 case PixelFormat_SignedGrayscale16: |
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1009 { |
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1010 memcpy(target, reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)), pitch); |
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1011 target += pitch; |
|
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1012 break; |
|
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1013 } |
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1014 |
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|
1015 case PixelFormat_RGBA32: |
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|
1016 { |
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1017 // The alpha channel is not supported by the DICOM standard |
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1018 const Uint8* source = reinterpret_cast<const Uint8*>(accessor.GetConstRow(y)); |
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1019 for (unsigned int x = 0; x < accessor.GetWidth(); x++, target += 3, source += 4) |
|
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|
1020 { |
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1021 target[0] = source[0]; |
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1022 target[1] = source[1]; |
|
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|
1023 target[2] = source[2]; |
|
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|
1024 } |
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|
1025 |
|
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|
1026 break; |
|
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|
1027 } |
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|
1028 |
|
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|
1029 default: |
|
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1030 throw OrthancException(ErrorCode_NotImplemented); |
|
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|
1031 } |
|
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1032 } |
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|
1033 |
|
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1034 if (!pimpl_->file_->getDataset()->insert(pixels.release(), false, false).good()) |
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|
1035 { |
|
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|
1036 throw OrthancException(ErrorCode_InternalError); |
|
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1037 } |
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|
1038 } |
|
874
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|
1039 |
|
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|
1040 |
|
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|
1041 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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|
1042 unsigned int frame) |
|
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|
1043 { |
|
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|
1044 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
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diff
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|
1045 |
|
87791ebc1f50
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parents:
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diff
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|
1046 if (!DicomImageDecoder::Decode(result, dataset, frame)) |
|
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parents:
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diff
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|
1047 { |
|
87791ebc1f50
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parents:
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|
1048 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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parents:
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diff
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|
1049 } |
|
87791ebc1f50
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parents:
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diff
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|
1050 } |
|
87791ebc1f50
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parents:
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diff
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|
1051 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1052 |
|
87791ebc1f50
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parents:
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diff
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|
1053 void ParsedDicomFile::ExtractImage(ImageBuffer& result, |
|
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parents:
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diff
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|
1054 unsigned int frame, |
|
87791ebc1f50
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parents:
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diff
changeset
|
1055 ImageExtractionMode mode) |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1056 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1057 DcmDataset& dataset = *pimpl_->file_->getDataset(); |
|
87791ebc1f50
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parents:
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diff
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|
1058 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1059 bool ok = false; |
|
87791ebc1f50
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parents:
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diff
changeset
|
1060 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1061 switch (mode) |
|
87791ebc1f50
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parents:
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diff
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|
1062 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1063 case ImageExtractionMode_UInt8: |
|
1015
f009f7c75069
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1064 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale8, false); |
|
874
87791ebc1f50
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parents:
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diff
changeset
|
1065 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1066 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1067 case ImageExtractionMode_UInt16: |
|
1015
f009f7c75069
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parents:
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diff
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|
1068 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_Grayscale16, false); |
|
874
87791ebc1f50
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parents:
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diff
changeset
|
1069 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1070 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1071 case ImageExtractionMode_Int16: |
|
1015
f009f7c75069
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
992
diff
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|
1072 ok = DicomImageDecoder::DecodeAndTruncate(result, dataset, frame, PixelFormat_SignedGrayscale16, false); |
|
874
87791ebc1f50
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parents:
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diff
changeset
|
1073 break; |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1074 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1075 case ImageExtractionMode_Preview: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1076 ok = DicomImageDecoder::DecodePreview(result, dataset, frame); |
|
87791ebc1f50
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parents:
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diff
changeset
|
1077 break; |
|
87791ebc1f50
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parents:
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diff
changeset
|
1078 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1079 default: |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1080 throw OrthancException(ErrorCode_ParameterOutOfRange); |
|
87791ebc1f50
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parents:
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diff
changeset
|
1081 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1082 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1083 if (!ok) |
|
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parents:
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diff
changeset
|
1084 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1085 throw OrthancException(ErrorCode_BadFileFormat); |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1086 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1087 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1088 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1089 |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
853
diff
changeset
|
1090 void ParsedDicomFile::ExtractPngImage(std::string& result, |
|
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parents:
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diff
changeset
|
1091 unsigned int frame, |
|
87791ebc1f50
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parents:
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diff
changeset
|
1092 ImageExtractionMode mode) |
|
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parents:
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diff
changeset
|
1093 { |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1094 ImageBuffer buffer; |
|
87791ebc1f50
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diff
changeset
|
1095 ExtractImage(buffer, frame, mode); |
|
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parents:
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diff
changeset
|
1096 |
|
87791ebc1f50
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parents:
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diff
changeset
|
1097 ImageAccessor accessor(buffer.GetConstAccessor()); |
|
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diff
changeset
|
1098 PngWriter writer; |
|
87791ebc1f50
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diff
changeset
|
1099 writer.WriteToMemory(result, accessor); |
|
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diff
changeset
|
1100 } |
|
87791ebc1f50
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1101 |
|
956
2fd5a163776d
primitives for proper encoding handling
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|
1102 |
|
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1103 Encoding ParsedDicomFile::GetEncoding() const |
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1104 { |
| 1695 | 1105 return FromDcmtkBridge::DetectEncoding(*pimpl_->file_->getDataset()); |
|
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1106 } |
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1090
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1107 |
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1108 |
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1109 void ParsedDicomFile::SetEncoding(Encoding encoding) |
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1110 { |
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1111 if (encoding == Encoding_Windows1251) |
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1112 { |
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1113 // This Cyrillic codepage is not officially supported by the |
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1114 // DICOM standard. Do not set the SpecificCharacterSet tag. |
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1115 return; |
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1116 } |
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1117 |
|
1565
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1118 std::string s = GetDicomSpecificCharacterSet(encoding); |
| 1091 | 1119 Replace(DICOM_TAG_SPECIFIC_CHARACTER_SET, s, DicomReplaceMode_InsertIfAbsent); |
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1120 } |
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1121 |
| 1686 | 1122 void ParsedDicomFile::ToJson(Json::Value& target, |
| 1123 DicomToJsonFormat format, | |
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1124 DicomToJsonFlags flags, |
| 1686 | 1125 unsigned int maxStringLength) |
|
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1126 { |
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1127 FromDcmtkBridge::ToJson(target, *pimpl_->file_->getDataset(), format, flags, maxStringLength); |
|
1160
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1128 } |
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1129 |
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1130 |
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1131 bool ParsedDicomFile::HasTag(const DicomTag& tag) const |
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1132 { |
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1133 DcmTag key(tag.GetGroup(), tag.GetElement()); |
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1134 return pimpl_->file_->getDataset()->tagExists(key); |
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1135 } |
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1136 |
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1137 |
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1138 void ParsedDicomFile::EmbedPdf(const std::string& pdf) |
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1139 { |
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1140 if (pdf.size() < 5 || // (*) |
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1141 strncmp("%PDF-", pdf.c_str(), 5) != 0) |
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1142 { |
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1143 LOG(ERROR) << "Not a PDF file"; |
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1144 throw OrthancException(ErrorCode_BadFileFormat); |
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1145 } |
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1146 |
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1147 Replace(DICOM_TAG_SOP_CLASS_UID, UID_EncapsulatedPDFStorage); |
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1148 Replace(FromDcmtkBridge::Convert(DCM_Modality), "OT"); |
|
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1149 Replace(FromDcmtkBridge::Convert(DCM_ConversionType), "WSD"); |
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1150 Replace(FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument), "application/pdf"); |
| 1566 | 1151 //Replace(FromDcmtkBridge::Convert(DCM_SeriesNumber), "1"); |
|
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1152 |
|
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|
1153 std::auto_ptr<DcmPolymorphOBOW> element(new DcmPolymorphOBOW(DCM_EncapsulatedDocument)); |
|
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|
1154 |
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1155 size_t s = pdf.size(); |
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|
1156 if (s & 1) |
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changeset
|
1157 { |
|
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Creation of DICOM files with encapsulated PDF
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|
1158 // The size of the buffer must be even |
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1159 s += 1; |
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1160 } |
|
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|
1161 |
|
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|
1162 Uint8* bytes = NULL; |
|
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|
1163 OFCondition result = element->createUint8Array(s, bytes); |
|
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|
1164 if (!result.good() || bytes == NULL) |
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|
1165 { |
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|
1166 throw OrthancException(ErrorCode_NotEnoughMemory); |
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|
1167 } |
|
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|
1168 |
|
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|
1169 // Blank pad byte (no access violation, as "pdf.size() >= 5" because of (*) ) |
|
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|
1170 bytes[s - 1] = 0; |
|
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|
1171 |
|
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|
1172 memcpy(bytes, pdf.c_str(), pdf.size()); |
|
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|
1173 |
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|
1174 DcmPolymorphOBOW* obj = element.release(); |
|
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|
1175 result = pimpl_->file_->getDataset()->insert(obj); |
|
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|
1176 |
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|
1177 if (!result.good()) |
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|
1178 { |
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|
1179 delete obj; |
|
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|
1180 throw OrthancException(ErrorCode_NotEnoughMemory); |
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|
1181 } |
|
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|
1182 } |
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|
1183 |
|
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1184 |
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|
1185 bool ParsedDicomFile::ExtractPdf(std::string& pdf) |
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|
1186 { |
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|
1187 std::string sop, mime; |
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|
1188 |
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1189 if (!GetTagValue(sop, DICOM_TAG_SOP_CLASS_UID) || |
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1190 !GetTagValue(mime, FromDcmtkBridge::Convert(DCM_MIMETypeOfEncapsulatedDocument)) || |
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1191 sop != UID_EncapsulatedPDFStorage || |
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1192 mime != "application/pdf") |
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1193 { |
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1194 return false; |
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1195 } |
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1196 |
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1197 if (!GetTagValue(pdf, DICOM_TAG_ENCAPSULATED_DOCUMENT)) |
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1198 { |
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1199 return false; |
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1200 } |
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|
1201 |
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1202 // Strip the possible pad byte at the end of file, because the |
|
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1203 // encapsulated documents must always have an even length. The PDF |
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1204 // format expects files to end with %%EOF followed by CR/LF. If |
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1205 // the last character of the file is not a CR or LF, we assume it |
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|
1206 // is a pad byte and remove it. |
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1207 if (pdf.size() > 0) |
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1208 { |
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1209 char last = *pdf.rbegin(); |
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1210 |
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1211 if (last != 10 && last != 13) |
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1212 { |
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parents:
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1213 pdf.resize(pdf.size() - 1); |
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changeset
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1214 } |
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1215 } |
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parents:
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changeset
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1216 |
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1217 return true; |
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1218 } |
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1662
09be34b2f30e
ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
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1219 |
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ParsedDicomFile::Convert()
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parents:
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1220 |
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ParsedDicomFile::Convert()
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1221 void ParsedDicomFile::Convert(DicomMap& tags) |
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09be34b2f30e
ParsedDicomFile::Convert()
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parents:
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1222 { |
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ParsedDicomFile::Convert()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1223 FromDcmtkBridge::Convert(tags, *pimpl_->file_->getDataset()); |
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ParsedDicomFile::Convert()
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1224 } |
| 790 | 1225 } |